HEADER VIRAL PROTEIN 28-SEP-13 4MYV TITLE FREE HSV-2 GD STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENVELOPE GLYCOPROTEIN D; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 26-310; COMPND 5 SYNONYM: GD; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN HERPESVIRUS 2; SOURCE 3 ORGANISM_COMMON: HHV-2; SOURCE 4 ORGANISM_TAXID: 10313; SOURCE 5 STRAIN: 333; SOURCE 6 GENE: GD, US6; SOURCE 7 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 8 EXPRESSION_SYSTEM_COMMON: CABBAGE LOOPER; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 7111; SOURCE 10 EXPRESSION_SYSTEM_CELL_LINE: BTI-TN-5B1-4; SOURCE 11 EXPRESSION_SYSTEM_CELL: HIGH5; SOURCE 12 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 13 EXPRESSION_SYSTEM_PLASMID: PFAST-BAC1 KEYWDS IGV-LIKE CORE, N-/C-TERMINAL EXTENSIONS, RECEPTOR BINDING, NECTIN-1, KEYWDS 2 HVEM, VIRAL SURFACE, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR G.LU,N.ZHANG,J.QI,Y.LI,Z.CHEN,C.ZHENG,J.YAN,G.F.GAO REVDAT 4 08-NOV-23 4MYV 1 REMARK REVDAT 3 24-AUG-22 4MYV 1 JRNL HETSYN REVDAT 2 29-JUL-20 4MYV 1 COMPND REMARK SEQADV HETNAM REVDAT 2 2 1 SITE REVDAT 1 01-OCT-14 4MYV 0 JRNL AUTH G.LU,N.ZHANG,J.QI,Y.LI,Z.CHEN,C.ZHENG,G.F.GAO,J.YAN JRNL TITL CRYSTAL STRUCTURE OF HERPES SIMPLEX VIRUS 2 GD BOUND TO JRNL TITL 2 NECTIN-1 REVEALS A CONSERVED MODE OF RECEPTOR RECOGNITION. JRNL REF J.VIROL. V. 88 13678 2014 JRNL REFN ESSN 1098-5514 JRNL PMID 25231300 JRNL DOI 10.1128/JVI.01906-14 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2_1309) 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.27 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 40596 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 2038 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 36.2752 - 4.4397 1.00 2741 139 0.1845 0.2167 REMARK 3 2 4.4397 - 3.5248 1.00 2693 141 0.1672 0.2149 REMARK 3 3 3.5248 - 3.0795 1.00 2650 146 0.1846 0.1941 REMARK 3 4 3.0795 - 2.7981 1.00 2680 154 0.1918 0.2583 REMARK 3 5 2.7981 - 2.5976 1.00 2666 120 0.1937 0.2366 REMARK 3 6 2.5976 - 2.4445 1.00 2619 151 0.1965 0.2300 REMARK 3 7 2.4445 - 2.3221 1.00 2650 137 0.1910 0.2711 REMARK 3 8 2.3221 - 2.2210 1.00 2653 137 0.1885 0.2789 REMARK 3 9 2.2210 - 2.1355 1.00 2640 126 0.1939 0.2105 REMARK 3 10 2.1355 - 2.0618 0.99 2604 140 0.1967 0.2306 REMARK 3 11 2.0618 - 1.9974 0.98 2562 137 0.1866 0.2424 REMARK 3 12 1.9974 - 1.9403 0.96 2565 143 0.1890 0.2012 REMARK 3 13 1.9403 - 1.8892 0.93 2466 124 0.1964 0.2048 REMARK 3 14 1.8892 - 1.8431 0.88 2302 134 0.2281 0.2731 REMARK 3 15 1.8431 - 1.8012 0.78 2067 109 0.2601 0.3343 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.480 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 : 0.008 2920 REMARK 3 ANGLE : 1.315 3986 REMARK 3 CHIRALITY : 0.094 447 REMARK 3 PLANARITY : 0.005 507 REMARK 3 DIHEDRAL : 16.681 1067 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 4MYV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-OCT-13. REMARK 100 THE DEPOSITION ID IS D_1000082538. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-NOV-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.2 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 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40614 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 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 (%) : 96.8 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.08500 REMARK 200 R SYM (I) : 0.08500 REMARK 200 FOR THE DATA SET : 15.8900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.29700 REMARK 200 R SYM FOR SHELL (I) : 0.29700 REMARK 200 FOR SHELL : 2.714 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 1L2G REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1MOL/L HEPES PH 7.2, 5% (V/V) MPD, REMARK 280 10% PEG 10000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 27.67550 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 ALA A -2 REMARK 465 ASP A -1 REMARK 465 LEU A 0 REMARK 465 LYS A 1 REMARK 465 TYR A 2 REMARK 465 ALA A 3 REMARK 465 LEU A 4 REMARK 465 ALA A 5 REMARK 465 ASP A 6 REMARK 465 PRO A 7 REMARK 465 SER A 8 REMARK 465 LEU A 9 REMARK 465 LYS A 10 REMARK 465 MET A 11 REMARK 465 ALA A 12 REMARK 465 ASP A 13 REMARK 465 PRO A 14 REMARK 465 ASN A 15 REMARK 465 ARG A 16 REMARK 465 PHE A 17 REMARK 465 ARG A 18 REMARK 465 GLY A 19 REMARK 465 LYS A 20 REMARK 465 ASN A 21 REMARK 465 LEU A 22 REMARK 465 PRO A 23 REMARK 465 VAL A 24 REMARK 465 LEU A 25 REMARK 465 ASP A 26 REMARK 465 GLN A 27 REMARK 465 LEU A 28 REMARK 465 THR A 29 REMARK 465 ASP A 30 REMARK 465 PRO A 31 REMARK 465 PRO A 32 REMARK 465 GLY A 33 REMARK 465 VAL A 34 REMARK 465 LYS A 35 REMARK 465 ARG A 36 REMARK 465 ALA A 185 REMARK 465 ARG A 186 REMARK 465 ALA A 187 REMARK 465 SER A 188 REMARK 465 CYS A 189 REMARK 465 LYS A 190 REMARK 465 TYR A 191 REMARK 465 ALA A 192 REMARK 465 LEU A 193 REMARK 465 PRO A 194 REMARK 465 PHE A 223 REMARK 465 ILE A 224 REMARK 465 PRO A 225 REMARK 465 GLU A 226 REMARK 465 ASN A 227 REMARK 465 GLN A 228 REMARK 465 ARG A 229 REMARK 465 THR A 230 REMARK 465 VAL A 231 REMARK 465 ALA A 232 REMARK 465 LEU A 233 REMARK 465 TYR A 234 REMARK 465 SER A 235 REMARK 465 LEU A 236 REMARK 465 LYS A 237 REMARK 465 ILE A 238 REMARK 465 ALA A 239 REMARK 465 GLY A 240 REMARK 465 TRP A 241 REMARK 465 HIS A 242 REMARK 465 GLY A 243 REMARK 465 PRO A 244 REMARK 465 LYS A 245 REMARK 465 PRO A 246 REMARK 465 PRO A 247 REMARK 465 TYR A 248 REMARK 465 THR A 249 REMARK 465 SER A 250 REMARK 465 THR A 251 REMARK 465 LEU A 252 REMARK 465 LEU A 253 REMARK 465 PRO A 254 REMARK 465 PRO A 255 REMARK 465 GLU A 256 REMARK 465 LEU A 257 REMARK 465 SER A 258 REMARK 465 ASP A 259 REMARK 465 THR A 260 REMARK 465 THR A 261 REMARK 465 ASN A 262 REMARK 465 ALA A 263 REMARK 465 THR A 264 REMARK 465 GLN A 265 REMARK 465 PRO A 266 REMARK 465 GLU A 267 REMARK 465 LEU A 268 REMARK 465 VAL A 269 REMARK 465 PRO A 270 REMARK 465 GLU A 271 REMARK 465 ASP A 272 REMARK 465 PRO A 273 REMARK 465 GLU A 274 REMARK 465 ASP A 275 REMARK 465 SER A 276 REMARK 465 ALA A 277 REMARK 465 LEU A 278 REMARK 465 LEU A 279 REMARK 465 GLU A 280 REMARK 465 ASP A 281 REMARK 465 PRO A 282 REMARK 465 ALA A 283 REMARK 465 GLY A 284 REMARK 465 THR A 285 REMARK 465 HIS A 286 REMARK 465 HIS A 287 REMARK 465 HIS A 288 REMARK 465 HIS A 289 REMARK 465 HIS A 290 REMARK 465 HIS A 291 REMARK 465 ALA B -2 REMARK 465 ASP B -1 REMARK 465 LEU B 0 REMARK 465 LYS B 1 REMARK 465 TYR B 2 REMARK 465 ALA B 3 REMARK 465 LEU B 4 REMARK 465 ALA B 5 REMARK 465 ASP B 6 REMARK 465 PRO B 7 REMARK 465 SER B 8 REMARK 465 LEU B 9 REMARK 465 LYS B 10 REMARK 465 MET B 11 REMARK 465 ALA B 12 REMARK 465 ASP B 13 REMARK 465 PRO B 14 REMARK 465 ASN B 15 REMARK 465 ARG B 16 REMARK 465 PHE B 17 REMARK 465 ARG B 18 REMARK 465 GLY B 19 REMARK 465 LYS B 20 REMARK 465 ASN B 21 REMARK 465 LEU B 22 REMARK 465 PRO B 23 REMARK 465 VAL B 24 REMARK 465 LEU B 25 REMARK 465 ASP B 26 REMARK 465 GLN B 27 REMARK 465 LEU B 28 REMARK 465 THR B 29 REMARK 465 ASP B 30 REMARK 465 PRO B 31 REMARK 465 PRO B 32 REMARK 465 GLY B 33 REMARK 465 VAL B 34 REMARK 465 LYS B 35 REMARK 465 ARG B 36 REMARK 465 ALA B 185 REMARK 465 ARG B 186 REMARK 465 ALA B 187 REMARK 465 SER B 188 REMARK 465 CYS B 189 REMARK 465 LYS B 190 REMARK 465 TYR B 191 REMARK 465 ALA B 192 REMARK 465 LEU B 193 REMARK 465 PRO B 194 REMARK 465 PHE B 223 REMARK 465 ILE B 224 REMARK 465 PRO B 225 REMARK 465 GLU B 226 REMARK 465 ASN B 227 REMARK 465 GLN B 228 REMARK 465 ARG B 229 REMARK 465 THR B 230 REMARK 465 VAL B 231 REMARK 465 ALA B 232 REMARK 465 LEU B 233 REMARK 465 TYR B 234 REMARK 465 SER B 235 REMARK 465 LEU B 236 REMARK 465 LYS B 237 REMARK 465 ILE B 238 REMARK 465 ALA B 239 REMARK 465 GLY B 240 REMARK 465 TRP B 241 REMARK 465 HIS B 242 REMARK 465 GLY B 243 REMARK 465 PRO B 244 REMARK 465 LYS B 245 REMARK 465 PRO B 246 REMARK 465 PRO B 247 REMARK 465 TYR B 248 REMARK 465 THR B 249 REMARK 465 SER B 250 REMARK 465 THR B 251 REMARK 465 LEU B 252 REMARK 465 LEU B 253 REMARK 465 PRO B 254 REMARK 465 PRO B 255 REMARK 465 GLU B 256 REMARK 465 LEU B 257 REMARK 465 SER B 258 REMARK 465 ASP B 259 REMARK 465 THR B 260 REMARK 465 THR B 261 REMARK 465 ASN B 262 REMARK 465 ALA B 263 REMARK 465 THR B 264 REMARK 465 GLN B 265 REMARK 465 PRO B 266 REMARK 465 GLU B 267 REMARK 465 LEU B 268 REMARK 465 VAL B 269 REMARK 465 PRO B 270 REMARK 465 GLU B 271 REMARK 465 ASP B 272 REMARK 465 PRO B 273 REMARK 465 GLU B 274 REMARK 465 ASP B 275 REMARK 465 SER B 276 REMARK 465 ALA B 277 REMARK 465 LEU B 278 REMARK 465 LEU B 279 REMARK 465 GLU B 280 REMARK 465 ASP B 281 REMARK 465 PRO B 282 REMARK 465 ALA B 283 REMARK 465 GLY B 284 REMARK 465 THR B 285 REMARK 465 HIS B 286 REMARK 465 HIS B 287 REMARK 465 HIS B 288 REMARK 465 HIS B 289 REMARK 465 HIS B 290 REMARK 465 HIS B 291 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 ASP A 86 OD1 OD2 REMARK 470 GLU A 87 CD OE1 OE2 REMARK 470 ASP B 86 OD1 OD2 REMARK 470 GLU B 87 CD OE1 OE2 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 O SER A 123 O HOH A 638 1.62 REMARK 500 SG CYS B 66 OG1 THR B 160 1.70 REMARK 500 NH1 ARG B 101 O GLU B 159 2.09 REMARK 500 O HOH B 645 O HOH B 683 2.09 REMARK 500 O HOH A 598 O HOH A 619 2.10 REMARK 500 O4 NAG B 401 O HOH B 638 2.16 REMARK 500 O HOH B 547 O HOH B 683 2.16 REMARK 500 O HIS B 91 O HOH B 583 2.17 REMARK 500 O HOH A 659 O HOH A 681 2.17 REMARK 500 O HOH A 686 O HOH B 655 2.18 REMARK 500 O HIS A 91 O HOH A 608 2.19 REMARK 500 OE1 GLU B 76 O HOH B 666 2.19 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 GLU B 87 N - CA - C ANGL. DEV. = 16.3 DEGREES REMARK 500 ALA B 88 N - CA - C ANGL. DEV. = -21.0 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 GLU A 63 -167.09 60.54 REMARK 500 ARG A 64 -129.73 37.34 REMARK 500 CYS A 66 -8.56 82.81 REMARK 500 ALA A 84 -147.51 62.62 REMARK 500 ASP A 86 117.76 -24.36 REMARK 500 ARG A 89 -24.06 -157.61 REMARK 500 LYS A 122 -178.66 -67.57 REMARK 500 ALA A 155 58.14 35.90 REMARK 500 ASN A 171 -123.54 49.59 REMARK 500 GLU B 63 -85.17 -118.15 REMARK 500 ALA B 65 -136.00 29.87 REMARK 500 ARG B 67 -113.88 -106.01 REMARK 500 GLU B 87 -14.09 79.32 REMARK 500 LYS B 90 -5.39 73.84 REMARK 500 ASN B 171 -123.18 51.99 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 NAG A 401 REMARK 610 NAG B 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4MYW RELATED DB: PDB REMARK 900 RELATED ID: 3U82 RELATED DB: PDB REMARK 900 STRUCTURE OF HSV-1 GD BOUND TO NECTIN-1 REMARK 900 RELATED ID: 1L2G RELATED DB: PDB REMARK 900 FREE HSV-1 GD STRUCTURE REMARK 999 REMARK 999 SEQUENCE REMARK 999 NATURAL VARIANT AT THIS POSITION. THE SEQUENCE IS BASED ON A RECORD REMARK 999 IN GENBANK WITH THE ACCESSION NUMBER EU018091 DBREF 4MYV A 1 285 UNP P03172 GD_HHV23 26 310 DBREF 4MYV B 1 285 UNP P03172 GD_HHV23 26 310 SEQADV 4MYV ALA A -2 UNP P03172 EXPRESSION TAG SEQADV 4MYV ASP A -1 UNP P03172 EXPRESSION TAG SEQADV 4MYV LEU A 0 UNP P03172 EXPRESSION TAG SEQADV 4MYV GLN A 27 UNP P03172 ARG 52 SEE REMARK 999 SEQADV 4MYV HIS A 286 UNP P03172 EXPRESSION TAG SEQADV 4MYV HIS A 287 UNP P03172 EXPRESSION TAG SEQADV 4MYV HIS A 288 UNP P03172 EXPRESSION TAG SEQADV 4MYV HIS A 289 UNP P03172 EXPRESSION TAG SEQADV 4MYV HIS A 290 UNP P03172 EXPRESSION TAG SEQADV 4MYV HIS A 291 UNP P03172 EXPRESSION TAG SEQADV 4MYV ALA B -2 UNP P03172 EXPRESSION TAG SEQADV 4MYV ASP B -1 UNP P03172 EXPRESSION TAG SEQADV 4MYV LEU B 0 UNP P03172 EXPRESSION TAG SEQADV 4MYV GLN B 27 UNP P03172 ARG 52 SEE REMARK 999 SEQADV 4MYV HIS B 286 UNP P03172 EXPRESSION TAG SEQADV 4MYV HIS B 287 UNP P03172 EXPRESSION TAG SEQADV 4MYV HIS B 288 UNP P03172 EXPRESSION TAG SEQADV 4MYV HIS B 289 UNP P03172 EXPRESSION TAG SEQADV 4MYV HIS B 290 UNP P03172 EXPRESSION TAG SEQADV 4MYV HIS B 291 UNP P03172 EXPRESSION TAG SEQRES 1 A 294 ALA ASP LEU LYS TYR ALA LEU ALA ASP PRO SER LEU LYS SEQRES 2 A 294 MET ALA ASP PRO ASN ARG PHE ARG GLY LYS ASN LEU PRO SEQRES 3 A 294 VAL LEU ASP GLN LEU THR ASP PRO PRO GLY VAL LYS ARG SEQRES 4 A 294 VAL TYR HIS ILE GLN PRO SER LEU GLU ASP PRO PHE GLN SEQRES 5 A 294 PRO PRO SER ILE PRO ILE THR VAL TYR TYR ALA VAL LEU SEQRES 6 A 294 GLU ARG ALA CYS ARG SER VAL LEU LEU HIS ALA PRO SER SEQRES 7 A 294 GLU ALA PRO GLN ILE VAL ARG GLY ALA SER ASP GLU ALA SEQRES 8 A 294 ARG LYS HIS THR TYR ASN LEU THR ILE ALA TRP TYR ARG SEQRES 9 A 294 MET GLY ASP ASN CYS ALA ILE PRO ILE THR VAL MET GLU SEQRES 10 A 294 TYR THR GLU CYS PRO TYR ASN LYS SER LEU GLY VAL CYS SEQRES 11 A 294 PRO ILE ARG THR GLN PRO ARG TRP SER TYR TYR ASP SER SEQRES 12 A 294 PHE SER ALA VAL SER GLU ASP ASN LEU GLY PHE LEU MET SEQRES 13 A 294 HIS ALA PRO ALA PHE GLU THR ALA GLY THR TYR LEU ARG SEQRES 14 A 294 LEU VAL LYS ILE ASN ASP TRP THR GLU ILE THR GLN PHE SEQRES 15 A 294 ILE LEU GLU HIS ARG ALA ARG ALA SER CYS LYS TYR ALA SEQRES 16 A 294 LEU PRO LEU ARG ILE PRO PRO ALA ALA CYS LEU THR SER SEQRES 17 A 294 LYS ALA TYR GLN GLN GLY VAL THR VAL ASP SER ILE GLY SEQRES 18 A 294 MET LEU PRO ARG PHE ILE PRO GLU ASN GLN ARG THR VAL SEQRES 19 A 294 ALA LEU TYR SER LEU LYS ILE ALA GLY TRP HIS GLY PRO SEQRES 20 A 294 LYS PRO PRO TYR THR SER THR LEU LEU PRO PRO GLU LEU SEQRES 21 A 294 SER ASP THR THR ASN ALA THR GLN PRO GLU LEU VAL PRO SEQRES 22 A 294 GLU ASP PRO GLU ASP SER ALA LEU LEU GLU ASP PRO ALA SEQRES 23 A 294 GLY THR HIS HIS HIS HIS HIS HIS SEQRES 1 B 294 ALA ASP LEU LYS TYR ALA LEU ALA ASP PRO SER LEU LYS SEQRES 2 B 294 MET ALA ASP PRO ASN ARG PHE ARG GLY LYS ASN LEU PRO SEQRES 3 B 294 VAL LEU ASP GLN LEU THR ASP PRO PRO GLY VAL LYS ARG SEQRES 4 B 294 VAL TYR HIS ILE GLN PRO SER LEU GLU ASP PRO PHE GLN SEQRES 5 B 294 PRO PRO SER ILE PRO ILE THR VAL TYR TYR ALA VAL LEU SEQRES 6 B 294 GLU ARG ALA CYS ARG SER VAL LEU LEU HIS ALA PRO SER SEQRES 7 B 294 GLU ALA PRO GLN ILE VAL ARG GLY ALA SER ASP GLU ALA SEQRES 8 B 294 ARG LYS HIS THR TYR ASN LEU THR ILE ALA TRP TYR ARG SEQRES 9 B 294 MET GLY ASP ASN CYS ALA ILE PRO ILE THR VAL MET GLU SEQRES 10 B 294 TYR THR GLU CYS PRO TYR ASN LYS SER LEU GLY VAL CYS SEQRES 11 B 294 PRO ILE ARG THR GLN PRO ARG TRP SER TYR TYR ASP SER SEQRES 12 B 294 PHE SER ALA VAL SER GLU ASP ASN LEU GLY PHE LEU MET SEQRES 13 B 294 HIS ALA PRO ALA PHE GLU THR ALA GLY THR TYR LEU ARG SEQRES 14 B 294 LEU VAL LYS ILE ASN ASP TRP THR GLU ILE THR GLN PHE SEQRES 15 B 294 ILE LEU GLU HIS ARG ALA ARG ALA SER CYS LYS TYR ALA SEQRES 16 B 294 LEU PRO LEU ARG ILE PRO PRO ALA ALA CYS LEU THR SER SEQRES 17 B 294 LYS ALA TYR GLN GLN GLY VAL THR VAL ASP SER ILE GLY SEQRES 18 B 294 MET LEU PRO ARG PHE ILE PRO GLU ASN GLN ARG THR VAL SEQRES 19 B 294 ALA LEU TYR SER LEU LYS ILE ALA GLY TRP HIS GLY PRO SEQRES 20 B 294 LYS PRO PRO TYR THR SER THR LEU LEU PRO PRO GLU LEU SEQRES 21 B 294 SER ASP THR THR ASN ALA THR GLN PRO GLU LEU VAL PRO SEQRES 22 B 294 GLU ASP PRO GLU ASP SER ALA LEU LEU GLU ASP PRO ALA SEQRES 23 B 294 GLY THR HIS HIS HIS HIS HIS HIS HET NAG A 401 14 HET NAG B 401 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 3 NAG 2(C8 H15 N O6) FORMUL 5 HOH *407(H2 O) HELIX 1 1 GLU A 76 VAL A 81 1 6 HELIX 2 2 ALA A 157 ALA A 161 5 5 HELIX 3 3 PRO A 198 CYS A 202 5 5 HELIX 4 4 THR A 204 GLY A 211 1 8 HELIX 5 5 GLU B 76 VAL B 81 1 6 HELIX 6 6 PRO B 198 CYS B 202 5 5 HELIX 7 7 THR B 204 GLY B 211 1 8 HELIX 8 8 VAL B 214 GLY B 218 5 5 SHEET 1 A 6 THR A 56 VAL A 61 0 SHEET 2 A 6 TRP A 173 GLU A 182 1 O ILE A 180 N TYR A 58 SHEET 3 A 6 GLY A 162 ILE A 170 -1 N ARG A 166 O THR A 177 SHEET 4 A 6 THR A 92 MET A 102 -1 N MET A 102 O THR A 163 SHEET 5 A 6 ALA A 107 PRO A 119 -1 O ILE A 110 N TRP A 99 SHEET 6 A 6 ILE A 129 ARG A 130 -1 O ILE A 129 N THR A 116 SHEET 1 B 6 THR A 56 VAL A 61 0 SHEET 2 B 6 TRP A 173 GLU A 182 1 O ILE A 180 N TYR A 58 SHEET 3 B 6 GLY A 162 ILE A 170 -1 N ARG A 166 O THR A 177 SHEET 4 B 6 THR A 92 MET A 102 -1 N MET A 102 O THR A 163 SHEET 5 B 6 ALA A 107 PRO A 119 -1 O ILE A 110 N TRP A 99 SHEET 6 B 6 ARG A 134 TRP A 135 -1 O ARG A 134 N VAL A 112 SHEET 1 C 3 VAL A 69 LEU A 71 0 SHEET 2 C 3 PHE A 151 MET A 153 -1 O PHE A 151 N LEU A 71 SHEET 3 C 3 ALA A 143 VAL A 144 -1 N ALA A 143 O LEU A 152 SHEET 1 D 6 THR B 56 LEU B 62 0 SHEET 2 D 6 TRP B 173 HIS B 183 1 O GLU B 182 N LEU B 62 SHEET 3 D 6 GLY B 162 ILE B 170 -1 N ARG B 166 O THR B 177 SHEET 4 D 6 TYR B 93 MET B 102 -1 N ALA B 98 O LEU B 167 SHEET 5 D 6 ALA B 107 CYS B 118 -1 O ILE B 108 N ARG B 101 SHEET 6 D 6 ILE B 129 ARG B 130 -1 O ILE B 129 N THR B 116 SHEET 1 E 6 THR B 56 LEU B 62 0 SHEET 2 E 6 TRP B 173 HIS B 183 1 O GLU B 182 N LEU B 62 SHEET 3 E 6 GLY B 162 ILE B 170 -1 N ARG B 166 O THR B 177 SHEET 4 E 6 TYR B 93 MET B 102 -1 N ALA B 98 O LEU B 167 SHEET 5 E 6 ALA B 107 CYS B 118 -1 O ILE B 108 N ARG B 101 SHEET 6 E 6 ARG B 134 TRP B 135 -1 O ARG B 134 N VAL B 112 SHEET 1 F 3 SER B 68 LEU B 71 0 SHEET 2 F 3 PHE B 151 HIS B 154 -1 O PHE B 151 N LEU B 71 SHEET 3 F 3 ALA B 143 VAL B 144 -1 N ALA B 143 O LEU B 152 SSBOND 1 CYS A 106 CYS A 202 1555 1555 2.07 SSBOND 2 CYS A 118 CYS A 127 1555 1555 2.04 SSBOND 3 CYS B 106 CYS B 202 1555 1555 2.08 SSBOND 4 CYS B 118 CYS B 127 1555 1555 2.06 CISPEP 1 ARG A 82 GLY A 83 0 -4.52 CISPEP 2 ASP A 86 GLU A 87 0 10.64 CISPEP 3 GLU A 87 ALA A 88 0 -8.42 CISPEP 4 ASP B 86 GLU B 87 0 -15.89 CRYST1 63.562 55.351 65.335 90.00 96.35 90.00 P 1 21 1 4 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 0.015733 0.000000 0.001751 0.00000 SCALE2 0.000000 0.018067 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015400 0.00000