PDB Short entry for 5SVR HEADER MEMBRANE PROTEIN 07-AUG-16 5SVR TITLE CRYSTAL STRUCTURE OF THE ATP-GATED HUMAN P2X3 ION CHANNEL BOUND TO TITLE 2 COMPETITIVE ANTAGONIST A-317491 COMPND MOL_ID: 1; COMPND 2 MOLECULE: P2X PURINOCEPTOR 3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: P2X3,ATP RECEPTOR,PURINERGIC RECEPTOR; COMPND 5 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: P2RX3; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: HEK293; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: BACMAM KEYWDS MEMBRANE PROTEIN ION CHANNEL ANTAGONIST STATE, MEMBRANE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.E.MANSOOR,W.LU,W.OOSTERHEERT,M.SHEKHAR,E.TAJKHORSHID,E.GOUAUX REVDAT 5 29-JUL-20 5SVR 1 COMPND REMARK HETNAM LINK REVDAT 5 2 1 SITE REVDAT 4 25-DEC-19 5SVR 1 REMARK REVDAT 3 20-SEP-17 5SVR 1 JRNL REMARK REVDAT 2 19-OCT-16 5SVR 1 JRNL REVDAT 1 05-OCT-16 5SVR 0 JRNL AUTH S.E.MANSOOR,W.LU,W.OOSTERHEERT,M.SHEKHAR,E.TAJKHORSHID, JRNL AUTH 2 E.GOUAUX JRNL TITL X-RAY STRUCTURES DEFINE HUMAN P2X3 RECEPTOR GATING CYCLE AND JRNL TITL 2 ANTAGONIST ACTION. JRNL REF NATURE V. 538 66 2016 JRNL REFN ESSN 1476-4687 JRNL PMID 27626375 JRNL DOI 10.1038/NATURE19367 REMARK 2 REMARK 2 RESOLUTION. 3.13 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10_2142: ???) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.13 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.67 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 12303 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.254 REMARK 3 R VALUE (WORKING SET) : 0.252 REMARK 3 FREE R VALUE : 0.283 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 590 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 39.6775 - 4.9661 0.98 3038 144 0.2286 0.2451 REMARK 3 2 4.9661 - 3.9429 0.98 2887 147 0.2373 0.2872 REMARK 3 3 3.9429 - 3.4448 0.98 2883 146 0.3020 0.3417 REMARK 3 4 3.4448 - 3.1300 1.00 2905 153 0.3526 0.3789 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.490 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.860 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 : 0.004 2572 REMARK 3 ANGLE : 0.955 3517 REMARK 3 CHIRALITY : 0.049 408 REMARK 3 PLANARITY : 0.004 448 REMARK 3 DIHEDRAL : 16.707 1496 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 5SVR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-AUG-16. REMARK 100 THE DEPOSITION ID IS D_1000223220. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-DEC-15 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 : ALS REMARK 200 BEAMLINE : 5.0.2 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 : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12308 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.130 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 10.67 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.3700 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: MOLECULAR REPLACEMENT 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 (%): 71.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 400, 100 MM GLYCINE, PH 8.5, REMARK 280 150 MM MGCL2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 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 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+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 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 61.58500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 35.55612 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 79.15333 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 61.58500 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 35.55612 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 79.15333 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 61.58500 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 35.55612 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 79.15333 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 61.58500 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 35.55612 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 79.15333 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 61.58500 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 35.55612 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 79.15333 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 61.58500 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 35.55612 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 79.15333 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 71.11223 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 158.30667 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 71.11223 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 158.30667 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 71.11223 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 158.30667 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 71.11223 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 158.30667 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 71.11223 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 158.30667 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 71.11223 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 158.30667 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 14410 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 45660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -66.0 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 NA NA A 404 LIES ON A SPECIAL POSITION. 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 3 REMARK 465 ARG A 4 REMARK 465 ALA A 5 REMARK 465 ASP A 6 REMARK 465 PHE A 7 REMARK 465 PHE A 8 REMARK 465 THR A 9 REMARK 465 TYR A 10 REMARK 465 GLU A 11 REMARK 465 THR A 12 REMARK 465 PRO A 13 REMARK 465 LYS A 14 REMARK 465 VAL A 15 REMARK 465 ILE A 16 REMARK 465 VAL A 17 REMARK 465 VAL A 18 REMARK 465 LYS A 19 REMARK 465 SER A 20 REMARK 465 LYS A 348 REMARK 465 GLY A 349 REMARK 465 ALA A 350 REMARK 465 ASP A 351 REMARK 465 GLN A 352 REMARK 465 TYR A 353 REMARK 465 LYS A 354 REMARK 465 ALA A 355 REMARK 465 LYS A 356 REMARK 465 LYS A 357 REMARK 465 PHE A 358 REMARK 465 GLU A 359 REMARK 465 GLU A 360 REMARK 465 VAL A 361 REMARK 465 ASN A 362 REMARK 465 GLU A 363 REMARK 465 THR A 364 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 TRP A 21 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 21 CZ3 CH2 REMARK 470 ILE A 23 CG1 CG2 CD1 REMARK 470 LYS A 47 CG CD CE NZ REMARK 470 LYS A 65 CE NZ REMARK 470 ASN A 72 CG OD1 ND2 REMARK 470 ARG A 73 CG CD NE CZ NH1 NH2 REMARK 470 MET A 103 CG SD CE REMARK 470 GLU A 109 CG CD OE1 OE2 REMARK 470 GLU A 111 CG CD OE1 OE2 REMARK 470 GLU A 112 CG CD OE1 OE2 REMARK 470 LYS A 113 CG CD CE NZ REMARK 470 TYR A 114 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ARG A 115 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 125 CG CD OE1 OE2 REMARK 470 ASN A 139 CG OD1 ND2 REMARK 470 VAL A 143 CG1 CG2 REMARK 470 ARG A 145 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 161 CG CD OE1 OE2 REMARK 470 LYS A 188 CG CD CE NZ REMARK 470 ASP A 199 CG OD1 OD2 REMARK 470 LYS A 201 CG CD CE NZ REMARK 470 THR A 202 OG1 CG2 REMARK 470 LYS A 209 CG CD CE NZ REMARK 470 LYS A 223 CG CD CE NZ REMARK 470 LYS A 231 CG CD CE NZ REMARK 470 LYS A 259 CG CD CE NZ REMARK 470 SER A 269 OG REMARK 470 GLU A 270 CG CD OE1 OE2 REMARK 470 LYS A 271 CG CD CE NZ REMARK 470 SER A 272 OG REMARK 470 SER A 275 OG REMARK 470 GLU A 289 CG CD OE1 OE2 REMARK 470 LEU A 343 CG CD1 CD2 REMARK 470 LEU A 344 CG CD1 CD2 REMARK 470 PHE A 346 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LEU A 347 CG CD1 CD2 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 ND2 ASN A 290 C2 NAG A 402 2.13 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 OD1 ASP A 79 OH TYR A 285 3555 2.02 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 CYS A 203 CA - CB - SG ANGL. DEV. = 7.6 DEGREES 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 ALA A 55 61.76 -112.48 REMARK 500 ALA A 71 -127.35 61.79 REMARK 500 ASP A 199 71.80 49.54 REMARK 500 SER A 272 -98.86 49.65 REMARK 500 PHE A 346 2.58 89.47 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ARG A 198 ASP A 199 -145.80 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5SVJ RELATED DB: PDB REMARK 900 RELATED ID: 5SVK RELATED DB: PDB REMARK 900 RELATED ID: 5SVL RELATED DB: PDB REMARK 900 RELATED ID: 5SVM RELATED DB: PDB REMARK 900 RELATED ID: 5SVP RELATED DB: PDB REMARK 900 RELATED ID: 5SVQ RELATED DB: PDB REMARK 900 RELATED ID: 5SVS RELATED DB: PDB REMARK 900 RELATED ID: 5SVT RELATED DB: PDB DBREF 5SVR A 6 364 UNP P56373 P2RX3_HUMAN 6 364 SEQADV 5SVR GLY A 2 UNP P56373 EXPRESSION TAG SEQADV 5SVR SER A 3 UNP P56373 EXPRESSION TAG SEQADV 5SVR ARG A 4 UNP P56373 EXPRESSION TAG SEQADV 5SVR ALA A 5 UNP P56373 EXPRESSION TAG SEQADV 5SVR PRO A 13 UNP P56373 THR 13 ENGINEERED MUTATION SEQADV 5SVR VAL A 15 UNP P56373 SER 15 ENGINEERED MUTATION SEQADV 5SVR ILE A 16 UNP P56373 VAL 16 ENGINEERED MUTATION SEQRES 1 A 363 GLY SER ARG ALA ASP PHE PHE THR TYR GLU THR PRO LYS SEQRES 2 A 363 VAL ILE VAL VAL LYS SER TRP THR ILE GLY ILE ILE ASN SEQRES 3 A 363 ARG VAL VAL GLN LEU LEU ILE ILE SER TYR PHE VAL GLY SEQRES 4 A 363 TRP VAL PHE LEU HIS GLU LYS ALA TYR GLN VAL ARG ASP SEQRES 5 A 363 THR ALA ILE GLU SER SER VAL VAL THR LYS VAL LYS GLY SEQRES 6 A 363 SER GLY LEU TYR ALA ASN ARG VAL MET ASP VAL SER ASP SEQRES 7 A 363 TYR VAL THR PRO PRO GLN GLY THR SER VAL PHE VAL ILE SEQRES 8 A 363 ILE THR LYS MET ILE VAL THR GLU ASN GLN MET GLN GLY SEQRES 9 A 363 PHE CYS PRO GLU SER GLU GLU LYS TYR ARG CYS VAL SER SEQRES 10 A 363 ASP SER GLN CYS GLY PRO GLU ARG LEU PRO GLY GLY GLY SEQRES 11 A 363 ILE LEU THR GLY ARG CYS VAL ASN TYR SER SER VAL LEU SEQRES 12 A 363 ARG THR CYS GLU ILE GLN GLY TRP CYS PRO THR GLU VAL SEQRES 13 A 363 ASP THR VAL GLU THR PRO ILE MET MET GLU ALA GLU ASN SEQRES 14 A 363 PHE THR ILE PHE ILE LYS ASN SER ILE ARG PHE PRO LEU SEQRES 15 A 363 PHE ASN PHE GLU LYS GLY ASN LEU LEU PRO ASN LEU THR SEQRES 16 A 363 ALA ARG ASP MET LYS THR CYS ARG PHE HIS PRO ASP LYS SEQRES 17 A 363 ASP PRO PHE CYS PRO ILE LEU ARG VAL GLY ASP VAL VAL SEQRES 18 A 363 LYS PHE ALA GLY GLN ASP PHE ALA LYS LEU ALA ARG THR SEQRES 19 A 363 GLY GLY VAL LEU GLY ILE LYS ILE GLY TRP VAL CYS ASP SEQRES 20 A 363 LEU ASP LYS ALA TRP ASP GLN CYS ILE PRO LYS TYR SER SEQRES 21 A 363 PHE THR ARG LEU ASP SER VAL SER GLU LYS SER SER VAL SEQRES 22 A 363 SER PRO GLY TYR ASN PHE ARG PHE ALA LYS TYR TYR LYS SEQRES 23 A 363 MET GLU ASN GLY SER GLU TYR ARG THR LEU LEU LYS ALA SEQRES 24 A 363 PHE GLY ILE ARG PHE ASP VAL LEU VAL TYR GLY ASN ALA SEQRES 25 A 363 GLY LYS PHE ASN ILE ILE PRO THR ILE ILE SER SER VAL SEQRES 26 A 363 ALA ALA PHE THR SER VAL GLY VAL GLY THR VAL LEU CYS SEQRES 27 A 363 ASP ILE ILE LEU LEU ASN PHE LEU LYS GLY ALA ASP GLN SEQRES 28 A 363 TYR LYS ALA LYS LYS PHE GLU GLU VAL ASN GLU THR HET NAG A 401 28 HET NAG A 402 28 HET MG A 403 1 HET NA A 404 1 HET 71C A 405 42 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION HETNAM 71C 5-{[(3-PHENOXYPHENYL)METHYL][(1S)-1,2,3,4- HETNAM 2 71C TETRAHYDRONAPHTHALEN-1-YL]CARBAMOYL}BENZENE-1,2,4- HETNAM 3 71C TRICARBOXYLIC ACID HETSYN 71C ANTAGONIST A-317491 FORMUL 2 NAG 2(C8 H15 N O6) FORMUL 4 MG MG 2+ FORMUL 5 NA NA 1+ FORMUL 6 71C C33 H27 N O8 FORMUL 7 HOH *2(H2 O) HELIX 1 AA1 TRP A 21 GLU A 46 1 26 HELIX 2 AA2 ASP A 76 TYR A 80 1 5 HELIX 3 AA3 GLU A 111 ARG A 115 5 5 HELIX 4 AA4 SER A 118 CYS A 122 5 5 HELIX 5 AA5 MET A 165 ASN A 170 5 6 HELIX 6 AA6 VAL A 218 ALA A 225 1 8 HELIX 7 AA7 ASP A 228 GLY A 236 1 9 HELIX 8 AA8 ALA A 252 CYS A 256 5 5 HELIX 9 AA9 ASN A 317 PHE A 346 1 30 SHEET 1 AA1 4 LEU A 133 VAL A 138 0 SHEET 2 AA1 4 THR A 146 CYS A 153 -1 O GLU A 148 N ARG A 136 SHEET 3 AA1 4 VAL A 89 PRO A 108 -1 N MET A 103 O CYS A 153 SHEET 4 AA1 4 VAL A 81 THR A 82 -1 N THR A 82 O VAL A 91 SHEET 1 AA2 4 THR A 146 CYS A 153 0 SHEET 2 AA2 4 VAL A 89 PRO A 108 -1 N MET A 103 O CYS A 153 SHEET 3 AA2 4 GLU A 293 PHE A 316 -1 O PHE A 301 N LYS A 95 SHEET 4 AA2 4 GLN A 50 ASP A 53 -1 N VAL A 51 O LYS A 315 SHEET 1 AA3 4 VAL A 81 THR A 82 0 SHEET 2 AA3 4 VAL A 89 PRO A 108 -1 O VAL A 91 N THR A 82 SHEET 3 AA3 4 GLU A 293 PHE A 316 -1 O PHE A 301 N LYS A 95 SHEET 4 AA3 4 ASN A 279 LYS A 287 -1 N PHE A 280 O ALA A 300 SHEET 1 AA4 4 ASN A 279 LYS A 287 0 SHEET 2 AA4 4 GLU A 293 PHE A 316 -1 O ALA A 300 N PHE A 280 SHEET 3 AA4 4 GLY A 237 ASP A 248 1 N LEU A 239 O ARG A 304 SHEET 4 AA4 4 LYS A 259 ARG A 264 -1 O SER A 261 N LYS A 242 SHEET 1 AA5 3 SER A 59 LYS A 65 0 SHEET 2 AA5 3 THR A 172 PHE A 181 -1 O LYS A 176 N VAL A 61 SHEET 3 AA5 3 PHE A 186 GLY A 189 -1 O PHE A 186 N PHE A 181 SHEET 1 AA6 3 SER A 59 LYS A 65 0 SHEET 2 AA6 3 THR A 172 PHE A 181 -1 O LYS A 176 N VAL A 61 SHEET 3 AA6 3 ILE A 215 ARG A 217 -1 O LEU A 216 N ILE A 173 SHEET 1 AA7 2 GLY A 68 TYR A 70 0 SHEET 2 AA7 2 ARG A 73 MET A 75 -1 O MET A 75 N GLY A 68 SSBOND 1 CYS A 107 CYS A 153 1555 1555 2.03 SSBOND 2 CYS A 116 CYS A 137 1555 1555 2.03 SSBOND 3 CYS A 122 CYS A 147 1555 1555 2.03 SSBOND 4 CYS A 203 CYS A 213 1555 1555 2.05 SSBOND 5 CYS A 247 CYS A 256 1555 1555 2.02 LINK ND2 ASN A 170 C1 NAG A 401 1555 1555 1.44 LINK ND2 ASN A 290 C1 NAG A 402 1555 1555 1.46 CISPEP 1 THR A 82 PRO A 83 0 -1.06 CISPEP 2 CYS A 153 PRO A 154 0 0.54 CRYST1 123.170 123.170 237.460 90.00 90.00 120.00 H 3 2 18 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 0.008119 0.004687 0.000000 0.00000 SCALE2 0.000000 0.009375 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004211 0.00000