HEADER TRANSPORT PROTEIN/INHIBITOR 16-JAN-15 4XNV
TITLE THE HUMAN P2Y1 RECEPTOR IN COMPLEX WITH BPTU
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: P2Y PURINOCEPTOR 1, RUBREDOXIN, P2Y PURINOCEPTOR 1;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: P2Y1, ATP RECEPTOR, PURINERGIC RECEPTOR;
COMPND 5 ENGINEERED: YES;
COMPND 6 MUTATION: YES;
COMPND 7 OTHER_DETAILS: CHIMERA PROTEIN OF P2Y PURINOCEPTOR 1 (P2RY1_HUMA)
COMPND 8 WITH RUBREDOXIN (RUBR_CLOPA) INSERTED INTO ICL3 DOMAIN BETWEEN
COMPND 9 RESIDUES 247LYS AND 253PRO, AND REPLACED RESIDUES 248ASN TO 252SER.
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS, CLOSTRIDIUM PASTEURIANUM;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606, 1501;
SOURCE 5 GENE: P2RY1;
SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7106;
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS
KEYWDS HUMAN P2Y1 RECEPTOR, G PROTEIN COUPLED RECEPTOR, PLATELET ACTIVATION,
KEYWDS 2 MEMBRANE PROTEIN, INHIBITOR COMPLEX, TRANSPORT PROTEIN-INHIBITOR
KEYWDS 3 COMPLEX, PSI-BIOLOGY, STRUCTURAL GENOMICS, GPCR NETWORK, GPCR
EXPDTA X-RAY DIFFRACTION
AUTHOR D.ZHANG,Z.GAO,K.JACOBSON,G.W.HAN,R.STEVENS,Q.ZHAO,B.WU,GPCR NETWORK
AUTHOR 2 (GPCR)
REVDAT 5 30-OCT-24 4XNV 1 REMARK
REVDAT 4 05-FEB-20 4XNV 1 SOURCE KEYWDS AUTHOR JRNL
REVDAT 4 2 1 REMARK
REVDAT 3 29-APR-15 4XNV 1 KEYWDS
REVDAT 2 22-APR-15 4XNV 1 JRNL
REVDAT 1 01-APR-15 4XNV 0
JRNL AUTH D.ZHANG,Z.G.GAO,K.ZHANG,E.KISELEV,S.CRANE,J.WANG,S.PAOLETTA,
JRNL AUTH 2 C.YI,L.MA,W.ZHANG,G.W.HAN,H.LIU,V.CHEREZOV,V.KATRITCH,
JRNL AUTH 3 H.JIANG,R.C.STEVENS,K.A.JACOBSON,Q.ZHAO,B.WU
JRNL TITL TWO DISPARATE LIGAND-BINDING SITES IN THE HUMAN P2Y1
JRNL TITL 2 RECEPTOR
JRNL REF NATURE V. 520 317 2015
JRNL REFN ESSN 1476-4687
JRNL PMID 25822790
JRNL DOI 10.1038/NATURE14287
REMARK 2
REMARK 2 RESOLUTION. 2.20 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : BUSTER 2.10.0
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) : 2.20
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.40
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 3 NUMBER OF REFLECTIONS : 19881
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) : 0.208
REMARK 3 R VALUE (WORKING SET) : 0.207
REMARK 3 FREE R VALUE : 0.230
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.120
REMARK 3 FREE R VALUE TEST SET COUNT : 1017
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 : 10
REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20
REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.32
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.94
REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2887
REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.3667
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2754
REMARK 3 BIN R VALUE (WORKING SET) : 0.3661
REMARK 3 BIN FREE R VALUE : 0.3786
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.61
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 133
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 : 2713
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 371
REMARK 3 SOLVENT ATOMS : 30
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 42.95
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 63.80
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -2.52040
REMARK 3 B22 (A**2) : -2.52040
REMARK 3 B33 (A**2) : 5.04090
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) : 0.369
REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.265
REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.190
REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.293
REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.200
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 : 0.941
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.931
REMARK 3
REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15
REMARK 3 TERM COUNT WEIGHT FUNCTION.
REMARK 3 BOND LENGTHS : 3164 ; 2.000 ; HARMONIC
REMARK 3 BOND ANGLES : 4262 ; 2.000 ; HARMONIC
REMARK 3 TORSION ANGLES : 1126 ; 2.000 ; SINUSOIDAL
REMARK 3 TRIGONAL CARBON PLANES : 38 ; 2.000 ; HARMONIC
REMARK 3 GENERAL PLANES : 440 ; 5.000 ; HARMONIC
REMARK 3 ISOTROPIC THERMAL FACTORS : 3164 ; 20.000 ; HARMONIC
REMARK 3 BAD NON-BONDED CONTACTS : 1 ; 5.000 ; SEMIHARMONIC
REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL
REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL
REMARK 3 CHIRAL IMPROPER TORSION : 406 ; 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 : 3716 ; 4.000 ; SEMIHARMONIC
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.010
REMARK 3 BOND ANGLES (DEGREES) : 1.04
REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.19
REMARK 3 OTHER TORSION ANGLES (DEGREES) : 17.56
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 1
REMARK 3
REMARK 3 TLS GROUP : 1
REMARK 3 SELECTION: { A|39 - A|334 }
REMARK 3 ORIGIN FOR THE GROUP (A): -11.1074 17.9445 9.7233
REMARK 3 T TENSOR
REMARK 3 T11: -0.1738 T22: -0.1537
REMARK 3 T33: -0.0538 T12: 0.0229
REMARK 3 T13: 0.0008 T23: -0.0413
REMARK 3 L TENSOR
REMARK 3 L11: 1.7026 L22: 2.2469
REMARK 3 L33: 1.0152 L12: 0.0833
REMARK 3 L13: 0.3764 L23: 0.0550
REMARK 3 S TENSOR
REMARK 3 S11: 0.0034 S12: -0.2893 S13: 0.2711
REMARK 3 S21: 0.2173 S22: 0.0210 S23: 0.2022
REMARK 3 S31: -0.0437 S32: -0.0951 S33: -0.0244
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 4XNV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-JAN-15.
REMARK 100 THE DEPOSITION ID IS D_1000205835.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 02-JUN-14
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 : SPRING-8
REMARK 200 BEAMLINE : BL41XU
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.0
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : XSCALE
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19881
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 200 DATA REDUNDANCY : 7.200
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.1000
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 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL
REMARK 200 SOFTWARE USED: PHASER
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 41.80
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PEG2000MME SODIUM CITRATE, LIPIDIC
REMARK 280 CUBIC PHASE, TEMPERATURE 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -Y,X-Y,Z
REMARK 290 3555 -X+Y,-X,Z
REMARK 290 4555 X+2/3,Y+1/3,Z+1/3
REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3
REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3
REMARK 290 7555 X+1/3,Y+2/3,Z+2/3
REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3
REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3
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 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.13500
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 19.13050
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 79.69000
REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 33.13500
REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 19.13050
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 79.69000
REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 33.13500
REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 19.13050
REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 79.69000
REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 38.26100
REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 159.38000
REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 38.26100
REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 159.38000
REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 38.26100
REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 159.38000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
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 TOTAL BURIED SURFACE AREA: 330 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 18390 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 KCAL/MOL
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 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 THR A 2
REMARK 465 GLU A 3
REMARK 465 VAL A 4
REMARK 465 LEU A 5
REMARK 465 TRP A 6
REMARK 465 PRO A 7
REMARK 465 ALA A 8
REMARK 465 VAL A 9
REMARK 465 PRO A 10
REMARK 465 ASN A 11
REMARK 465 GLY A 12
REMARK 465 THR A 13
REMARK 465 ASP A 14
REMARK 465 ALA A 15
REMARK 465 ALA A 16
REMARK 465 PHE A 17
REMARK 465 LEU A 18
REMARK 465 ALA A 19
REMARK 465 GLY A 20
REMARK 465 PRO A 21
REMARK 465 GLY A 22
REMARK 465 SER A 23
REMARK 465 SER A 24
REMARK 465 TRP A 25
REMARK 465 GLY A 26
REMARK 465 ASN A 27
REMARK 465 SER A 28
REMARK 465 THR A 29
REMARK 465 VAL A 30
REMARK 465 ALA A 31
REMARK 465 SER A 32
REMARK 465 THR A 33
REMARK 465 ALA A 34
REMARK 465 ALA A 35
REMARK 465 VAL A 36
REMARK 465 SER A 37
REMARK 465 SER A 38
REMARK 465 LEU A 157
REMARK 465 PRO A 1034
REMARK 465 ASP A 1035
REMARK 465 ASP A 1036
REMARK 465 TRP A 1037
REMARK 465 LEU A 335
REMARK 465 SER A 336
REMARK 465 ARG A 337
REMARK 465 ALA A 338
REMARK 465 THR A 339
REMARK 465 ARG A 340
REMARK 465 LYS A 341
REMARK 465 ALA A 342
REMARK 465 SER A 343
REMARK 465 ARG A 344
REMARK 465 ARG A 345
REMARK 465 SER A 346
REMARK 465 GLU A 347
REMARK 465 ALA A 348
REMARK 465 ASN A 349
REMARK 465 LEU A 350
REMARK 465 GLN A 351
REMARK 465 SER A 352
REMARK 465 LYS A 353
REMARK 465 SER A 354
REMARK 465 GLU A 355
REMARK 465 ASP A 356
REMARK 465 MET A 357
REMARK 465 THR A 358
REMARK 465 LEU A 359
REMARK 465 ASN A 360
REMARK 465 ILE A 361
REMARK 465 LEU A 362
REMARK 465 PRO A 363
REMARK 465 GLU A 364
REMARK 465 PHE A 365
REMARK 465 LYS A 366
REMARK 465 GLN A 367
REMARK 465 ASN A 368
REMARK 465 GLY A 369
REMARK 465 ASP A 370
REMARK 465 THR A 371
REMARK 465 SER A 372
REMARK 465 LEU A 373
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 45 OG1 CG2
REMARK 470 LYS A 158 CG CD CE NZ
REMARK 470 LEU A 160 CG CD1 CD2
REMARK 470 THR A 330 OG1 CG2
REMARK 470 ARG A 332 CG CD NE CZ NH1 NH2
REMARK 470 ARG A 334 CG CD NE CZ NH1 NH2
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 ALA A 43 81.26 -67.33
REMARK 500 TYR A 155 68.17 -114.33
REMARK 500 LEU A 160 43.60 -100.99
REMARK 500 THR A 205 -95.87 -106.43
REMARK 500 PHE A 226 -62.25 -125.78
REMARK 500 LEU A1041 -75.93 -77.95
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 OLC A 1106
REMARK 610 OLC A 1107
REMARK 610 OLC A 1112
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A1115 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A1006 SG
REMARK 620 2 CYS A1009 SG 104.5
REMARK 620 3 CYS A1039 SG 109.8 113.7
REMARK 620 4 CYS A1042 SG 98.5 119.5 109.3
REMARK 620 N 1 2 3
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue BUR A 1101
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue CLR A 1102
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue Y01 A 1103
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue Y01 A 1104
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue Y01 A 1105
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue OLC A 1106
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue OLC A 1107
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue OLC A 1108
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue OLC A 1109
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue OLC A 1110
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue OLC A 1111
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue OLC A 1112
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue OLC A 1113
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue 1PE A 1114
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 1115
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 4XNW RELATED DB: PDB
REMARK 900 RELATED ID: GPCR-86 RELATED DB: TARGETTRACK
DBREF 4XNV A 2 247 UNP P47900 P2RY1_HUMAN 2 247
DBREF 4XNV A 1001 1054 UNP P00268 RUBR_CLOPA 1 54
DBREF 4XNV A 253 373 UNP P47900 P2RY1_HUMAN 253 373
SEQADV 4XNV ASN A 320 UNP P47900 ASP 320 ENGINEERED MUTATION
SEQRES 1 A 421 THR GLU VAL LEU TRP PRO ALA VAL PRO ASN GLY THR ASP
SEQRES 2 A 421 ALA ALA PHE LEU ALA GLY PRO GLY SER SER TRP GLY ASN
SEQRES 3 A 421 SER THR VAL ALA SER THR ALA ALA VAL SER SER SER PHE
SEQRES 4 A 421 LYS CYS ALA LEU THR LYS THR GLY PHE GLN PHE TYR TYR
SEQRES 5 A 421 LEU PRO ALA VAL TYR ILE LEU VAL PHE ILE ILE GLY PHE
SEQRES 6 A 421 LEU GLY ASN SER VAL ALA ILE TRP MET PHE VAL PHE HIS
SEQRES 7 A 421 MET LYS PRO TRP SER GLY ILE SER VAL TYR MET PHE ASN
SEQRES 8 A 421 LEU ALA LEU ALA ASP PHE LEU TYR VAL LEU THR LEU PRO
SEQRES 9 A 421 ALA LEU ILE PHE TYR TYR PHE ASN LYS THR ASP TRP ILE
SEQRES 10 A 421 PHE GLY ASP ALA MET CYS LYS LEU GLN ARG PHE ILE PHE
SEQRES 11 A 421 HIS VAL ASN LEU TYR GLY SER ILE LEU PHE LEU THR CYS
SEQRES 12 A 421 ILE SER ALA HIS ARG TYR SER GLY VAL VAL TYR PRO LEU
SEQRES 13 A 421 LYS SER LEU GLY ARG LEU LYS LYS LYS ASN ALA ILE CYS
SEQRES 14 A 421 ILE SER VAL LEU VAL TRP LEU ILE VAL VAL VAL ALA ILE
SEQRES 15 A 421 SER PRO ILE LEU PHE TYR SER GLY THR GLY VAL ARG LYS
SEQRES 16 A 421 ASN LYS THR ILE THR CYS TYR ASP THR THR SER ASP GLU
SEQRES 17 A 421 TYR LEU ARG SER TYR PHE ILE TYR SER MET CYS THR THR
SEQRES 18 A 421 VAL ALA MET PHE CYS VAL PRO LEU VAL LEU ILE LEU GLY
SEQRES 19 A 421 CYS TYR GLY LEU ILE VAL ARG ALA LEU ILE TYR LYS MET
SEQRES 20 A 421 LYS LYS TYR THR CYS THR VAL CYS GLY TYR ILE TYR ASN
SEQRES 21 A 421 PRO GLU ASP GLY ASP PRO ASP ASN GLY VAL ASN PRO GLY
SEQRES 22 A 421 THR ASP PHE LYS ASP ILE PRO ASP ASP TRP VAL CYS PRO
SEQRES 23 A 421 LEU CYS GLY VAL GLY LYS ASP GLN PHE GLU GLU VAL GLU
SEQRES 24 A 421 GLU PRO LEU ARG ARG LYS SER ILE TYR LEU VAL ILE ILE
SEQRES 25 A 421 VAL LEU THR VAL PHE ALA VAL SER TYR ILE PRO PHE HIS
SEQRES 26 A 421 VAL MET LYS THR MET ASN LEU ARG ALA ARG LEU ASP PHE
SEQRES 27 A 421 GLN THR PRO ALA MET CYS ALA PHE ASN ASP ARG VAL TYR
SEQRES 28 A 421 ALA THR TYR GLN VAL THR ARG GLY LEU ALA SER LEU ASN
SEQRES 29 A 421 SER CYS VAL ASN PRO ILE LEU TYR PHE LEU ALA GLY ASP
SEQRES 30 A 421 THR PHE ARG ARG ARG LEU SER ARG ALA THR ARG LYS ALA
SEQRES 31 A 421 SER ARG ARG SER GLU ALA ASN LEU GLN SER LYS SER GLU
SEQRES 32 A 421 ASP MET THR LEU ASN ILE LEU PRO GLU PHE LYS GLN ASN
SEQRES 33 A 421 GLY ASP THR SER LEU
HET BUR A1101 32
HET CLR A1102 28
HET Y01 A1103 35
HET Y01 A1104 35
HET Y01 A1105 35
HET OLC A1106 21
HET OLC A1107 21
HET OLC A1108 25
HET OLC A1109 25
HET OLC A1110 25
HET OLC A1111 25
HET OLC A1112 22
HET OLC A1113 25
HET 1PE A1114 16
HET ZN A1115 1
HETNAM BUR 1-[2-(2-TERT-BUTYLPHENOXY)PYRIDIN-3-YL]-3-[4-
HETNAM 2 BUR (TRIFLUOROMETHOXY)PHENYL]UREA
HETNAM CLR CHOLESTEROL
HETNAM Y01 CHOLESTEROL HEMISUCCINATE
HETNAM OLC (2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTADEC-9-ENOATE
HETNAM 1PE PENTAETHYLENE GLYCOL
HETNAM ZN ZINC ION
HETSYN OLC 1-OLEOYL-R-GLYCEROL
HETSYN 1PE PEG400
FORMUL 2 BUR C23 H22 F3 N3 O3
FORMUL 3 CLR C27 H46 O
FORMUL 4 Y01 3(C31 H50 O4)
FORMUL 7 OLC 8(C21 H40 O4)
FORMUL 15 1PE C10 H22 O6
FORMUL 16 ZN ZN 2+
FORMUL 17 HOH *30(H2 O)
HELIX 1 AA1 PHE A 49 HIS A 79 1 31
HELIX 2 AA2 SER A 84 ASN A 113 1 30
HELIX 3 AA3 GLY A 120 TYR A 155 1 36
HELIX 4 AA4 LEU A 160 SER A 184 1 25
HELIX 5 AA5 PRO A 185 SER A 190 1 6
HELIX 6 AA6 TYR A 210 PHE A 226 1 17
HELIX 7 AA7 PHE A 226 TYR A 246 1 21
HELIX 8 AA8 ASP A 1029 ILE A 1033 5 5
HELIX 9 AA9 GLY A 1045 ASP A 1047 5 3
HELIX 10 AB1 GLU A 1054 SER A 272 1 21
HELIX 11 AB2 SER A 272 PHE A 290 1 19
HELIX 12 AB3 THR A 292 ALA A 294 5 3
HELIX 13 AB4 MET A 295 ASN A 320 1 26
HELIX 14 AB5 ASN A 320 ALA A 327 1 8
SHEET 1 AA1 2 GLY A 191 VAL A 194 0
SHEET 2 AA1 2 ILE A 200 TYR A 203 -1 O TYR A 203 N GLY A 191
SHEET 1 AA2 3 ILE A1012 TYR A1013 0
SHEET 2 AA2 3 TYR A1004 CYS A1006 -1 N TYR A1004 O TYR A1013
SHEET 3 AA2 3 PHE A1049 GLU A1051 -1 O GLU A1050 N THR A1005
SSBOND 1 CYS A 42 CYS A 296 1555 1555 2.04
SSBOND 2 CYS A 124 CYS A 202 1555 1555 2.03
LINK SG CYS A1006 ZN ZN A1115 1555 1555 2.88
LINK SG CYS A1009 ZN ZN A1115 1555 1555 2.18
LINK SG CYS A1039 ZN ZN A1115 1555 1555 2.60
LINK SG CYS A1042 ZN ZN A1115 1555 1555 2.35
CISPEP 1 LYS A 81 PRO A 82 0 -1.35
SITE 1 AC1 13 PHE A 62 PHE A 66 LEU A 102 THR A 103
SITE 2 AC1 13 PRO A 105 ALA A 106 MET A 123 GLN A 127
SITE 3 AC1 13 Y01 A1105 OLC A1107 OLC A1110 OLC A1113
SITE 4 AC1 13 1PE A1114
SITE 1 AC2 5 PRO A 185 TYR A 189 SER A 213 TYR A 217
SITE 2 AC2 5 Y01 A1103
SITE 1 AC3 8 ILE A 216 CYS A 220 ALA A 270 MET A 279
SITE 2 AC3 8 ARG A 301 THR A 305 CLR A1102 1PE A1114
SITE 1 AC4 7 TYR A 89 CYS A 144 HIS A 148 ALA A 224
SITE 2 AC4 7 LEU A 232 TYR A 246 LEU A 266
SITE 1 AC5 9 PHE A 62 ILE A 108 PHE A 109 PHE A 112
SITE 2 AC5 9 ASN A 113 ARG A 301 BUR A1101 OLC A1113
SITE 3 AC5 9 1PE A1114
SITE 1 AC6 5 ARG A 212 PHE A 215 ILE A 216 ASP A 289
SITE 2 AC6 5 OLC A1112
SITE 1 AC7 9 PHE A 109 SER A 184 PHE A 188 TYR A 189
SITE 2 AC7 9 TYR A 210 SER A 213 ARG A 301 BUR A1101
SITE 3 AC7 9 1PE A1114
SITE 1 AC8 4 ASP A 121 PHE A 129 OLC A1110 HOH A1206
SITE 1 AC9 6 LYS A 46 PHE A 49 TYR A 53 PHE A 112
SITE 2 AC9 6 CYS A 318 OLC A1111
SITE 1 AD1 10 ILE A 118 PHE A 119 ASP A 121 MET A 123
SITE 2 AD1 10 LYS A 125 SER A 184 LEU A 187 PHE A 188
SITE 3 AD1 10 BUR A1101 OLC A1108
SITE 1 AD2 6 PHE A 51 TYR A 52 PRO A 55 TYR A 111
SITE 2 AD2 6 PHE A 112 OLC A1109
SITE 1 AD3 5 PHE A 226 THR A 281 MET A 282 ARG A 285
SITE 2 AD3 5 OLC A1106
SITE 1 AD4 9 THR A 267 ALA A 270 ARG A 301 THR A 305
SITE 2 AD4 9 VAL A 308 BUR A1101 Y01 A1105 1PE A1114
SITE 3 AD4 9 HOH A1217
SITE 1 AD5 6 ARG A 301 BUR A1101 Y01 A1103 Y01 A1105
SITE 2 AD5 6 OLC A1107 OLC A1113
SITE 1 AD6 4 CYS A1006 CYS A1009 CYS A1039 CYS A1042
CRYST1 66.270 66.270 239.070 90.00 90.00 120.00 H 3 9
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 0.015090 0.008712 0.000000 0.00000
SCALE2 0.000000 0.017424 0.000000 0.00000
SCALE3 0.000000 0.000000 0.004183 0.00000