HEADER CELL ADHESION 15-OCT-11 3U83 TITLE CRYSTAL STRUCTURE OF NECTIN-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLIOVIRUS RECEPTOR-RELATED PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 30-335; COMPND 5 SYNONYM: HERPES VIRUS ENTRY MEDIATOR C, HERPESVIRUS ENTRY MEDIATOR C, COMPND 6 HVEC, HERPESVIRUS IG-LIKE RECEPTOR, HIGR, NECTIN-1; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 GENE: PVRL1, HVEC, PRR1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NECTIN-1, HINGE REGION PLASITICITY, CELL ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR N.ZHANG,J.YAN,G.LU,Z.GUO,Z.FAN,J.WANG,Y.SHI,J.QI,G.F.GAO REVDAT 3 09-OCT-24 3U83 1 REMARK REVDAT 2 01-NOV-23 3U83 1 REMARK SEQADV REVDAT 1 21-MAR-12 3U83 0 JRNL AUTH N.ZHANG,J.YAN,G.LU,Z.GUO,Z.FAN,J.WANG,Y.SHI,J.QI,G.F.GAO JRNL TITL BINDING OF HERPES SIMPLEX VIRUS GLYCOPROTEIN D TO NECTIN-1 JRNL TITL 2 EXPLOITS HOST CELL ADHESION. JRNL REF NAT COMMUN V. 2 577 2011 JRNL REFN ESSN 2041-1723 JRNL PMID 22146396 JRNL DOI 10.1038/NCOMMS1571 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.5_2) 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.77 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.180 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 3 NUMBER OF REFLECTIONS : 20026 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.110 REMARK 3 FREE R VALUE TEST SET COUNT : 1023 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 40.7794 - 4.7781 0.99 2938 134 0.1640 0.1797 REMARK 3 2 4.7781 - 3.7934 0.99 2830 145 0.1559 0.1844 REMARK 3 3 3.7934 - 3.3141 0.99 2799 164 0.1788 0.2552 REMARK 3 4 3.3141 - 3.0112 0.97 2711 158 0.1976 0.2484 REMARK 3 5 3.0112 - 2.7955 0.96 2698 142 0.2040 0.2589 REMARK 3 6 2.7955 - 2.6307 0.93 2578 134 0.2179 0.2613 REMARK 3 7 2.6307 - 2.4989 0.88 2449 146 0.2385 0.3096 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 : 0.33 REMARK 3 B_SOL : 26.47 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.920 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) : 4.07720 REMARK 3 B22 (A**2) : 4.07720 REMARK 3 B33 (A**2) : -8.15440 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 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 : 0.005 2432 REMARK 3 ANGLE : 1.003 3304 REMARK 3 CHIRALITY : 0.065 369 REMARK 3 PLANARITY : 0.003 431 REMARK 3 DIHEDRAL : 19.579 887 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -16.7312 -5.0264 -33.4212 REMARK 3 T TENSOR REMARK 3 T11: 0.1732 T22: 0.1680 REMARK 3 T33: 0.1613 T12: 0.0091 REMARK 3 T13: -0.0097 T23: 0.0080 REMARK 3 L TENSOR REMARK 3 L11: 0.7305 L22: 0.3987 REMARK 3 L33: 0.5724 L12: -0.5312 REMARK 3 L13: 0.6813 L23: -0.4776 REMARK 3 S TENSOR REMARK 3 S11: -0.0348 S12: -0.0218 S13: -0.0121 REMARK 3 S21: -0.0284 S22: 0.0288 S23: 0.0111 REMARK 3 S31: -0.0186 S32: -0.0045 S33: -0.0000 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 3U83 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-OCT-11. REMARK 100 THE DEPOSITION ID IS D_1000068424. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-MAY-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97916 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20827 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.499 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 9.100 REMARK 200 R MERGE (I) : 0.12300 REMARK 200 R SYM (I) : 0.12300 REMARK 200 FOR THE DATA SET : 20.9330 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 9.20 REMARK 200 R MERGE FOR SHELL (I) : 0.59400 REMARK 200 R SYM FOR SHELL (I) : 0.59400 REMARK 200 FOR SHELL : 4.739 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: 3ALP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 69.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 2000, 0.2M TRIMETHYLAMINE N REMARK 280 -OXIDEDIHYDRATE, 0.1M TRIS, PH 8.5, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 289K 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 63.76000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 36.81185 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 63.51833 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 63.76000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 36.81185 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 63.51833 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 63.76000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 36.81185 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 63.51833 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 63.76000 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 36.81185 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 63.51833 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 63.76000 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 36.81185 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 63.51833 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 63.76000 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 36.81185 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 63.51833 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 73.62371 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 127.03667 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 73.62371 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 127.03667 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 73.62371 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 127.03667 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 73.62371 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 127.03667 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 73.62371 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 127.03667 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 73.62371 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 127.03667 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32280 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 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 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 16 REMARK 465 ALA A 17 REMARK 465 SER A 18 REMARK 465 MET A 19 REMARK 465 THR A 20 REMARK 465 GLY A 21 REMARK 465 GLY A 22 REMARK 465 GLN A 23 REMARK 465 GLN A 24 REMARK 465 MET A 25 REMARK 465 GLY A 26 REMARK 465 ARG A 27 REMARK 465 ASP A 28 REMARK 465 PRO A 29 REMARK 465 SER A 30 REMARK 465 GLN A 31 REMARK 465 VAL A 32 REMARK 465 VAL A 33 REMARK 465 GLN A 34 REMARK 465 VAL A 35 REMARK 465 ALA A 336 REMARK 465 ALA A 337 REMARK 465 ALA A 338 REMARK 465 LEU A 339 REMARK 465 GLU A 340 REMARK 465 HIS A 341 REMARK 465 HIS A 342 REMARK 465 HIS A 343 REMARK 465 HIS A 344 REMARK 465 HIS A 345 REMARK 465 HIS A 346 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 LYS A 161 CG CD CE NZ REMARK 470 LYS A 190 CG CD CE NZ 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 OD1 ASN A 72 O HOH A 469 1.17 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 CYS A 51 112.24 -163.49 REMARK 500 ALA A 54 -98.40 -50.15 REMARK 500 GLN A 64 145.74 -171.25 REMARK 500 ASN A 72 37.16 -53.35 REMARK 500 PRO A 92 32.93 -93.68 REMARK 500 LYS A 178 115.92 -160.07 REMARK 500 GLN A 221 -6.91 74.82 REMARK 500 HIS A 231 -125.31 50.72 REMARK 500 GLN A 261 -8.20 81.61 REMARK 500 ASN A 286 69.81 -115.41 REMARK 500 SER A 288 -159.63 -117.05 REMARK 500 ASN A 297 -126.39 38.98 REMARK 500 SER A 309 1.62 -64.88 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 THR A 71 ASN A 72 -121.93 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 PG6 A 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PG6 A 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3ALP RELATED DB: PDB REMARK 900 HOMODIMER STRUCTURE OF NECTIN-1 REMARK 900 RELATED ID: 3U82 RELATED DB: PDB REMARK 900 HSV-1 GD IN COMPLEX WITH NECTIN-1 DBREF 3U83 A 30 335 UNP Q15223 PVRL1_HUMAN 30 335 SEQADV 3U83 MET A 16 UNP Q15223 EXPRESSION TAG SEQADV 3U83 ALA A 17 UNP Q15223 EXPRESSION TAG SEQADV 3U83 SER A 18 UNP Q15223 EXPRESSION TAG SEQADV 3U83 MET A 19 UNP Q15223 EXPRESSION TAG SEQADV 3U83 THR A 20 UNP Q15223 EXPRESSION TAG SEQADV 3U83 GLY A 21 UNP Q15223 EXPRESSION TAG SEQADV 3U83 GLY A 22 UNP Q15223 EXPRESSION TAG SEQADV 3U83 GLN A 23 UNP Q15223 EXPRESSION TAG SEQADV 3U83 GLN A 24 UNP Q15223 EXPRESSION TAG SEQADV 3U83 MET A 25 UNP Q15223 EXPRESSION TAG SEQADV 3U83 GLY A 26 UNP Q15223 EXPRESSION TAG SEQADV 3U83 ARG A 27 UNP Q15223 EXPRESSION TAG SEQADV 3U83 ASP A 28 UNP Q15223 EXPRESSION TAG SEQADV 3U83 PRO A 29 UNP Q15223 EXPRESSION TAG SEQADV 3U83 ALA A 336 UNP Q15223 EXPRESSION TAG SEQADV 3U83 ALA A 337 UNP Q15223 EXPRESSION TAG SEQADV 3U83 ALA A 338 UNP Q15223 EXPRESSION TAG SEQADV 3U83 LEU A 339 UNP Q15223 EXPRESSION TAG SEQADV 3U83 GLU A 340 UNP Q15223 EXPRESSION TAG SEQADV 3U83 HIS A 341 UNP Q15223 EXPRESSION TAG SEQADV 3U83 HIS A 342 UNP Q15223 EXPRESSION TAG SEQADV 3U83 HIS A 343 UNP Q15223 EXPRESSION TAG SEQADV 3U83 HIS A 344 UNP Q15223 EXPRESSION TAG SEQADV 3U83 HIS A 345 UNP Q15223 EXPRESSION TAG SEQADV 3U83 HIS A 346 UNP Q15223 EXPRESSION TAG SEQRES 1 A 331 MET ALA SER MET THR GLY GLY GLN GLN MET GLY ARG ASP SEQRES 2 A 331 PRO SER GLN VAL VAL GLN VAL ASN ASP SER MET TYR GLY SEQRES 3 A 331 PHE ILE GLY THR ASP VAL VAL LEU HIS CYS SER PHE ALA SEQRES 4 A 331 ASN PRO LEU PRO SER VAL LYS ILE THR GLN VAL THR TRP SEQRES 5 A 331 GLN LYS SER THR ASN GLY SER LYS GLN ASN VAL ALA ILE SEQRES 6 A 331 TYR ASN PRO SER MET GLY VAL SER VAL LEU ALA PRO TYR SEQRES 7 A 331 ARG GLU ARG VAL GLU PHE LEU ARG PRO SER PHE THR ASP SEQRES 8 A 331 GLY THR ILE ARG LEU SER ARG LEU GLU LEU GLU ASP GLU SEQRES 9 A 331 GLY VAL TYR ILE CYS GLU PHE ALA THR PHE PRO THR GLY SEQRES 10 A 331 ASN ARG GLU SER GLN LEU ASN LEU THR VAL MET ALA LYS SEQRES 11 A 331 PRO THR ASN TRP ILE GLU GLY THR GLN ALA VAL LEU ARG SEQRES 12 A 331 ALA LYS LYS GLY GLN ASP ASP LYS VAL LEU VAL ALA THR SEQRES 13 A 331 CYS THR SER ALA ASN GLY LYS PRO PRO SER VAL VAL SER SEQRES 14 A 331 TRP GLU THR ARG LEU LYS GLY GLU ALA GLU TYR GLN GLU SEQRES 15 A 331 ILE ARG ASN PRO ASN GLY THR VAL THR VAL ILE SER ARG SEQRES 16 A 331 TYR ARG LEU VAL PRO SER ARG GLU ALA HIS GLN GLN SER SEQRES 17 A 331 LEU ALA CYS ILE VAL ASN TYR HIS MET ASP ARG PHE LYS SEQRES 18 A 331 GLU SER LEU THR LEU ASN VAL GLN TYR GLU PRO GLU VAL SEQRES 19 A 331 THR ILE GLU GLY PHE ASP GLY ASN TRP TYR LEU GLN ARG SEQRES 20 A 331 MET ASP VAL LYS LEU THR CYS LYS ALA ASP ALA ASN PRO SEQRES 21 A 331 PRO ALA THR GLU TYR HIS TRP THR THR LEU ASN GLY SER SEQRES 22 A 331 LEU PRO LYS GLY VAL GLU ALA GLN ASN ARG THR LEU PHE SEQRES 23 A 331 PHE LYS GLY PRO ILE ASN TYR SER LEU ALA GLY THR TYR SEQRES 24 A 331 ILE CYS GLU ALA THR ASN PRO ILE GLY THR ARG SER GLY SEQRES 25 A 331 GLN VAL GLU VAL ASN ILE THR GLU ALA ALA ALA LEU GLU SEQRES 26 A 331 HIS HIS HIS HIS HIS HIS HET PG6 A 1 16 HETNAM PG6 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]- HETNAM 2 PG6 ETHOXY}-ETHANE FORMUL 2 PG6 C12 H26 O6 FORMUL 3 HOH *178(H2 O) HELIX 1 1 GLU A 115 GLU A 119 5 5 HELIX 2 2 SER A 216 HIS A 220 5 5 HELIX 3 3 ASN A 307 ALA A 311 5 5 SHEET 1 A 6 ASP A 37 PHE A 42 0 SHEET 2 A 6 GLY A 132 MET A 143 1 O ASN A 139 N MET A 39 SHEET 3 A 6 GLY A 120 PHE A 129 -1 N PHE A 126 O ARG A 134 SHEET 4 A 6 LYS A 61 THR A 71 -1 N THR A 63 O ALA A 127 SHEET 5 A 6 SER A 74 ASN A 82 -1 O ALA A 79 N TRP A 67 SHEET 6 A 6 GLY A 86 VAL A 89 -1 O SER A 88 N ILE A 80 SHEET 1 B 3 VAL A 47 LEU A 49 0 SHEET 2 B 3 ILE A 109 LEU A 111 -1 O ILE A 109 N LEU A 49 SHEET 3 B 3 VAL A 97 PHE A 99 -1 N GLU A 98 O ARG A 110 SHEET 1 C 4 THR A 147 GLY A 152 0 SHEET 2 C 4 VAL A 167 GLY A 177 -1 O ALA A 175 N THR A 147 SHEET 3 C 4 VAL A 205 LEU A 213 -1 O VAL A 205 N GLY A 177 SHEET 4 C 4 GLU A 192 ARG A 199 -1 N ILE A 198 O THR A 206 SHEET 1 D 5 LEU A 157 ALA A 159 0 SHEET 2 D 5 VAL A 243 GLU A 252 1 O GLN A 244 N ALA A 159 SHEET 3 D 5 VAL A 265 ASN A 274 -1 O LYS A 270 N THR A 250 SHEET 4 D 5 THR A 299 PHE A 302 -1 O PHE A 302 N VAL A 265 SHEET 5 D 5 VAL A 293 GLN A 296 -1 N GLU A 294 O PHE A 301 SHEET 1 E 3 VAL A 182 THR A 187 0 SHEET 2 E 3 SER A 223 TYR A 230 -1 O ILE A 227 N SER A 184 SHEET 3 E 3 ASP A 233 THR A 240 -1 O ASP A 233 N TYR A 230 SHEET 1 F 3 GLU A 279 THR A 284 0 SHEET 2 F 3 GLY A 312 ASN A 320 -1 O ILE A 315 N THR A 283 SHEET 3 F 3 GLY A 323 VAL A 331 -1 O VAL A 331 N GLY A 312 SSBOND 1 CYS A 51 CYS A 124 1555 1555 2.05 SSBOND 2 CYS A 172 CYS A 226 1555 1555 2.04 SSBOND 3 CYS A 269 CYS A 316 1555 1555 2.06 CISPEP 1 ALA A 91 PRO A 92 0 4.00 CISPEP 2 PHE A 129 PRO A 130 0 6.62 CISPEP 3 LYS A 178 PRO A 179 0 -4.11 CISPEP 4 ASN A 274 PRO A 275 0 -1.70 CISPEP 5 GLY A 304 PRO A 305 0 2.96 SITE 1 AC1 6 MET A 143 TYR A 195 GLU A 197 ASN A 229 SITE 2 AC1 6 TYR A 230 HIS A 231 CRYST1 127.520 127.520 190.555 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 0.007842 0.004528 0.000000 0.00000 SCALE2 0.000000 0.009055 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005248 0.00000