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HEADER HYDROLASE/HYDROLASE INHIBITOR 11-AUG-16 5SYN
TITLE COCRYSTAL STRUCTURE OF THE HUMAN ACYL PROTEIN THIOESTERASE 2 WITH AN
TITLE 2 ISOFORM-SELECTIVE INHIBITOR, ML349
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: ACYL-PROTEIN THIOESTERASE 2;
COMPND 3 CHAIN: A, B, C, D;
COMPND 4 SYNONYM: APT-2,LYSOPHOSPHOLIPASE II,LYSOPLA II;
COMPND 5 EC: 3.1.2.-;
COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 GENE: LYPLA2, APT2;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS HYDROLASE, INHIBITOR, THIOESTERASE, HYDROLASE-HYDROLASE INHIBITOR
KEYWDS 2 COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR J.A.STUCKEY,K.J.LABBY,J.L.MEAGHER,S.J.WON,B.R.MARTIN
REVDAT 1 26-OCT-16 5SYN 0
JRNL AUTH S.J.WON,D.DAVDA,K.J.LABBY,S.Y.HWANG,R.PRICER,J.D.MAJMUDAR,
JRNL AUTH 2 K.A.ARMACOST,J.PALAKURTHI,L.A.RODRIGUEZ,C.L.RODRIGUEZ,
JRNL AUTH 3 F.S.CHONG,K.A.TORROSIAN,E.S.HUR,J.L.MEAGHER,C.L.BROOKS,
JRNL AUTH 4 J.A.STUCKEY,B.R.MARTIN
JRNL TITL MOLECULAR MECHANISM FOR ISOFORM-SELECTIVE INHIBITION OF ACYL
JRNL TITL 2 PROTEIN THIOESTERASES 1 AND 2 (APT1 AND APT2)
JRNL REF ACS CHEM.BIOL. 2016
JRNL REFN ESSN 1554-8937
REMARK 2
REMARK 2 RESOLUTION. 1.64 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : BUSTER
REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER,
REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN,
REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.64
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 55.81
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 93.2
REMARK 3 NUMBER OF REFLECTIONS : 97049
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE
REMARK 3 FREE R VALUE TEST SET SELECTION : NULL
REMARK 3 R VALUE (WORKING + TEST SET) : NULL
REMARK 3 R VALUE (WORKING SET) : 0.220
REMARK 3 FREE R VALUE : 0.250
REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT : NULL
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : NULL
REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : NULL
REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : NULL
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : NULL
REMARK 3 BIN R VALUE (WORKING + TEST SET) : NULL
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL
REMARK 3 BIN R VALUE (WORKING SET) : NULL
REMARK 3 BIN FREE R VALUE : NULL
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 6547
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 148
REMARK 3 SOLVENT ATOMS : 310
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.55
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : NULL
REMARK 3 B22 (A**2) : NULL
REMARK 3 B33 (A**2) : NULL
REMARK 3 B12 (A**2) : NULL
REMARK 3 B13 (A**2) : NULL
REMARK 3 B23 (A**2) : NULL
REMARK 3
REMARK 3 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL
REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : NULL
REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : NULL
REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : NULL
REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : NULL
REMARK 3
REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797
REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : NULL
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : NULL
REMARK 3
REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15
REMARK 3 TERM COUNT WEIGHT FUNCTION.
REMARK 3 BOND LENGTHS : NULL ; NULL ; NULL
REMARK 3 BOND ANGLES : NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES : NULL ; NULL ; NULL
REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL
REMARK 3 GENERAL PLANES : NULL ; NULL ; NULL
REMARK 3 ISOTROPIC THERMAL FACTORS : NULL ; NULL ; NULL
REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL
REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL
REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL
REMARK 3 CHIRAL IMPROPER TORSION : NULL ; NULL ; NULL
REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL
REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL
REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL
REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL
REMARK 3 IDEAL-DIST CONTACT TERM : NULL ; NULL ; NULL
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : NULL
REMARK 3 BOND ANGLES (DEGREES) : NULL
REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : NULL
REMARK 3 OTHER TORSION ANGLES (DEGREES) : NULL
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 5SYN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-AUG-16.
REMARK 100 THE DEPOSITION ID IS D_1000222867.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 04-JUN-14
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 5.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : APS
REMARK 200 BEAMLINE : 21-ID-G
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.9786
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL
REMARK 200 DATA SCALING SOFTWARE : SCALA
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 97049
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.640
REMARK 200 RESOLUTION RANGE LOW (A) : 55.810
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 93.2
REMARK 200 DATA REDUNDANCY : 3.700
REMARK 200 R MERGE (I) : 0.09500
REMARK 200 R SYM (I) : NULL
REMARK 200 FOR THE DATA SET : 7.1000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL
REMARK 200 COMPLETENESS FOR SHELL (%) : NULL
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: BALBES
REMARK 200 STARTING MODEL: PDB:1FJ2 CHAIN A
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 43.56
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 MM SODIUM CITRATE PH 5.5, 20-24%
REMARK 280 PEG 3350., VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,Y,-Z
REMARK 290 3555 X+1/2,Y+1/2,Z
REMARK 290 4555 -X+1/2,Y+1/2,-Z
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 39.10500
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.89500
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 39.10500
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 39.89500
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1, 2, 3, 4
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 350
REMARK 350 BIOMOLECULE: 2
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 APPLY THE FOLLOWING TO CHAINS: B
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 350
REMARK 350 BIOMOLECULE: 3
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 APPLY THE FOLLOWING TO CHAINS: C
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 350
REMARK 350 BIOMOLECULE: 4
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 APPLY THE FOLLOWING TO CHAINS: D
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465 M RES C SSSEQI
REMARK 465 MET A 1
REMARK 465 CYS A 2
REMARK 465 GLY A 3
REMARK 465 ASN A 4
REMARK 465 THR A 5
REMARK 465 MET A 6
REMARK 465 SER A 7
REMARK 465 VAL A 8
REMARK 465 MET B 1
REMARK 465 CYS B 2
REMARK 465 GLY B 3
REMARK 465 ASN B 4
REMARK 465 THR B 5
REMARK 465 MET B 6
REMARK 465 SER B 7
REMARK 465 VAL B 8
REMARK 465 MET C 1
REMARK 465 CYS C 2
REMARK 465 GLY C 3
REMARK 465 ASN C 4
REMARK 465 THR C 5
REMARK 465 MET C 6
REMARK 465 SER C 7
REMARK 465 VAL C 8
REMARK 465 PRO C 9
REMARK 465 ALA C 159
REMARK 465 MET D 1
REMARK 465 CYS D 2
REMARK 465 GLY D 3
REMARK 465 ASN D 4
REMARK 465 THR D 5
REMARK 465 MET D 6
REMARK 465 SER D 7
REMARK 465 VAL D 8
REMARK 465 PRO D 9
REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 470 I=INSERTION CODE):
REMARK 470 M RES CSSEQI ATOMS
REMARK 470 LEU A 11 CG CD1 CD2
REMARK 470 GLU A 21 OE1 OE2
REMARK 470 LYS A 69 CE NZ
REMARK 470 MET A 70 CG SD CE
REMARK 470 VAL A 71 CG1 CG2
REMARK 470 LYS A 94 NZ
REMARK 470 GLU A 104 CD OE1 OE2
REMARK 470 SER A 162 OG
REMARK 470 LYS A 164 CG CD CE NZ
REMARK 470 ARG A 182 CD NE CZ NH1 NH2
REMARK 470 LEU A 186 CG CD1 CD2
REMARK 470 SER A 193 OG
REMARK 470 THR A 196 OG1 CG2
REMARK 470 GLU A 225 OE1 OE2
REMARK 470 LEU B 11 CD1 CD2
REMARK 470 LYS B 69 CE NZ
REMARK 470 ARG B 153 CG CD NE CZ NH1 NH2
REMARK 470 SER B 162 OG
REMARK 470 LYS B 164 CE NZ
REMARK 470 LEU B 175 CD1 CD2
REMARK 470 ARG B 182 CD NE CZ NH1 NH2
REMARK 470 SER B 193 OG
REMARK 470 THR B 196 OG1 CG2
REMARK 470 ARG B 199 CD NE CZ NH1 NH2
REMARK 470 GLU B 225 OE1 OE2
REMARK 470 LEU C 11 CG CD1 CD2
REMARK 470 GLU C 21 OE1 OE2
REMARK 470 ARG C 22 NH1 NH2
REMARK 470 GLU C 23 CG CD OE1 OE2
REMARK 470 LYS C 69 CE NZ
REMARK 470 MET C 70 CG SD CE
REMARK 470 LYS C 94 NZ
REMARK 470 ARG C 153 CG CD NE CZ NH1 NH2
REMARK 470 SER C 162 OG
REMARK 470 LYS C 164 CG CD CE NZ
REMARK 470 ARG C 182 CD NE CZ NH1 NH2
REMARK 470 THR C 196 OG1 CG2
REMARK 470 ARG C 199 CD NE CZ NH1 NH2
REMARK 470 GLU C 225 OE1 OE2
REMARK 470 LEU D 11 CG CD1 CD2
REMARK 470 GLU D 21 OE1 OE2
REMARK 470 ARG D 22 CG CD NE CZ NH1 NH2
REMARK 470 LYS D 69 CE NZ
REMARK 470 ASP D 84 CG OD1 OD2
REMARK 470 GLU D 104 CD OE1 OE2
REMARK 470 SER D 162 OG
REMARK 470 LYS D 164 CG CD CE NZ
REMARK 470 ARG D 182 CD NE CZ NH1 NH2
REMARK 470 THR D 196 OG1 CG2
REMARK 470 ARG D 199 CD NE CZ NH1 NH2
REMARK 480
REMARK 480 ZERO OCCUPANCY ATOM
REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO
REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS
REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME;
REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 480 M RES C SSEQI ATOMS
REMARK 480 LEU A 66 CD1
REMARK 480 LEU B 66 CD1
REMARK 480 LEU B 81 CD1
REMARK 480 LEU C 66 CD1
REMARK 480 LEU D 66 CD1
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 ASN A 67 46.39 -97.24
REMARK 500 SER A 122 -115.40 46.68
REMARK 500 MET A 209 -140.27 -100.04
REMARK 500 ASN B 67 45.16 -107.63
REMARK 500 SER B 122 -116.67 52.22
REMARK 500 MET B 209 -137.68 -99.89
REMARK 500 SER C 122 -118.76 45.39
REMARK 500 ASP C 165 65.22 -117.42
REMARK 500 MET C 209 -138.66 -99.08
REMARK 500 ASN D 67 44.41 -101.49
REMARK 500 SER D 122 -115.78 48.92
REMARK 500 MET D 209 -136.94 -100.15
REMARK 500 MET D 209 -135.50 -101.92
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue 71T A 301
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 302
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue 71T B 301
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 302
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 303
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 304
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 305
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue 71T C 301
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO C 302
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue 71T D 301
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 5SYM RELATED DB: PDB
DBREF 5SYN A 1 231 UNP O95372 LYPA2_HUMAN 1 231
DBREF 5SYN B 1 231 UNP O95372 LYPA2_HUMAN 1 231
DBREF 5SYN C 1 231 UNP O95372 LYPA2_HUMAN 1 231
DBREF 5SYN D 1 231 UNP O95372 LYPA2_HUMAN 1 231
SEQRES 1 A 231 MET CYS GLY ASN THR MET SER VAL PRO LEU LEU THR ASP
SEQRES 2 A 231 ALA ALA THR VAL SER GLY ALA GLU ARG GLU THR ALA ALA
SEQRES 3 A 231 VAL ILE PHE LEU HIS GLY LEU GLY ASP THR GLY HIS SER
SEQRES 4 A 231 TRP ALA ASP ALA LEU SER THR ILE ARG LEU PRO HIS VAL
SEQRES 5 A 231 LYS TYR ILE CYS PRO HIS ALA PRO ARG ILE PRO VAL THR
SEQRES 6 A 231 LEU ASN MET LYS MET VAL MET PRO SER TRP PHE ASP LEU
SEQRES 7 A 231 MET GLY LEU SER PRO ASP ALA PRO GLU ASP GLU ALA GLY
SEQRES 8 A 231 ILE LYS LYS ALA ALA GLU ASN ILE LYS ALA LEU ILE GLU
SEQRES 9 A 231 HIS GLU MET LYS ASN GLY ILE PRO ALA ASN ARG ILE VAL
SEQRES 10 A 231 LEU GLY GLY PHE SER GLN GLY GLY ALA LEU SER LEU TYR
SEQRES 11 A 231 THR ALA LEU THR CYS PRO HIS PRO LEU ALA GLY ILE VAL
SEQRES 12 A 231 ALA LEU SER CYS TRP LEU PRO LEU HIS ARG ALA PHE PRO
SEQRES 13 A 231 GLN ALA ALA ASN GLY SER ALA LYS ASP LEU ALA ILE LEU
SEQRES 14 A 231 GLN CYS HIS GLY GLU LEU ASP PRO MET VAL PRO VAL ARG
SEQRES 15 A 231 PHE GLY ALA LEU THR ALA GLU LYS LEU ARG SER VAL VAL
SEQRES 16 A 231 THR PRO ALA ARG VAL GLN PHE LYS THR TYR PRO GLY VAL
SEQRES 17 A 231 MET HIS SER SER CYS PRO GLN GLU MET ALA ALA VAL LYS
SEQRES 18 A 231 GLU PHE LEU GLU LYS LEU LEU PRO PRO VAL
SEQRES 1 B 231 MET CYS GLY ASN THR MET SER VAL PRO LEU LEU THR ASP
SEQRES 2 B 231 ALA ALA THR VAL SER GLY ALA GLU ARG GLU THR ALA ALA
SEQRES 3 B 231 VAL ILE PHE LEU HIS GLY LEU GLY ASP THR GLY HIS SER
SEQRES 4 B 231 TRP ALA ASP ALA LEU SER THR ILE ARG LEU PRO HIS VAL
SEQRES 5 B 231 LYS TYR ILE CYS PRO HIS ALA PRO ARG ILE PRO VAL THR
SEQRES 6 B 231 LEU ASN MET LYS MET VAL MET PRO SER TRP PHE ASP LEU
SEQRES 7 B 231 MET GLY LEU SER PRO ASP ALA PRO GLU ASP GLU ALA GLY
SEQRES 8 B 231 ILE LYS LYS ALA ALA GLU ASN ILE LYS ALA LEU ILE GLU
SEQRES 9 B 231 HIS GLU MET LYS ASN GLY ILE PRO ALA ASN ARG ILE VAL
SEQRES 10 B 231 LEU GLY GLY PHE SER GLN GLY GLY ALA LEU SER LEU TYR
SEQRES 11 B 231 THR ALA LEU THR CYS PRO HIS PRO LEU ALA GLY ILE VAL
SEQRES 12 B 231 ALA LEU SER CYS TRP LEU PRO LEU HIS ARG ALA PHE PRO
SEQRES 13 B 231 GLN ALA ALA ASN GLY SER ALA LYS ASP LEU ALA ILE LEU
SEQRES 14 B 231 GLN CYS HIS GLY GLU LEU ASP PRO MET VAL PRO VAL ARG
SEQRES 15 B 231 PHE GLY ALA LEU THR ALA GLU LYS LEU ARG SER VAL VAL
SEQRES 16 B 231 THR PRO ALA ARG VAL GLN PHE LYS THR TYR PRO GLY VAL
SEQRES 17 B 231 MET HIS SER SER CYS PRO GLN GLU MET ALA ALA VAL LYS
SEQRES 18 B 231 GLU PHE LEU GLU LYS LEU LEU PRO PRO VAL
SEQRES 1 C 231 MET CYS GLY ASN THR MET SER VAL PRO LEU LEU THR ASP
SEQRES 2 C 231 ALA ALA THR VAL SER GLY ALA GLU ARG GLU THR ALA ALA
SEQRES 3 C 231 VAL ILE PHE LEU HIS GLY LEU GLY ASP THR GLY HIS SER
SEQRES 4 C 231 TRP ALA ASP ALA LEU SER THR ILE ARG LEU PRO HIS VAL
SEQRES 5 C 231 LYS TYR ILE CYS PRO HIS ALA PRO ARG ILE PRO VAL THR
SEQRES 6 C 231 LEU ASN MET LYS MET VAL MET PRO SER TRP PHE ASP LEU
SEQRES 7 C 231 MET GLY LEU SER PRO ASP ALA PRO GLU ASP GLU ALA GLY
SEQRES 8 C 231 ILE LYS LYS ALA ALA GLU ASN ILE LYS ALA LEU ILE GLU
SEQRES 9 C 231 HIS GLU MET LYS ASN GLY ILE PRO ALA ASN ARG ILE VAL
SEQRES 10 C 231 LEU GLY GLY PHE SER GLN GLY GLY ALA LEU SER LEU TYR
SEQRES 11 C 231 THR ALA LEU THR CYS PRO HIS PRO LEU ALA GLY ILE VAL
SEQRES 12 C 231 ALA LEU SER CYS TRP LEU PRO LEU HIS ARG ALA PHE PRO
SEQRES 13 C 231 GLN ALA ALA ASN GLY SER ALA LYS ASP LEU ALA ILE LEU
SEQRES 14 C 231 GLN CYS HIS GLY GLU LEU ASP PRO MET VAL PRO VAL ARG
SEQRES 15 C 231 PHE GLY ALA LEU THR ALA GLU LYS LEU ARG SER VAL VAL
SEQRES 16 C 231 THR PRO ALA ARG VAL GLN PHE LYS THR TYR PRO GLY VAL
SEQRES 17 C 231 MET HIS SER SER CYS PRO GLN GLU MET ALA ALA VAL LYS
SEQRES 18 C 231 GLU PHE LEU GLU LYS LEU LEU PRO PRO VAL
SEQRES 1 D 231 MET CYS GLY ASN THR MET SER VAL PRO LEU LEU THR ASP
SEQRES 2 D 231 ALA ALA THR VAL SER GLY ALA GLU ARG GLU THR ALA ALA
SEQRES 3 D 231 VAL ILE PHE LEU HIS GLY LEU GLY ASP THR GLY HIS SER
SEQRES 4 D 231 TRP ALA ASP ALA LEU SER THR ILE ARG LEU PRO HIS VAL
SEQRES 5 D 231 LYS TYR ILE CYS PRO HIS ALA PRO ARG ILE PRO VAL THR
SEQRES 6 D 231 LEU ASN MET LYS MET VAL MET PRO SER TRP PHE ASP LEU
SEQRES 7 D 231 MET GLY LEU SER PRO ASP ALA PRO GLU ASP GLU ALA GLY
SEQRES 8 D 231 ILE LYS LYS ALA ALA GLU ASN ILE LYS ALA LEU ILE GLU
SEQRES 9 D 231 HIS GLU MET LYS ASN GLY ILE PRO ALA ASN ARG ILE VAL
SEQRES 10 D 231 LEU GLY GLY PHE SER GLN GLY GLY ALA LEU SER LEU TYR
SEQRES 11 D 231 THR ALA LEU THR CYS PRO HIS PRO LEU ALA GLY ILE VAL
SEQRES 12 D 231 ALA LEU SER CYS TRP LEU PRO LEU HIS ARG ALA PHE PRO
SEQRES 13 D 231 GLN ALA ALA ASN GLY SER ALA LYS ASP LEU ALA ILE LEU
SEQRES 14 D 231 GLN CYS HIS GLY GLU LEU ASP PRO MET VAL PRO VAL ARG
SEQRES 15 D 231 PHE GLY ALA LEU THR ALA GLU LYS LEU ARG SER VAL VAL
SEQRES 16 D 231 THR PRO ALA ARG VAL GLN PHE LYS THR TYR PRO GLY VAL
SEQRES 17 D 231 MET HIS SER SER CYS PRO GLN GLU MET ALA ALA VAL LYS
SEQRES 18 D 231 GLU PHE LEU GLU LYS LEU LEU PRO PRO VAL
HET 71T A 301 53
HET EDO A 302 4
HET 71T B 301 53
HET EDO B 302 4
HET EDO B 303 4
HET EDO B 304 4
HET EDO B 305 4
HET 71T C 301 53
HET EDO C 302 4
HET 71T D 301 53
HETNAM 71T 2-[4-(4-METHOXYPHENYL)PIPERAZINE-1-CARBONYL]-
HETNAM 2 71T 5LAMBDA~6~-THIENO[3,2-C][1]BENZOTHIOPYRAN-5,5(4H)-
HETNAM 3 71T DIONE
HETNAM EDO 1,2-ETHANEDIOL
HETSYN EDO ETHYLENE GLYCOL
FORMUL 5 71T 4(C23 H22 N2 O4 S2)
FORMUL 6 EDO 6(C2 H6 O2)
FORMUL 15 HOH *310(H2 O)
HELIX 1 AA1 GLY A 37 THR A 46 1 10
HELIX 2 AA2 THR A 65 MET A 68 5 4
HELIX 3 AA3 ASP A 88 ASN A 109 1 22
HELIX 4 AA4 PRO A 112 ASN A 114 5 3
HELIX 5 AA5 SER A 122 THR A 134 1 13
HELIX 6 AA6 LEU A 151 PHE A 155 5 5
HELIX 7 AA7 ASN A 160 LEU A 166 5 7
HELIX 8 AA8 PRO A 180 SER A 193 1 14
HELIX 9 AA9 THR A 196 ALA A 198 5 3
HELIX 10 AB1 CYS A 213 LEU A 228 1 16
HELIX 11 AB2 GLY B 37 THR B 46 1 10
HELIX 12 AB3 THR B 65 MET B 68 5 4
HELIX 13 AB4 ASP B 88 ASN B 109 1 22
HELIX 14 AB5 PRO B 112 ASN B 114 5 3
HELIX 15 AB6 SER B 122 THR B 134 1 13
HELIX 16 AB7 LEU B 151 PHE B 155 5 5
HELIX 17 AB8 ASN B 160 LYS B 164 5 5
HELIX 18 AB9 PRO B 180 SER B 193 1 14
HELIX 19 AC1 THR B 196 ALA B 198 5 3
HELIX 20 AC2 CYS B 213 LEU B 228 1 16
HELIX 21 AC3 GLY C 37 THR C 46 1 10
HELIX 22 AC4 ASP C 88 ASN C 109 1 22
HELIX 23 AC5 PRO C 112 ASN C 114 5 3
HELIX 24 AC6 SER C 122 THR C 134 1 13
HELIX 25 AC7 LEU C 151 PHE C 155 5 5
HELIX 26 AC8 PRO C 180 VAL C 195 1 16
HELIX 27 AC9 THR C 196 ALA C 198 5 3
HELIX 28 AD1 CYS C 213 LEU C 228 1 16
HELIX 29 AD2 GLY D 37 THR D 46 1 10
HELIX 30 AD3 THR D 65 MET D 68 5 4
HELIX 31 AD4 ASP D 88 ASN D 109 1 22
HELIX 32 AD5 PRO D 112 ASN D 114 5 3
HELIX 33 AD6 SER D 122 THR D 134 1 13
HELIX 34 AD7 LEU D 151 PHE D 155 5 5
HELIX 35 AD8 ASN D 160 LEU D 166 5 7
HELIX 36 AD9 PRO D 180 ARG D 192 1 13
HELIX 37 AE1 THR D 196 ALA D 198 5 3
HELIX 38 AE2 CYS D 213 LEU D 228 1 16
SHEET 1 AA114 VAL A 200 TYR A 205 0
SHEET 2 AA114 ALA A 167 GLY A 173 1 N GLN A 170 O GLN A 201
SHEET 3 AA114 GLY A 141 LEU A 145 1 N ALA A 144 O LEU A 169
SHEET 4 AA114 ILE A 116 PHE A 121 1 N GLY A 120 O LEU A 145
SHEET 5 AA114 ALA A 25 LEU A 30 1 N ALA A 26 O VAL A 117
SHEET 6 AA114 VAL A 52 PRO A 57 1 O ILE A 55 N VAL A 27
SHEET 7 AA114 LEU A 11 VAL A 17 -1 N VAL A 17 O TYR A 54
SHEET 8 AA114 LEU B 11 VAL B 17 -1 O THR B 12 N THR A 16
SHEET 9 AA114 VAL B 52 PRO B 57 -1 O TYR B 54 N VAL B 17
SHEET 10 AA114 ALA B 25 LEU B 30 1 N VAL B 27 O ILE B 55
SHEET 11 AA114 ILE B 116 PHE B 121 1 O VAL B 117 N ILE B 28
SHEET 12 AA114 GLY B 141 LEU B 145 1 O LEU B 145 N GLY B 120
SHEET 13 AA114 ALA B 167 GLY B 173 1 O LEU B 169 N ILE B 142
SHEET 14 AA114 VAL B 200 TYR B 205 1 O GLN B 201 N ILE B 168
SHEET 1 AA2 2 ARG A 61 PRO A 63 0
SHEET 2 AA2 2 VAL A 71 PRO A 73 -1 O MET A 72 N ILE A 62
SHEET 1 AA3 2 ARG B 61 PRO B 63 0
SHEET 2 AA3 2 VAL B 71 PRO B 73 -1 O MET B 72 N ILE B 62
SHEET 1 AA4 7 ALA C 14 VAL C 17 0
SHEET 2 AA4 7 VAL C 52 PRO C 57 -1 O TYR C 54 N VAL C 17
SHEET 3 AA4 7 ALA C 25 LEU C 30 1 N VAL C 27 O ILE C 55
SHEET 4 AA4 7 ILE C 116 PHE C 121 1 O VAL C 117 N ILE C 28
SHEET 5 AA4 7 GLY C 141 LEU C 145 1 O LEU C 145 N GLY C 120
SHEET 6 AA4 7 ALA C 167 GLY C 173 1 O LEU C 169 N ALA C 144
SHEET 7 AA4 7 VAL C 200 TYR C 205 1 O GLN C 201 N GLN C 170
SHEET 1 AA5 2 ARG C 61 PRO C 63 0
SHEET 2 AA5 2 VAL C 71 PRO C 73 -1 O MET C 72 N ILE C 62
SHEET 1 AA6 7 ALA D 14 VAL D 17 0
SHEET 2 AA6 7 VAL D 52 PRO D 57 -1 O TYR D 54 N VAL D 17
SHEET 3 AA6 7 ALA D 25 LEU D 30 1 N VAL D 27 O ILE D 55
SHEET 4 AA6 7 ILE D 116 PHE D 121 1 O VAL D 117 N ILE D 28
SHEET 5 AA6 7 GLY D 141 LEU D 145 1 O LEU D 145 N GLY D 120
SHEET 6 AA6 7 ALA D 167 GLY D 173 1 O LEU D 169 N ILE D 142
SHEET 7 AA6 7 VAL D 200 TYR D 205 1 O GLN D 201 N ILE D 168
SHEET 1 AA7 2 ARG D 61 PRO D 63 0
SHEET 2 AA7 2 VAL D 71 PRO D 73 -1 O MET D 72 N ILE D 62
CISPEP 1 PHE A 155 PRO A 156 0 5.82
CISPEP 2 PHE B 155 PRO B 156 0 7.42
CISPEP 3 PHE C 155 PRO C 156 0 5.69
CISPEP 4 ASN C 160 GLY C 161 0 -1.65
CISPEP 5 PHE D 155 PRO D 156 0 4.40
SITE 1 AC1 18 LEU A 33 GLY A 80 LEU A 81 SER A 82
SITE 2 AC1 18 PRO A 83 SER A 122 TRP A 148 LEU A 149
SITE 3 AC1 18 HIS A 152 MET A 178 VAL A 179 PHE A 183
SITE 4 AC1 18 LEU A 186 THR A 187 HIS A 210 HOH A 429
SITE 5 AC1 18 HOH A 431 HOH A 452
SITE 1 AC2 5 GLY A 110 HOH A 469 THR B 24 PRO B 112
SITE 2 AC2 5 ARG B 115
SITE 1 AC3 21 LEU B 33 LEU B 66 LEU B 78 GLY B 80
SITE 2 AC3 21 LEU B 81 SER B 82 PRO B 83 GLU B 87
SITE 3 AC3 21 SER B 122 TRP B 148 LEU B 149 HIS B 152
SITE 4 AC3 21 MET B 178 VAL B 179 PHE B 183 LEU B 186
SITE 5 AC3 21 THR B 187 HIS B 210 HOH B 416 HOH B 434
SITE 6 AC3 21 HOH B 443
SITE 1 AC4 4 TRP B 75 ASN B 98 ILE B 99 HOH B 402
SITE 1 AC5 5 MET A 68 SER B 39 TRP B 40 ALA B 43
SITE 2 AC5 5 SER B 212
SITE 1 AC6 4 GLY A 19 GLU B 104 HIS B 105 LYS B 108
SITE 1 AC7 5 SER A 39 TRP A 40 ALA A 43 SER A 212
SITE 2 AC7 5 MET B 68
SITE 1 AC8 19 LEU C 66 GLY C 80 LEU C 81 SER C 82
SITE 2 AC8 19 PRO C 83 GLU C 87 SER C 122 TRP C 148
SITE 3 AC8 19 LEU C 149 HIS C 152 MET C 178 VAL C 179
SITE 4 AC8 19 PHE C 183 LEU C 186 THR C 187 HIS C 210
SITE 5 AC8 19 HOH C 406 HOH C 414 HOH C 420
SITE 1 AC9 5 SER C 39 TRP C 40 SER C 212 HOH C 410
SITE 2 AC9 5 MET D 68
SITE 1 AD1 19 LEU D 33 LEU D 78 GLY D 80 LEU D 81
SITE 2 AD1 19 SER D 82 PRO D 83 SER D 122 TRP D 148
SITE 3 AD1 19 LEU D 149 HIS D 152 MET D 178 VAL D 179
SITE 4 AD1 19 PHE D 183 LEU D 186 THR D 187 HIS D 210
SITE 5 AD1 19 HOH D 412 HOH D 413 HOH D 420
CRYST1 78.210 79.790 138.610 90.00 93.30 90.00 C 1 2 1 16
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.012786 0.000000 0.000737 0.00000
SCALE2 0.000000 0.012533 0.000000 0.00000
SCALE3 0.000000 0.000000 0.007226 0.00000
TER 1663 VAL A 231
TER 3331 VAL B 231
TER 4961 VAL C 231
TER 6619 VAL D 231
MASTER 424 0 10 38 36 0 31 6 7005 4 236 72
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