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HEADER HYDROLASE 12-JAN-19 6QGQ
TITLE CRYSTAL STRUCTURE OF APT1 C2S MUTANT BOUND TO PALMITIC ACID.
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: ACYL-PROTEIN THIOESTERASE 1;
COMPND 3 CHAIN: A, C, D;
COMPND 4 SYNONYM: HAPT1,LYSOPHOSPHOLIPASE 1,LYSOPHOSPHOLIPASE I,LYSOPLA I;
COMPND 5 EC: 3.1.2.-;
COMPND 6 ENGINEERED: YES;
COMPND 7 MUTATION: YES;
COMPND 8 MOL_ID: 2;
COMPND 9 MOLECULE: ACYL-PROTEIN THIOESTERASE 1;
COMPND 10 CHAIN: B;
COMPND 11 SYNONYM: HAPT1,LYSOPHOSPHOLIPASE 1,LYSOPHOSPHOLIPASE I,LYSOPLA I;
COMPND 12 EC: 3.1.2.-;
COMPND 13 ENGINEERED: YES;
COMPND 14 MUTATION: 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;
SOURCE 8 MOL_ID: 2;
SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 10 ORGANISM_COMMON: HUMAN;
SOURCE 11 ORGANISM_TAXID: 9606;
SOURCE 12 GENE: LYPLA1, APT1, LPL1;
SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS ACYL-PROTEIN THIOESTERASE, PALMITIC ACID, DEPALMITOYLATION, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR M.AUDAGNOTTO,M.J.MARCAIDA,S.HO,F.POJER,G.VAN DER GOOT,M.DAL PERARO
REVDAT 3 31-MAR-21 6QGQ 1 JRNL
REVDAT 2 17-MAR-21 6QGQ 1 JRNL
REVDAT 1 05-FEB-20 6QGQ 0
JRNL AUTH L.ABRAMI,M.AUDAGNOTTO,S.HO,M.J.MARCAIDA,F.S.MESQUITA,
JRNL AUTH 2 M.U.ANWAR,P.A.SANDOZ,G.FONTI,F.POJER,M.DAL PERARO,
JRNL AUTH 3 F.G.VAN DER GOOT
JRNL TITL PALMITOYLATED ACYL PROTEIN THIOESTERASE APT2 DEFORMS
JRNL TITL 2 MEMBRANES TO EXTRACT SUBSTRATE ACYL CHAINS.
JRNL REF NAT.CHEM.BIOL. 2021
JRNL REFN ESSN 1552-4469
JRNL PMID 33707782
JRNL DOI 10.1038/S41589-021-00753-2
REMARK 2
REMARK 2 RESOLUTION. 2.60 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX (1.14_3260)
REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN
REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE,
REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER,
REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY,
REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON,
REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI,
REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT
REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART
REMARK 3
REMARK 3 REFINEMENT TARGET : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.62
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 3 NUMBER OF REFLECTIONS : 30461
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.193
REMARK 3 R VALUE (WORKING SET) : 0.191
REMARK 3 FREE R VALUE : 0.238
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.860
REMARK 3 FREE R VALUE TEST SET COUNT : 1481
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS).
REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE
REMARK 3 1 46.6263 - 5.7822 1.00 2836 133 0.1884 0.2263
REMARK 3 2 5.7822 - 4.5908 1.00 2683 146 0.1719 0.2338
REMARK 3 3 4.5908 - 4.0109 1.00 2673 129 0.1551 0.1810
REMARK 3 4 4.0109 - 3.6443 1.00 2653 121 0.1762 0.2184
REMARK 3 5 3.6443 - 3.3832 1.00 2565 163 0.1853 0.2267
REMARK 3 6 3.3832 - 3.1838 1.00 2651 118 0.2057 0.2429
REMARK 3 7 3.1838 - 3.0244 1.00 2608 128 0.2205 0.2824
REMARK 3 8 3.0244 - 2.8927 1.00 2534 148 0.2313 0.2894
REMARK 3 9 2.8927 - 2.7814 1.00 2614 149 0.2295 0.2994
REMARK 3 10 2.7814 - 2.6854 1.00 2572 117 0.2303 0.3104
REMARK 3 11 2.6854 - 2.6015 0.99 2591 129 0.2258 0.2432
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : NULL
REMARK 3 SOLVENT RADIUS : 1.11
REMARK 3 SHRINKAGE RADIUS : 0.90
REMARK 3 K_SOL : NULL
REMARK 3 B_SOL : NULL
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.260
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.470
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL
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 TWINNING INFORMATION.
REMARK 3 FRACTION: NULL
REMARK 3 OPERATOR: NULL
REMARK 3
REMARK 3 DEVIATIONS FROM IDEAL VALUES.
REMARK 3 RMSD COUNT
REMARK 3 BOND : 0.003 6883
REMARK 3 ANGLE : 0.541 9343
REMARK 3 CHIRALITY : 0.042 1065
REMARK 3 PLANARITY : 0.004 1205
REMARK 3 DIHEDRAL : 6.818 4162
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 NCS DETAILS
REMARK 3 NUMBER OF NCS GROUPS : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 6QGQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-JAN-19.
REMARK 100 THE DEPOSITION ID IS D_1292100145.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 27-JUN-16
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SLS
REMARK 200 BEAMLINE : X06DA
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M-F
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : SCALA
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30525
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600
REMARK 200 RESOLUTION RANGE LOW (A) : 48.710
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 200 DATA REDUNDANCY : 7.900
REMARK 200 R MERGE (I) : 0.18000
REMARK 200 R SYM (I) : NULL
REMARK 200 FOR THE DATA SET : 9.6000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.74
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: PHASER
REMARK 200 STARTING MODEL: 1FJ2
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 50.90
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 25% OF OF POLYETHYLENE GLYCOL (PEG)
REMARK 280 2000 MME, 0.3 M SODIUM ACETATE, 0.1 M SODIUM CACODYLATE PH 6.5;,
REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2
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 73.06900
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 80.36900
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 73.06900
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 80.36900
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 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 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 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 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 GLY A -2
REMARK 465 SER A -1
REMARK 465 ARG A 0
REMARK 465 MET A 1
REMARK 465 SER 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 GLY B -2
REMARK 465 SER B -1
REMARK 465 ARG B 0
REMARK 465 MET B 1
REMARK 465 SER 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 465 THR B 8
REMARK 465 GLY C -2
REMARK 465 SER C -1
REMARK 465 ARG C 0
REMARK 465 MET C 1
REMARK 465 SER C 2
REMARK 465 GLY C 3
REMARK 465 ASN C 4
REMARK 465 ASN C 5
REMARK 465 MET C 6
REMARK 465 SER C 7
REMARK 465 THR C 8
REMARK 465 ASP C 230
REMARK 465 GLY D -2
REMARK 465 SER D -1
REMARK 465 ARG D 0
REMARK 465 MET D 1
REMARK 465 SER D 2
REMARK 465 GLY D 3
REMARK 465 ASN D 4
REMARK 465 ASN D 5
REMARK 465 MET D 6
REMARK 465 SER D 7
REMARK 465 THR D 8
REMARK 465 ASP D 230
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500 OD2 ASP C 174 O HOH C 701 1.87
REMARK 500 OG SER D 143 O HOH D 401 1.93
REMARK 500 O CYS A 169 O HOH A 401 1.94
REMARK 500 O ASP B 74 O HOH B 501 2.01
REMARK 500 NE2 GLN B 102 O HOH B 502 2.01
REMARK 500 NZ LYS B 50 O HOH B 503 2.03
REMARK 500 CA GLY B 159 O HOH B 510 2.04
REMARK 500 O2 GOL D 301 O HOH D 402 2.05
REMARK 500 O HOH C 733 O HOH C 737 2.09
REMARK 500 ND2 ASN A 106 O HOH A 402 2.10
REMARK 500 OD1 ASN D 161 O HOH D 403 2.12
REMARK 500 O HOH B 531 O HOH B 532 2.13
REMARK 500 O LEU C 148 OG SER C 151 2.15
REMARK 500 OE2 GLU C 84 O HOH C 702 2.15
REMARK 500 OE1 GLU B 103 O HOH B 502 2.18
REMARK 500 O THR B 33 O HOH B 504 2.18
REMARK 500 O PRO D 228 O HOH D 404 2.19
REMARK 500
REMARK 500 REMARK: NULL
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 O HOH A 406 O HOH C 703 4456 1.76
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 ARG A 18 -75.47 -127.93
REMARK 500 ILE A 44 27.50 -144.14
REMARK 500 ASN A 64 58.30 -117.84
REMARK 500 SER A 119 -126.98 56.03
REMARK 500 ASN A 161 30.22 -99.95
REMARK 500 MET A 207 -151.50 -103.13
REMARK 500 ARG B 18 -109.08 -119.67
REMARK 500 SER B 119 -125.53 54.65
REMARK 500 CYS B 144 -161.35 -129.99
REMARK 500 SER B 151 -5.54 -57.37
REMARK 500 LYS B 190 1.35 -67.36
REMARK 500 MET B 207 -137.86 -93.68
REMARK 500 SER B 209 -147.56 -166.40
REMARK 500 ASP B 230 -5.64 -141.74
REMARK 500 ARG C 18 -99.10 -104.47
REMARK 500 ASN C 64 62.42 -114.85
REMARK 500 ASN C 111 0.86 -69.12
REMARK 500 SER C 119 -128.28 52.55
REMARK 500 ARG C 162 -57.55 -26.11
REMARK 500 PRO C 178 152.02 -48.95
REMARK 500 MET C 207 -149.99 -101.44
REMARK 500 ARG D 18 -156.44 -86.47
REMARK 500 LYS D 105 4.19 -68.65
REMARK 500 SER D 119 -123.21 55.91
REMARK 500 CYS D 144 -159.68 -129.28
REMARK 500 ASN D 194 109.14 -54.89
REMARK 500 MET D 207 -142.69 -92.91
REMARK 500 SER D 209 -155.40 -158.93
REMARK 500
REMARK 500 REMARK: NULL
REMARK 610
REMARK 610 MISSING HETEROATOM
REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 610 I=INSERTION CODE):
REMARK 610 M RES C SSEQI
REMARK 610 PLM D 302
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 301
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 302
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue PLM B 401
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue GOL C 601
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue GOL D 301
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue PLM D 302
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 6QGO RELATED DB: PDB
REMARK 900 RELATED ID: 6QGN RELATED DB: PDB
DBREF 6QGQ A 1 230 UNP O75608 LYPA1_HUMAN 1 230
DBREF 6QGQ B 1 230 UNP O75608 LYPA1_HUMAN 1 230
DBREF 6QGQ C 1 230 UNP O75608 LYPA1_HUMAN 1 230
DBREF 6QGQ D 1 230 UNP O75608 LYPA1_HUMAN 1 230
SEQADV 6QGQ GLY A -2 UNP O75608 EXPRESSION TAG
SEQADV 6QGQ SER A -1 UNP O75608 EXPRESSION TAG
SEQADV 6QGQ ARG A 0 UNP O75608 EXPRESSION TAG
SEQADV 6QGQ SER A 2 UNP O75608 CYS 2 ENGINEERED MUTATION
SEQADV 6QGQ GLY B -2 UNP O75608 EXPRESSION TAG
SEQADV 6QGQ SER B -1 UNP O75608 EXPRESSION TAG
SEQADV 6QGQ ARG B 0 UNP O75608 EXPRESSION TAG
SEQADV 6QGQ SER B 2 UNP O75608 CYS 2 ENGINEERED MUTATION
SEQADV 6QGQ ALA B 231 UNP O75608 EXPRESSION TAG
SEQADV 6QGQ GLY C -2 UNP O75608 EXPRESSION TAG
SEQADV 6QGQ SER C -1 UNP O75608 EXPRESSION TAG
SEQADV 6QGQ ARG C 0 UNP O75608 EXPRESSION TAG
SEQADV 6QGQ SER C 2 UNP O75608 CYS 2 ENGINEERED MUTATION
SEQADV 6QGQ GLY D -2 UNP O75608 EXPRESSION TAG
SEQADV 6QGQ SER D -1 UNP O75608 EXPRESSION TAG
SEQADV 6QGQ ARG D 0 UNP O75608 EXPRESSION TAG
SEQADV 6QGQ SER D 2 UNP O75608 CYS 2 ENGINEERED MUTATION
SEQRES 1 A 233 GLY SER ARG MET SER GLY ASN ASN MET SER THR PRO LEU
SEQRES 2 A 233 PRO ALA ILE VAL PRO ALA ALA ARG LYS ALA THR ALA ALA
SEQRES 3 A 233 VAL ILE PHE LEU HIS GLY LEU GLY ASP THR GLY HIS GLY
SEQRES 4 A 233 TRP ALA GLU ALA PHE ALA GLY ILE ARG SER SER HIS ILE
SEQRES 5 A 233 LYS TYR ILE CYS PRO HIS ALA PRO VAL ARG PRO VAL THR
SEQRES 6 A 233 LEU ASN MET ASN VAL ALA MET PRO SER TRP PHE ASP ILE
SEQRES 7 A 233 ILE GLY LEU SER PRO ASP SER GLN GLU ASP GLU SER GLY
SEQRES 8 A 233 ILE LYS GLN ALA ALA GLU ASN ILE LYS ALA LEU ILE ASP
SEQRES 9 A 233 GLN GLU VAL LYS ASN GLY ILE PRO SER ASN ARG ILE ILE
SEQRES 10 A 233 LEU GLY GLY PHE SER GLN GLY GLY ALA LEU SER LEU TYR
SEQRES 11 A 233 THR ALA LEU THR THR GLN GLN LYS LEU ALA GLY VAL THR
SEQRES 12 A 233 ALA LEU SER CYS TRP LEU PRO LEU ARG ALA SER PHE PRO
SEQRES 13 A 233 GLN GLY PRO ILE GLY GLY ALA ASN ARG ASP ILE SER ILE
SEQRES 14 A 233 LEU GLN CYS HIS GLY ASP CYS ASP PRO LEU VAL PRO LEU
SEQRES 15 A 233 MET PHE GLY SER LEU THR VAL GLU LYS LEU LYS THR LEU
SEQRES 16 A 233 VAL ASN PRO ALA ASN VAL THR PHE LYS THR TYR GLU GLY
SEQRES 17 A 233 MET MET HIS SER SER CYS GLN GLN GLU MET MET ASP VAL
SEQRES 18 A 233 LYS GLN PHE ILE ASP LYS LEU LEU PRO PRO ILE ASP
SEQRES 1 B 234 GLY SER ARG MET SER GLY ASN ASN MET SER THR PRO LEU
SEQRES 2 B 234 PRO ALA ILE VAL PRO ALA ALA ARG LYS ALA THR ALA ALA
SEQRES 3 B 234 VAL ILE PHE LEU HIS GLY LEU GLY ASP THR GLY HIS GLY
SEQRES 4 B 234 TRP ALA GLU ALA PHE ALA GLY ILE ARG SER SER HIS ILE
SEQRES 5 B 234 LYS TYR ILE CYS PRO HIS ALA PRO VAL ARG PRO VAL THR
SEQRES 6 B 234 LEU ASN MET ASN VAL ALA MET PRO SER TRP PHE ASP ILE
SEQRES 7 B 234 ILE GLY LEU SER PRO ASP SER GLN GLU ASP GLU SER GLY
SEQRES 8 B 234 ILE LYS GLN ALA ALA GLU ASN ILE LYS ALA LEU ILE ASP
SEQRES 9 B 234 GLN GLU VAL LYS ASN GLY ILE PRO SER ASN ARG ILE ILE
SEQRES 10 B 234 LEU GLY GLY PHE SER GLN GLY GLY ALA LEU SER LEU TYR
SEQRES 11 B 234 THR ALA LEU THR THR GLN GLN LYS LEU ALA GLY VAL THR
SEQRES 12 B 234 ALA LEU SER CYS TRP LEU PRO LEU ARG ALA SER PHE PRO
SEQRES 13 B 234 GLN GLY PRO ILE GLY GLY ALA ASN ARG ASP ILE SER ILE
SEQRES 14 B 234 LEU GLN CYS HIS GLY ASP CYS ASP PRO LEU VAL PRO LEU
SEQRES 15 B 234 MET PHE GLY SER LEU THR VAL GLU LYS LEU LYS THR LEU
SEQRES 16 B 234 VAL ASN PRO ALA ASN VAL THR PHE LYS THR TYR GLU GLY
SEQRES 17 B 234 MET MET HIS SER SER CYS GLN GLN GLU MET MET ASP VAL
SEQRES 18 B 234 LYS GLN PHE ILE ASP LYS LEU LEU PRO PRO ILE ASP ALA
SEQRES 1 C 233 GLY SER ARG MET SER GLY ASN ASN MET SER THR PRO LEU
SEQRES 2 C 233 PRO ALA ILE VAL PRO ALA ALA ARG LYS ALA THR ALA ALA
SEQRES 3 C 233 VAL ILE PHE LEU HIS GLY LEU GLY ASP THR GLY HIS GLY
SEQRES 4 C 233 TRP ALA GLU ALA PHE ALA GLY ILE ARG SER SER HIS ILE
SEQRES 5 C 233 LYS TYR ILE CYS PRO HIS ALA PRO VAL ARG PRO VAL THR
SEQRES 6 C 233 LEU ASN MET ASN VAL ALA MET PRO SER TRP PHE ASP ILE
SEQRES 7 C 233 ILE GLY LEU SER PRO ASP SER GLN GLU ASP GLU SER GLY
SEQRES 8 C 233 ILE LYS GLN ALA ALA GLU ASN ILE LYS ALA LEU ILE ASP
SEQRES 9 C 233 GLN GLU VAL LYS ASN GLY ILE PRO SER ASN ARG ILE ILE
SEQRES 10 C 233 LEU GLY GLY PHE SER GLN GLY GLY ALA LEU SER LEU TYR
SEQRES 11 C 233 THR ALA LEU THR THR GLN GLN LYS LEU ALA GLY VAL THR
SEQRES 12 C 233 ALA LEU SER CYS TRP LEU PRO LEU ARG ALA SER PHE PRO
SEQRES 13 C 233 GLN GLY PRO ILE GLY GLY ALA ASN ARG ASP ILE SER ILE
SEQRES 14 C 233 LEU GLN CYS HIS GLY ASP CYS ASP PRO LEU VAL PRO LEU
SEQRES 15 C 233 MET PHE GLY SER LEU THR VAL GLU LYS LEU LYS THR LEU
SEQRES 16 C 233 VAL ASN PRO ALA ASN VAL THR PHE LYS THR TYR GLU GLY
SEQRES 17 C 233 MET MET HIS SER SER CYS GLN GLN GLU MET MET ASP VAL
SEQRES 18 C 233 LYS GLN PHE ILE ASP LYS LEU LEU PRO PRO ILE ASP
SEQRES 1 D 233 GLY SER ARG MET SER GLY ASN ASN MET SER THR PRO LEU
SEQRES 2 D 233 PRO ALA ILE VAL PRO ALA ALA ARG LYS ALA THR ALA ALA
SEQRES 3 D 233 VAL ILE PHE LEU HIS GLY LEU GLY ASP THR GLY HIS GLY
SEQRES 4 D 233 TRP ALA GLU ALA PHE ALA GLY ILE ARG SER SER HIS ILE
SEQRES 5 D 233 LYS TYR ILE CYS PRO HIS ALA PRO VAL ARG PRO VAL THR
SEQRES 6 D 233 LEU ASN MET ASN VAL ALA MET PRO SER TRP PHE ASP ILE
SEQRES 7 D 233 ILE GLY LEU SER PRO ASP SER GLN GLU ASP GLU SER GLY
SEQRES 8 D 233 ILE LYS GLN ALA ALA GLU ASN ILE LYS ALA LEU ILE ASP
SEQRES 9 D 233 GLN GLU VAL LYS ASN GLY ILE PRO SER ASN ARG ILE ILE
SEQRES 10 D 233 LEU GLY GLY PHE SER GLN GLY GLY ALA LEU SER LEU TYR
SEQRES 11 D 233 THR ALA LEU THR THR GLN GLN LYS LEU ALA GLY VAL THR
SEQRES 12 D 233 ALA LEU SER CYS TRP LEU PRO LEU ARG ALA SER PHE PRO
SEQRES 13 D 233 GLN GLY PRO ILE GLY GLY ALA ASN ARG ASP ILE SER ILE
SEQRES 14 D 233 LEU GLN CYS HIS GLY ASP CYS ASP PRO LEU VAL PRO LEU
SEQRES 15 D 233 MET PHE GLY SER LEU THR VAL GLU LYS LEU LYS THR LEU
SEQRES 16 D 233 VAL ASN PRO ALA ASN VAL THR PHE LYS THR TYR GLU GLY
SEQRES 17 D 233 MET MET HIS SER SER CYS GLN GLN GLU MET MET ASP VAL
SEQRES 18 D 233 LYS GLN PHE ILE ASP LYS LEU LEU PRO PRO ILE ASP
HET GOL A 301 14
HET GOL A 302 14
HET PLM B 401 49
HET GOL C 601 14
HET GOL D 301 14
HET PLM D 302 27
HETNAM GOL GLYCEROL
HETNAM PLM PALMITIC ACID
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 5 GOL 4(C3 H8 O3)
FORMUL 7 PLM 2(C16 H32 O2)
FORMUL 11 HOH *132(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 GLY A 159 ILE A 164 5 6
HELIX 8 AA8 PRO A 178 VAL A 193 1 16
HELIX 9 AA9 ASN A 194 ALA A 196 5 3
HELIX 10 AB1 CYS A 211 LEU A 226 1 16
HELIX 11 AB2 GLY B 34 GLY B 43 1 10
HELIX 12 AB3 THR B 62 MET B 65 5 4
HELIX 13 AB4 ASP B 85 ASN B 106 1 22
HELIX 14 AB5 PRO B 109 ASN B 111 5 3
HELIX 15 AB6 SER B 119 THR B 131 1 13
HELIX 16 AB7 LEU B 148 PHE B 152 5 5
HELIX 17 AB8 PRO B 178 VAL B 193 1 16
HELIX 18 AB9 ASN B 194 ALA B 196 5 3
HELIX 19 AC1 CYS B 211 LEU B 226 1 16
HELIX 20 AC2 GLY C 34 GLY C 43 1 10
HELIX 21 AC3 THR C 62 MET C 65 5 4
HELIX 22 AC4 ASP C 85 ASN C 106 1 22
HELIX 23 AC5 PRO C 109 ASN C 111 5 3
HELIX 24 AC6 SER C 119 THR C 132 1 14
HELIX 25 AC7 LEU C 148 PHE C 152 5 5
HELIX 26 AC8 PRO C 178 VAL C 193 1 16
HELIX 27 AC9 ASN C 194 ALA C 196 5 3
HELIX 28 AD1 CYS C 211 LEU C 226 1 16
HELIX 29 AD2 GLY D 34 GLY D 43 1 10
HELIX 30 AD3 THR D 62 MET D 65 5 4
HELIX 31 AD4 ASP D 85 LYS D 105 1 21
HELIX 32 AD5 PRO D 109 ASN D 111 5 3
HELIX 33 AD6 SER D 119 THR D 132 1 14
HELIX 34 AD7 LEU D 148 PHE D 152 5 5
HELIX 35 AD8 PRO D 178 VAL D 193 1 16
HELIX 36 AD9 ASN D 194 ALA D 196 5 3
HELIX 37 AE1 CYS D 211 LEU D 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 LYS A 50
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 GLY A 138 N LEU A 115
SHEET 6 AA1 7 ILE A 166 GLY A 171 1 O LEU A 167 N VAL A 139
SHEET 7 AA1 7 VAL A 198 TYR A 203 1 O LYS A 201 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 TYR B 51 N VAL B 14
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 PHE B 118 N LEU B 27
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 VAL B 139
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
SHEET 1 AA5 7 ALA C 12 VAL C 14 0
SHEET 2 AA5 7 ILE C 49 CYS C 53 -1 O CYS C 53 N ALA C 12
SHEET 3 AA5 7 ALA C 22 LEU C 27 1 N VAL C 24 O ILE C 52
SHEET 4 AA5 7 ILE C 113 PHE C 118 1 O ILE C 114 N ALA C 23
SHEET 5 AA5 7 GLY C 138 LEU C 142 1 O LEU C 142 N GLY C 117
SHEET 6 AA5 7 SER C 165 GLY C 171 1 O LEU C 167 N VAL C 139
SHEET 7 AA5 7 VAL C 198 TYR C 203 1 O TYR C 203 N HIS C 170
SHEET 1 AA6 2 VAL C 58 PRO C 60 0
SHEET 2 AA6 2 ALA C 68 PRO C 70 -1 O MET C 69 N ARG C 59
SHEET 1 AA7 7 ALA D 12 VAL D 14 0
SHEET 2 AA7 7 ILE D 49 CYS D 53 -1 O CYS D 53 N ALA D 12
SHEET 3 AA7 7 ALA D 22 LEU D 27 1 N VAL D 24 O ILE D 52
SHEET 4 AA7 7 ILE D 113 PHE D 118 1 O ILE D 114 N ILE D 25
SHEET 5 AA7 7 GLY D 138 LEU D 142 1 O LEU D 142 N GLY D 117
SHEET 6 AA7 7 ILE D 166 GLY D 171 1 O LEU D 167 N VAL D 139
SHEET 7 AA7 7 VAL D 198 TYR D 203 1 O THR D 199 N GLN D 168
SHEET 1 AA8 2 VAL D 58 PRO D 60 0
SHEET 2 AA8 2 ALA D 68 PRO D 70 -1 O MET D 69 N ARG D 59
SITE 1 AC1 2 TRP A 37 MET B 65
SITE 1 AC2 3 MET A 65 HOH A 403 GLY B 36
SITE 1 AC3 9 LEU B 30 LEU B 78 SER B 119 GLN B 120
SITE 2 AC3 9 TRP B 145 ARG B 149 PHE B 181 THR B 185
SITE 3 AC3 9 HOH B 505
SITE 1 AC4 5 ASP C 32 GLY C 36 TRP C 37 SER C 210
SITE 2 AC4 5 HOH C 722
SITE 1 AC5 6 MET C 65 ASP D 32 GLY D 36 TRP D 37
SITE 2 AC5 6 SER D 210 HOH D 402
SITE 1 AC6 11 LEU D 30 ILE D 75 GLY D 77 LEU D 78
SITE 2 AC6 11 SER D 79 SER D 119 GLN D 120 TRP D 145
SITE 3 AC6 11 VAL D 177 PHE D 181 HOH D 407
CRYST1 146.138 160.738 40.679 90.00 90.00 90.00 P 21 21 2 12
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 0.006843 0.000000 0.000000 0.00000
SCALE2 0.000000 0.006221 0.000000 0.00000
SCALE3 0.000000 0.000000 0.024583 0.00000
TER 1679 ASP A 230
TER 3356 ALA B 231
TER 5020 ILE C 229
TER 6684 ILE D 229
MASTER 397 0 6 37 36 0 12 6 6865 4 132 72
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