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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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