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HEADER HYDROLASE/HYDROLASE INHIBITOR 11-AUG-16 5SYM
TITLE COCRYSTAL STRUCTURE OF THE HUMAN ACYL PROTEIN THIOESTERASE 1 WITH AN
TITLE 2 ISOFORM-SELECTIVE INHIBITOR, ML348
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: ACYL-PROTEIN THIOESTERASE 1;
COMPND 3 CHAIN: A, B;
COMPND 4 SYNONYM: HAPT1,LYSOPHOSPHOLIPASE 1,LYSOPHOSPHOLIPASE I,LYSOPLA I;
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: LYPLA1, APT1, LPL1;
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 5SYM 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. 1.55 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : BUSTER-TNT 2.10.2
REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER,
REMARK 3 : PACIOREK,ROVERSI,SMART,VONRHEIN,WOMACK,
REMARK 3 : MATTHEWS,TEN EYCK,TRONRUD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.55
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.51
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 3 NUMBER OF REFLECTIONS : 63533
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING + TEST SET) : 0.180
REMARK 3 R VALUE (WORKING SET) : 0.179
REMARK 3 FREE R VALUE : 0.199
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980
REMARK 3 FREE R VALUE TEST SET COUNT : 3167
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.000
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 20
REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.55
REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.59
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0
REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 4621
REMARK 3 BIN R VALUE (WORKING + TEST SET) : NULL
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4411
REMARK 3 BIN R VALUE (WORKING SET) : 0.2000
REMARK 3 BIN FREE R VALUE : 0.2310
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.54
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 210
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 : 3350
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 88
REMARK 3 SOLVENT ATOMS : 363
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 18.10
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.12
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -1.99180
REMARK 3 B22 (A**2) : 1.03250
REMARK 3 B33 (A**2) : 0.95930
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.00000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.190
REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.082
REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.078
REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.093
REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.076
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 : 0.951
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.941
REMARK 3
REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15
REMARK 3 TERM COUNT WEIGHT FUNCTION.
REMARK 3 BOND LENGTHS : 7082 ; 2.000 ; HARMONIC
REMARK 3 BOND ANGLES : 12882 ; 2.000 ; HARMONIC
REMARK 3 TORSION ANGLES : 1963 ; 2.000 ; SINUSOIDAL
REMARK 3 TRIGONAL CARBON PLANES : 80 ; 2.000 ; HARMONIC
REMARK 3 GENERAL PLANES : 1085 ; 5.000 ; HARMONIC
REMARK 3 ISOTROPIC THERMAL FACTORS : 7082 ; 20.000 ; HARMONIC
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 : 482 ; 5.000 ; SEMIHARMONIC
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 : 7945 ; 4.000 ; SEMIHARMONIC
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.009
REMARK 3 BOND ANGLES (DEGREES) : 1.09
REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.75
REMARK 3 OTHER TORSION ANGLES (DEGREES) : 2.52
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 8
REMARK 3
REMARK 3 TLS GROUP : 1
REMARK 3 SELECTION: {A|8 - 82}
REMARK 3 ORIGIN FOR THE GROUP (A): -16.2310 -25.6110 -10.7310
REMARK 3 T TENSOR
REMARK 3 T11: -0.0488 T22: -0.0244
REMARK 3 T33: -0.0310 T12: -0.0094
REMARK 3 T13: -0.0057 T23: 0.0255
REMARK 3 L TENSOR
REMARK 3 L11: 0.6627 L22: 0.6237
REMARK 3 L33: 3.2617 L12: 0.3059
REMARK 3 L13: 1.0604 L23: 0.8732
REMARK 3 S TENSOR
REMARK 3 S11: 0.0790 S12: -0.0593 S13: -0.1133
REMARK 3 S21: 0.0287 S22: 0.0457 S23: -0.0060
REMARK 3 S31: 0.2033 S32: -0.1073 S33: -0.1247
REMARK 3
REMARK 3 TLS GROUP : 2
REMARK 3 SELECTION: {A|83 - 106}
REMARK 3 ORIGIN FOR THE GROUP (A): -3.5634 -26.5602 -12.8091
REMARK 3 T TENSOR
REMARK 3 T11: -0.0696 T22: -0.0216
REMARK 3 T33: -0.0167 T12: 0.0180
REMARK 3 T13: -0.0233 T23: 0.0085
REMARK 3 L TENSOR
REMARK 3 L11: 1.6986 L22: 0.6272
REMARK 3 L33: 2.4997 L12: -0.6992
REMARK 3 L13: -0.5291 L23: -0.3465
REMARK 3 S TENSOR
REMARK 3 S11: 0.0425 S12: -0.0936 S13: -0.2358
REMARK 3 S21: 0.0150 S22: 0.0429 S23: 0.0322
REMARK 3 S31: 0.2337 S32: 0.2395 S33: -0.0855
REMARK 3
REMARK 3 TLS GROUP : 3
REMARK 3 SELECTION: {A|107 - 218}
REMARK 3 ORIGIN FOR THE GROUP (A): -11.4076 -13.2519 -16.7087
REMARK 3 T TENSOR
REMARK 3 T11: -0.0454 T22: -0.0400
REMARK 3 T33: -0.0421 T12: -0.0169
REMARK 3 T13: -0.0036 T23: -0.0012
REMARK 3 L TENSOR
REMARK 3 L11: 0.8668 L22: 1.0220
REMARK 3 L33: 0.9695 L12: -0.0558
REMARK 3 L13: 0.0705 L23: -0.0495
REMARK 3 S TENSOR
REMARK 3 S11: 0.0217 S12: 0.0029 S13: 0.0552
REMARK 3 S21: 0.0253 S22: 0.0038 S23: -0.0366
REMARK 3 S31: -0.1767 S32: 0.0175 S33: -0.0255
REMARK 3
REMARK 3 TLS GROUP : 4
REMARK 3 SELECTION: {A|219 - 230}
REMARK 3 ORIGIN FOR THE GROUP (A): -18.4517 -20.0982 -30.5072
REMARK 3 T TENSOR
REMARK 3 T11: -0.0265 T22: -0.0012
REMARK 3 T33: -0.0056 T12: -0.0195
REMARK 3 T13: -0.0091 T23: -0.0345
REMARK 3 L TENSOR
REMARK 3 L11: 0.0989 L22: 0.2865
REMARK 3 L33: 1.3361 L12: -1.4681
REMARK 3 L13: 1.2269 L23: -1.3653
REMARK 3 S TENSOR
REMARK 3 S11: 0.0053 S12: 0.0798 S13: 0.0224
REMARK 3 S21: -0.1045 S22: 0.0233 S23: 0.0402
REMARK 3 S31: 0.0431 S32: -0.0689 S33: -0.0286
REMARK 3
REMARK 3 TLS GROUP : 5
REMARK 3 SELECTION: {B|8 - 19}
REMARK 3 ORIGIN FOR THE GROUP (A): -25.1258 -33.6258 26.2076
REMARK 3 T TENSOR
REMARK 3 T11: 0.0124 T22: 0.0344
REMARK 3 T33: -0.0365 T12: 0.0209
REMARK 3 T13: 0.0173 T23: -0.0081
REMARK 3 L TENSOR
REMARK 3 L11: 0.5382 L22: 1.0898
REMARK 3 L33: 0.6609 L12: 1.0910
REMARK 3 L13: 0.0438 L23: -0.4527
REMARK 3 S TENSOR
REMARK 3 S11: -0.0547 S12: -0.0497 S13: -0.0537
REMARK 3 S21: -0.0047 S22: 0.0955 S23: 0.0813
REMARK 3 S31: 0.0969 S32: 0.0212 S33: -0.0408
REMARK 3
REMARK 3 TLS GROUP : 6
REMARK 3 SELECTION: {B|20 - 153}
REMARK 3 ORIGIN FOR THE GROUP (A): -26.9115 -19.1052 18.1021
REMARK 3 T TENSOR
REMARK 3 T11: -0.0932 T22: -0.0012
REMARK 3 T33: -0.0394 T12: 0.0001
REMARK 3 T13: 0.0109 T23: 0.0374
REMARK 3 L TENSOR
REMARK 3 L11: 0.2033 L22: 0.6395
REMARK 3 L33: 1.8293 L12: 0.0090
REMARK 3 L13: -0.1884 L23: -0.5155
REMARK 3 S TENSOR
REMARK 3 S11: -0.0035 S12: 0.0485 S13: 0.0378
REMARK 3 S21: 0.0084 S22: 0.1083 S23: 0.0774
REMARK 3 S31: -0.0547 S32: -0.1476 S33: -0.1049
REMARK 3
REMARK 3 TLS GROUP : 7
REMARK 3 SELECTION: {B|154 - 163}
REMARK 3 ORIGIN FOR THE GROUP (A): -33.1449 -4.2839 29.0024
REMARK 3 T TENSOR
REMARK 3 T11: -0.0117 T22: 0.0061
REMARK 3 T33: 0.0682 T12: 0.0769
REMARK 3 T13: 0.1129 T23: 0.0323
REMARK 3 L TENSOR
REMARK 3 L11: 0.4550 L22: 0.8222
REMARK 3 L33: 0.2281 L12: -1.0637
REMARK 3 L13: 0.6488 L23: 0.9862
REMARK 3 S TENSOR
REMARK 3 S11: 0.0034 S12: 0.0106 S13: 0.0321
REMARK 3 S21: -0.0139 S22: 0.0145 S23: 0.0468
REMARK 3 S31: -0.0777 S32: 0.0008 S33: -0.0179
REMARK 3
REMARK 3 TLS GROUP : 8
REMARK 3 SELECTION: {B|164 - 230}
REMARK 3 ORIGIN FOR THE GROUP (A): -16.5144 -11.1907 24.0500
REMARK 3 T TENSOR
REMARK 3 T11: -0.0528 T22: -0.0267
REMARK 3 T33: -0.0385 T12: -0.0162
REMARK 3 T13: 0.0191 T23: -0.0124
REMARK 3 L TENSOR
REMARK 3 L11: 1.0363 L22: 1.1202
REMARK 3 L33: 1.3511 L12: 0.2214
REMARK 3 L13: -0.7133 L23: -0.8454
REMARK 3 S TENSOR
REMARK 3 S11: 0.0983 S12: -0.0390 S13: 0.1818
REMARK 3 S21: 0.1320 S22: -0.0038 S23: 0.0143
REMARK 3 S31: -0.2476 S32: 0.0812 S33: -0.0945
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 5SYM 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_1000222850.
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-D
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792
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 : 63533
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550
REMARK 200 RESOLUTION RANGE LOW (A) : 43.510
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 200 DATA REDUNDANCY : 8.100
REMARK 200 R MERGE (I) : 0.05700
REMARK 200 R SYM (I) : NULL
REMARK 200 FOR THE DATA SET : 18.5000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.57
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : 7.80
REMARK 200 R MERGE FOR SHELL (I) : 0.44900
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: MOLREP
REMARK 200 STARTING MODEL: APT1-CHAINA, PDB:1FJ2
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 43.77
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM CITRATE, 22-24% PEG 3350,
REMARK 280 200 MM MGCL2, PH 5.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE
REMARK 280 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21
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,Y+1/2,-Z+1/2
REMARK 290 4555 -X,-Y+1/2,Z+1/2
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 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.84500
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 40.91000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.84500
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 40.91000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1, 2
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 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 ASN A 5
REMARK 465 MET A 6
REMARK 465 SER A 7
REMARK 465 MET B 1
REMARK 465 CYS B 2
REMARK 465 GLY B 3
REMARK 465 ASN B 4
REMARK 465 ASN B 5
REMARK 465 MET B 6
REMARK 465 SER B 7
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 THR A 8 OG1 CG2
REMARK 470 LEU A 10 CG CD1 CD2
REMARK 470 ASP B 230 CG OD1 OD2
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC
REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15
REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A
REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375
REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE
REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS.
REMARK 500
REMARK 500 DISTANCE CUTOFF:
REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS
REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE
REMARK 500 H GLN A 212 OD2 ASP B 101 4444 1.59
REMARK 500
REMARK 500 REMARK: NULL
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 LYS A 19 118.65 -31.97
REMARK 500 ASN A 64 59.55 -118.07
REMARK 500 SER A 119 -124.39 55.21
REMARK 500 MET A 207 -145.06 -101.58
REMARK 500 ASN B 64 58.73 -116.73
REMARK 500 SER B 119 -119.46 54.36
REMARK 500 MET B 207 -146.04 -101.75
REMARK 500 SER B 209 -163.04 -160.84
REMARK 500
REMARK 500 REMARK: NULL
REMARK 525
REMARK 525 SOLVENT
REMARK 525
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
REMARK 525
REMARK 525 M RES CSSEQI
REMARK 525 HOH A 588 DISTANCE = 5.89 ANGSTROMS
REMARK 525 HOH A 589 DISTANCE = 6.63 ANGSTROMS
REMARK 525 HOH B 573 DISTANCE = 6.05 ANGSTROMS
REMARK 525 HOH B 574 DISTANCE = 6.36 ANGSTROMS
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue 71Q 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 EDO A 303
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 304
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 305
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 306
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 307
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 308
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 309
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 310
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue 71Q B 301
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 302
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue CL B 303
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 5SYN RELATED DB: PDB
DBREF 5SYM A 1 230 UNP O75608 LYPA1_HUMAN 1 230
DBREF 5SYM B 1 230 UNP O75608 LYPA1_HUMAN 1 230
SEQRES 1 A 230 MET CYS GLY ASN ASN MET SER THR PRO LEU PRO ALA ILE
SEQRES 2 A 230 VAL PRO ALA ALA ARG LYS ALA THR ALA ALA VAL ILE PHE
SEQRES 3 A 230 LEU HIS GLY LEU GLY ASP THR GLY HIS GLY TRP ALA GLU
SEQRES 4 A 230 ALA PHE ALA GLY ILE ARG SER SER HIS ILE LYS TYR ILE
SEQRES 5 A 230 CYS PRO HIS ALA PRO VAL ARG PRO VAL THR LEU ASN MET
SEQRES 6 A 230 ASN VAL ALA MET PRO SER TRP PHE ASP ILE ILE GLY LEU
SEQRES 7 A 230 SER PRO ASP SER GLN GLU ASP GLU SER GLY ILE LYS GLN
SEQRES 8 A 230 ALA ALA GLU ASN ILE LYS ALA LEU ILE ASP GLN GLU VAL
SEQRES 9 A 230 LYS ASN GLY ILE PRO SER ASN ARG ILE ILE LEU GLY GLY
SEQRES 10 A 230 PHE SER GLN GLY GLY ALA LEU SER LEU TYR THR ALA LEU
SEQRES 11 A 230 THR THR GLN GLN LYS LEU ALA GLY VAL THR ALA LEU SER
SEQRES 12 A 230 CYS TRP LEU PRO LEU ARG ALA SER PHE PRO GLN GLY PRO
SEQRES 13 A 230 ILE GLY GLY ALA ASN ARG ASP ILE SER ILE LEU GLN CYS
SEQRES 14 A 230 HIS GLY ASP CYS ASP PRO LEU VAL PRO LEU MET PHE GLY
SEQRES 15 A 230 SER LEU THR VAL GLU LYS LEU LYS THR LEU VAL ASN PRO
SEQRES 16 A 230 ALA ASN VAL THR PHE LYS THR TYR GLU GLY MET MET HIS
SEQRES 17 A 230 SER SER CYS GLN GLN GLU MET MET ASP VAL LYS GLN PHE
SEQRES 18 A 230 ILE ASP LYS LEU LEU PRO PRO ILE ASP
SEQRES 1 B 230 MET CYS GLY ASN ASN MET SER THR PRO LEU PRO ALA ILE
SEQRES 2 B 230 VAL PRO ALA ALA ARG LYS ALA THR ALA ALA VAL ILE PHE
SEQRES 3 B 230 LEU HIS GLY LEU GLY ASP THR GLY HIS GLY TRP ALA GLU
SEQRES 4 B 230 ALA PHE ALA GLY ILE ARG SER SER HIS ILE LYS TYR ILE
SEQRES 5 B 230 CYS PRO HIS ALA PRO VAL ARG PRO VAL THR LEU ASN MET
SEQRES 6 B 230 ASN VAL ALA MET PRO SER TRP PHE ASP ILE ILE GLY LEU
SEQRES 7 B 230 SER PRO ASP SER GLN GLU ASP GLU SER GLY ILE LYS GLN
SEQRES 8 B 230 ALA ALA GLU ASN ILE LYS ALA LEU ILE ASP GLN GLU VAL
SEQRES 9 B 230 LYS ASN GLY ILE PRO SER ASN ARG ILE ILE LEU GLY GLY
SEQRES 10 B 230 PHE SER GLN GLY GLY ALA LEU SER LEU TYR THR ALA LEU
SEQRES 11 B 230 THR THR GLN GLN LYS LEU ALA GLY VAL THR ALA LEU SER
SEQRES 12 B 230 CYS TRP LEU PRO LEU ARG ALA SER PHE PRO GLN GLY PRO
SEQRES 13 B 230 ILE GLY GLY ALA ASN ARG ASP ILE SER ILE LEU GLN CYS
SEQRES 14 B 230 HIS GLY ASP CYS ASP PRO LEU VAL PRO LEU MET PHE GLY
SEQRES 15 B 230 SER LEU THR VAL GLU LYS LEU LYS THR LEU VAL ASN PRO
SEQRES 16 B 230 ALA ASN VAL THR PHE LYS THR TYR GLU GLY MET MET HIS
SEQRES 17 B 230 SER SER CYS GLN GLN GLU MET MET ASP VAL LYS GLN PHE
SEQRES 18 B 230 ILE ASP LYS LEU LEU PRO PRO ILE ASP
HET 71Q A 301 38
HET EDO A 302 4
HET EDO A 303 4
HET EDO A 304 4
HET EDO A 305 4
HET EDO A 306 4
HET CL A 307 1
HET CL A 308 1
HET CL A 309 1
HET EDO A 310 4
HET 71Q B 301 38
HET EDO B 302 4
HET CL B 303 1
HETNAM 71Q N-[2-CHLORO-5-(TRIFLUOROMETHYL)PHENYL]-2-[4-(FURAN-2-
HETNAM 2 71Q CARBONYL)PIPERAZIN-1-YL]ACETAMIDE
HETNAM EDO 1,2-ETHANEDIOL
HETNAM CL CHLORIDE ION
HETSYN EDO ETHYLENE GLYCOL
FORMUL 3 71Q 2(C18 H17 CL F3 N3 O3)
FORMUL 4 EDO 7(C2 H6 O2)
FORMUL 9 CL 4(CL 1-)
FORMUL 16 HOH *363(H2 O)
HELIX 1 AA1 GLY A 34 GLY A 43 1 10
HELIX 2 AA2 THR A 62 MET A 65 5 4
HELIX 3 AA3 ASP A 85 ASN A 106 1 22
HELIX 4 AA4 PRO A 109 ASN A 111 5 3
HELIX 5 AA5 SER A 119 LEU A 130 1 12
HELIX 6 AA6 LEU A 148 PHE A 152 5 5
HELIX 7 AA7 PRO A 178 VAL A 193 1 16
HELIX 8 AA8 ASN A 194 ALA A 196 5 3
HELIX 9 AA9 CYS A 211 LEU A 226 1 16
HELIX 10 AB1 GLY B 34 GLY B 43 1 10
HELIX 11 AB2 THR B 62 MET B 65 5 4
HELIX 12 AB3 ASP B 85 ASN B 106 1 22
HELIX 13 AB4 PRO B 109 ASN B 111 5 3
HELIX 14 AB5 SER B 119 THR B 132 1 14
HELIX 15 AB6 LEU B 148 PHE B 152 5 5
HELIX 16 AB7 PRO B 178 VAL B 193 1 16
HELIX 17 AB8 ASN B 194 ALA B 196 5 3
HELIX 18 AB9 CYS B 211 LEU B 226 1 16
SHEET 1 AA1 7 ALA A 12 VAL A 14 0
SHEET 2 AA1 7 ILE A 49 CYS A 53 -1 O CYS A 53 N ALA A 12
SHEET 3 AA1 7 ALA A 22 LEU A 27 1 N VAL A 24 O ILE A 52
SHEET 4 AA1 7 ILE A 113 PHE A 118 1 O ILE A 114 N ILE A 25
SHEET 5 AA1 7 GLY A 138 LEU A 142 1 O LEU A 142 N GLY A 117
SHEET 6 AA1 7 SER A 165 GLY A 171 1 O LEU A 167 N VAL A 139
SHEET 7 AA1 7 VAL A 198 TYR A 203 1 O THR A 199 N GLN A 168
SHEET 1 AA2 2 VAL A 58 PRO A 60 0
SHEET 2 AA2 2 ALA A 68 PRO A 70 -1 O MET A 69 N ARG A 59
SHEET 1 AA3 7 ALA B 12 VAL B 14 0
SHEET 2 AA3 7 ILE B 49 CYS B 53 -1 O CYS B 53 N ALA B 12
SHEET 3 AA3 7 ALA B 22 LEU B 27 1 N VAL B 24 O ILE B 52
SHEET 4 AA3 7 ILE B 113 PHE B 118 1 O ILE B 114 N ILE B 25
SHEET 5 AA3 7 GLY B 138 LEU B 142 1 O LEU B 142 N GLY B 117
SHEET 6 AA3 7 SER B 165 GLY B 171 1 O LEU B 167 N ALA B 141
SHEET 7 AA3 7 VAL B 198 TYR B 203 1 O THR B 199 N GLN B 168
SHEET 1 AA4 2 VAL B 58 PRO B 60 0
SHEET 2 AA4 2 ALA B 68 PRO B 70 -1 O MET B 69 N ARG B 59
CISPEP 1 THR A 8 PRO A 9 0 5.14
SITE 1 AC1 15 ILE A 75 GLY A 77 LEU A 78 SER A 79
SITE 2 AC1 15 PRO A 80 TRP A 145 LEU A 146 ARG A 149
SITE 3 AC1 15 LEU A 176 VAL A 177 PHE A 181 THR A 185
SITE 4 AC1 15 CL A 308 HOH A 431 HOH A 456
SITE 1 AC2 4 GLY A 36 TRP A 37 SER A 210 MET B 65
SITE 1 AC3 4 SER A 210 CYS A 211 MET A 215 HOH A 531
SITE 1 AC4 8 LYS A 97 THR A 131 THR A 132 GLN A 133
SITE 2 AC4 8 HOH A 403 HOH A 423 GLU B 204 GLN B 213
SITE 1 AC5 6 LYS A 19 ALA A 20 ASN A 106 CL A 307
SITE 2 AC5 6 HOH A 428 ARG B 45
SITE 1 AC6 3 GLN A 83 GLU A 84 HOH A 459
SITE 1 AC7 4 ALA A 20 EDO A 305 ARG B 45 HOH B 547
SITE 1 AC8 5 LEU A 30 SER A 119 GLN A 120 71Q A 301
SITE 2 AC8 5 HOH B 414
SITE 1 AC9 4 ARG A 18 THR A 21 PRO A 228 ILE A 229
SITE 1 AD1 5 MET A 65 HOH A 466 GLY B 36 TRP B 37
SITE 2 AD1 5 SER B 210
SITE 1 AD2 16 LEU B 30 ILE B 75 GLY B 77 LEU B 78
SITE 2 AD2 16 SER B 79 PRO B 80 TRP B 145 LEU B 146
SITE 3 AD2 16 ARG B 149 LEU B 176 VAL B 177 PHE B 181
SITE 4 AD2 16 THR B 185 CL B 303 HOH B 408 HOH B 411
SITE 1 AD3 7 ASN A 66 GLY A 159 MET B 207 SER B 209
SITE 2 AD3 7 HOH B 417 HOH B 426 HOH B 450
SITE 1 AD4 5 HOH A 420 LEU B 30 SER B 119 GLN B 120
SITE 2 AD4 5 71Q B 301
CRYST1 71.670 73.690 81.820 90.00 90.00 90.00 P 2 21 21 8
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 0.013953 0.000000 0.000000 0.00000
SCALE2 0.000000 0.013570 0.000000 0.00000
SCALE3 0.000000 0.000000 0.012222 0.00000
TER 3460 ASP A 230
TER 6890 ASP B 230
MASTER 497 0 13 18 18 0 25 6 3801 2 104 36
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