HEADER VIRAL PROTEIN 05-OCT-05 2C3A TITLE STRUCTURE OF UNLIGANDED HSV GD REVEALS A MECHANISM FOR RECEPTOR- TITLE 2 MEDIATED ACTIVATION OF VIRUS ENTRY COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLYCOPROTEIN D; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 OTHER_DETAILS: N-ACETYL-D-GLUCOSAMINE LINKED TO ASN94 FOR BOTH CHAINS COMPND 7 A AND B SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN HERPESVIRUS 1; SOURCE 3 ORGANISM_COMMON: HUMAN HERPES SIMPLEX VIRUS 1; SOURCE 4 ORGANISM_TAXID: 10298; SOURCE 5 STRAIN: PATTON; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: SF9; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PDL485 KEYWDS VIRUS, HERPES SIMPLEX VIRUS, HSV-1, GLYCOPROTEIN D, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.KRUMMENACHER,V.M.SUPEKAR,J.C.WHITBECK,E.LAZEAR,S.A.CONNOLLY, AUTHOR 2 R.J.EISENBERG,G.H.COHEN,D.C.WILEY,A.CARFI REVDAT 3 29-JUL-20 2C3A 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE ATOM REVDAT 2 24-FEB-09 2C3A 1 VERSN REVDAT 1 21-DEC-05 2C3A 0 JRNL AUTH C.KRUMMENACHER,V.M.SUPEKAR,J.C.WHITBECK,E.LAZEAR, JRNL AUTH 2 S.A.CONNOLLY,R.J.EISENBERG,G.H.COHEN,D.C.WILEY,A.CARFI JRNL TITL STRUCTURE OF UNLIGANDED HSV GD REVEALS A MECHANISM FOR JRNL TITL 2 RECEPTOR-MEDIATED ACTIVATION OF VIRUS ENTRY. JRNL REF EMBO J. V. 24 4144 2005 JRNL REFN ISSN 0261-4189 JRNL PMID 16292345 JRNL DOI 10.1038/SJ.EMBOJ.7600875 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 22271 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) : 0.228 REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.275 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1212 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.56 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1565 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2780 REMARK 3 BIN FREE R VALUE SET COUNT : 81 REMARK 3 BIN FREE R VALUE : 0.4310 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4067 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 65 REMARK 3 SOLVENT ATOMS : 53 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.37000 REMARK 3 B22 (A**2) : 0.60000 REMARK 3 B33 (A**2) : -1.97000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.517 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.307 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.193 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.386 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.928 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.896 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4279 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 3833 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5878 ; 1.685 ; 1.979 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8929 ; 0.931 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 519 ; 7.806 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 654 ; 0.105 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4667 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 819 ; 0.005 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 788 ; 0.206 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 4271 ; 0.235 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 2539 ; 0.090 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 114 ; 0.174 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 18 ; 0.323 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 46 ; 0.243 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 2 ; 0.007 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2644 ; 0.903 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4317 ; 1.655 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1635 ; 2.011 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1561 ; 3.412 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 100 A 200 2 REMARK 3 1 B 100 B 200 2 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 1 A (A): 593 ; 0.04 ; 0.05 REMARK 3 MEDIUM POSITIONAL 1 A (A): 931 ; 0.26 ; 0.50 REMARK 3 TIGHT THERMAL 1 A (A**2): 593 ; 0.17 ; 0.50 REMARK 3 MEDIUM THERMAL 1 A (A**2): 931 ; 0.73 ; 2.00 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. FIRST 22 RESIDUES DISORDERED FOR BOTH CHAINS A,B. REMARK 3 RESIDUES 256-267 DISORDERED FOR BOTH CHAINS A,B REMARK 4 REMARK 4 2C3A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-OCT-05. REMARK 100 THE DEPOSITION ID IS D_1290025867. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-OCT-04 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 4.60 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.931 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23602 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 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 (%) : 99.6 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.0000 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 (%) : 98.2 REMARK 200 DATA REDUNDANCY IN SHELL : 7.10 REMARK 200 R MERGE FOR SHELL (I) : 0.34000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.070 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1L2G REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM NA ACETATE PH 4.6, 10MM ZNCL2, REMARK 280 24% PEG &K, PH 4.60 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 33.81450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 61.78150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.55250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 61.78150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.81450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.55250 REMARK 290 SMTRY3 4 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: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D 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 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, VAL 62 TO CYS REMARK 400 ENGINEERED RESIDUE IN CHAIN A, ALA 327 TO CYS REMARK 400 ENGINEERED RESIDUE IN CHAIN B, VAL 62 TO CYS REMARK 400 ENGINEERED RESIDUE IN CHAIN B, ALA 327 TO CYS 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 LEU A 22 REMARK 465 PRO A 23 REMARK 465 GLU A 256 REMARK 465 LEU A 257 REMARK 465 SER A 258 REMARK 465 GLU A 259 REMARK 465 THR A 260 REMARK 465 PRO 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 ALA 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 VAL A 283 REMARK 465 GLY A 284 REMARK 465 THR A 285 REMARK 465 HIS A 307 REMARK 465 SER B 258 REMARK 465 GLU B 259 REMARK 465 THR B 260 REMARK 465 PRO 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 ALA B 269 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 ASN A 121 CG OD1 ND2 REMARK 470 GLU A 146 CA C CG OE1 REMARK 470 ASP A 147 N REMARK 470 ARG A 184 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 186 CG CD CE NZ REMARK 470 LYS A 190 CG CD CE NZ REMARK 470 GLU A 226 C CG OE1 REMARK 470 LYS A 245 CG CD CE NZ REMARK 470 ARG B 82 CD NE CZ NH1 NH2 REMARK 470 GLU B 86 CG CD OE1 OE2 REMARK 470 ASP B 87 OD1 OD2 REMARK 470 ARG B 89 CD NE CZ NH1 NH2 REMARK 470 LYS B 90 CE NZ REMARK 470 GLN B 91 CD OE1 NE2 REMARK 470 ASN B 121 CG OD1 ND2 REMARK 470 LYS B 186 CD CE NZ REMARK 470 TYR B 306 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 HIS B 307 CG ND1 CD2 CE1 NE2 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 NH2 ARG B 35 O THR B 304 2.13 REMARK 500 OG SER B 85 O HOH B 2011 2.14 REMARK 500 CE MET A 102 O HOH B 2019 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 226 CA GLU A 226 CB -0.375 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 A 226 N - CA - CB ANGL. DEV. = 15.5 DEGREES REMARK 500 ASP A 301 CB - CG - OD2 ANGL. DEV. = 9.5 DEGREES REMARK 500 ASP B 30 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP B 275 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ASP B 281 CB - CG - OD2 ANGL. DEV. = 5.9 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 ILE A 40 -59.01 -123.19 REMARK 500 ASN A 121 41.41 -97.10 REMARK 500 TYR A 137 -40.00 78.08 REMARK 500 PHE A 141 15.96 -146.38 REMARK 500 ALA A 155 54.45 37.18 REMARK 500 ASN A 171 -105.83 54.28 REMARK 500 ARG A 222 -134.40 -113.02 REMARK 500 PRO A 291 147.90 -38.65 REMARK 500 PRO A 297 -178.73 -66.71 REMARK 500 VAL B 24 -61.67 -157.64 REMARK 500 LEU B 25 77.85 60.52 REMARK 500 ILE B 40 -63.82 -123.79 REMARK 500 PRO B 78 0.97 -66.46 REMARK 500 GLU B 86 -38.69 -36.23 REMARK 500 ARG B 89 -0.27 -59.87 REMARK 500 PRO B 92 132.46 -31.58 REMARK 500 TYR B 137 -32.95 73.12 REMARK 500 ASN B 148 13.56 57.19 REMARK 500 ASN B 171 -116.86 53.18 REMARK 500 ARG B 222 -134.46 -117.79 REMARK 500 GLU B 256 -93.52 -9.97 REMARK 500 ASP B 275 -37.24 179.17 REMARK 500 REMARK 500 REMARK: NULL 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 B1315 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 39 NE2 REMARK 620 2 ASP A 215 OD2 106.5 REMARK 620 3 ASP B 301 OD2 93.0 126.6 REMARK 620 4 ASP B 301 OD1 143.5 102.5 51.5 REMARK 620 5 HOH B2035 O 103.0 104.7 118.8 90.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1314 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 301 OD1 REMARK 620 2 ASP A 301 OD2 53.8 REMARK 620 3 HIS B 39 NE2 110.7 164.3 REMARK 620 4 ASP B 215 OD2 131.0 91.4 102.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B1311 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 146 OE1 REMARK 620 2 GLU B 226 OE2 83.2 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1313 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 147 OD1 REMARK 620 2 ASP B 281 OD1 121.8 REMARK 620 3 ASP B 281 OD2 78.3 53.5 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1316 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 242 ND1 REMARK 620 2 ASP B 272 OD2 100.2 REMARK 620 N 1 REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1JMA RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE HERPES SIMPLEX VIRUS GLYCOPROTEIND BOUND REMARK 900 TO THE CELLULAR RECEPTOR HVEA/HVEM REMARK 900 RELATED ID: 1L2G RELATED DB: PDB REMARK 900 STRUCTURE OF A C-TERMINALLY TRUNCATED FORM OF GLYCOPROTEIND FROM REMARK 900 HSV-1 REMARK 900 RELATED ID: 2C36 RELATED DB: PDB REMARK 900 STRUCTURE OF UNLIGANDED HSV GD REVEALS A MECHANISM FOR RECEPTOR- REMARK 900 MEDIATED ACTIVATION OF VIRUS ENTRY DBREF 2C3A A 22 307 UNP P57083 VGLD_HHV1P 47 332 DBREF 2C3A B 22 307 UNP P57083 VGLD_HHV1P 47 332 SEQADV 2C3A CYS A 37 UNP P57083 VAL 62 ENGINEERED MUTATION SEQADV 2C3A CYS A 302 UNP P57083 ALA 327 ENGINEERED MUTATION SEQADV 2C3A CYS B 37 UNP P57083 VAL 62 ENGINEERED MUTATION SEQADV 2C3A CYS B 302 UNP P57083 ALA 327 ENGINEERED MUTATION SEQRES 1 A 286 LEU PRO VAL LEU ASP GLN LEU THR ASP PRO PRO GLY VAL SEQRES 2 A 286 ARG ARG CYS TYR HIS ILE GLN ALA GLY LEU PRO ASP PRO SEQRES 3 A 286 PHE GLN PRO PRO SER LEU PRO ILE THR VAL TYR TYR ALA SEQRES 4 A 286 VAL LEU GLU ARG ALA CYS ARG SER VAL LEU LEU ASN ALA SEQRES 5 A 286 PRO SER GLU ALA PRO GLN ILE VAL ARG GLY ALA SER GLU SEQRES 6 A 286 ASP VAL ARG LYS GLN PRO TYR ASN LEU THR ILE ALA TRP SEQRES 7 A 286 PHE ARG MET GLY GLY ASN CYS ALA ILE PRO ILE THR VAL SEQRES 8 A 286 MET GLU TYR THR GLU CYS SER TYR ASN LYS SER LEU GLY SEQRES 9 A 286 ALA CYS PRO ILE ARG THR GLN PRO ARG TRP ASN TYR TYR SEQRES 10 A 286 ASP SER PHE SER ALA VAL SER GLU ASP ASN LEU GLY PHE SEQRES 11 A 286 LEU MET HIS ALA PRO ALA PHE GLU THR ALA GLY THR TYR SEQRES 12 A 286 LEU ARG LEU VAL LYS ILE ASN ASP TRP THR GLU ILE THR SEQRES 13 A 286 GLN PHE ILE LEU GLU HIS ARG ALA LYS GLY SER CYS LYS SEQRES 14 A 286 TYR ALA LEU PRO LEU ARG ILE PRO PRO SER ALA CYS LEU SEQRES 15 A 286 SER PRO GLN ALA TYR GLN GLN GLY VAL THR VAL ASP SER SEQRES 16 A 286 ILE GLY MET LEU PRO ARG PHE ILE PRO GLU ASN GLN ARG SEQRES 17 A 286 THR VAL ALA VAL TYR SER LEU LYS ILE ALA GLY TRP HIS SEQRES 18 A 286 GLY PRO LYS ALA PRO TYR THR SER THR LEU LEU PRO PRO SEQRES 19 A 286 GLU LEU SER GLU THR PRO ASN ALA THR GLN PRO GLU LEU SEQRES 20 A 286 ALA PRO GLU ASP PRO GLU ASP SER ALA LEU LEU GLU ASP SEQRES 21 A 286 PRO VAL GLY THR VAL ALA PRO GLN ILE PRO PRO ASN TRP SEQRES 22 A 286 HIS ILE PRO SER ILE GLN ASP CYS ALA THR PRO TYR HIS SEQRES 1 B 286 LEU PRO VAL LEU ASP GLN LEU THR ASP PRO PRO GLY VAL SEQRES 2 B 286 ARG ARG CYS TYR HIS ILE GLN ALA GLY LEU PRO ASP PRO SEQRES 3 B 286 PHE GLN PRO PRO SER LEU PRO ILE THR VAL TYR TYR ALA SEQRES 4 B 286 VAL LEU GLU ARG ALA CYS ARG SER VAL LEU LEU ASN ALA SEQRES 5 B 286 PRO SER GLU ALA PRO GLN ILE VAL ARG GLY ALA SER GLU SEQRES 6 B 286 ASP VAL ARG LYS GLN PRO TYR ASN LEU THR ILE ALA TRP SEQRES 7 B 286 PHE ARG MET GLY GLY ASN CYS ALA ILE PRO ILE THR VAL SEQRES 8 B 286 MET GLU TYR THR GLU CYS SER TYR ASN LYS SER LEU GLY SEQRES 9 B 286 ALA CYS PRO ILE ARG THR GLN PRO ARG TRP ASN TYR TYR SEQRES 10 B 286 ASP SER PHE SER ALA VAL SER GLU ASP ASN LEU GLY PHE SEQRES 11 B 286 LEU MET HIS ALA PRO ALA PHE GLU THR ALA GLY THR TYR SEQRES 12 B 286 LEU ARG LEU VAL LYS ILE ASN ASP TRP THR GLU ILE THR SEQRES 13 B 286 GLN PHE ILE LEU GLU HIS ARG ALA LYS GLY SER CYS LYS SEQRES 14 B 286 TYR ALA LEU PRO LEU ARG ILE PRO PRO SER ALA CYS LEU SEQRES 15 B 286 SER PRO GLN ALA TYR GLN GLN GLY VAL THR VAL ASP SER SEQRES 16 B 286 ILE GLY MET LEU PRO ARG PHE ILE PRO GLU ASN GLN ARG SEQRES 17 B 286 THR VAL ALA VAL TYR SER LEU LYS ILE ALA GLY TRP HIS SEQRES 18 B 286 GLY PRO LYS ALA PRO TYR THR SER THR LEU LEU PRO PRO SEQRES 19 B 286 GLU LEU SER GLU THR PRO ASN ALA THR GLN PRO GLU LEU SEQRES 20 B 286 ALA PRO GLU ASP PRO GLU ASP SER ALA LEU LEU GLU ASP SEQRES 21 B 286 PRO VAL GLY THR VAL ALA PRO GLN ILE PRO PRO ASN TRP SEQRES 22 B 286 HIS ILE PRO SER ILE GLN ASP CYS ALA THR PRO TYR HIS MODRES 2C3A ASN A 94 ASN GLYCOSYLATION SITE MODRES 2C3A ASN B 94 ASN GLYCOSYLATION SITE HET NAG C 1 14 HET NAG C 2 14 HET NAG D 1 14 HET NAG D 2 14 HET CL A1309 1 HET ZN A1310 1 HET CL B1310 1 HET NA B1311 1 HET NA B1312 1 HET ZN B1313 1 HET ZN B1314 1 HET ZN B1315 1 HET ZN B1316 1 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM CL CHLORIDE ION HETNAM ZN ZINC ION HETNAM NA SODIUM ION FORMUL 3 NAG 4(C8 H15 N O6) FORMUL 5 CL 2(CL 1-) FORMUL 6 ZN 5(ZN 2+) FORMUL 8 NA 2(NA 1+) FORMUL 14 HOH *53(H2 O) HELIX 1 1 GLU A 76 GLY A 83 1 8 HELIX 2 2 ASP A 87 GLN A 91 5 5 HELIX 3 3 ALA A 157 ALA A 161 5 5 HELIX 4 4 PRO A 198 CYS A 202 5 5 HELIX 5 5 SER A 204 GLY A 211 1 8 HELIX 6 6 ASN A 227 ALA A 239 1 13 HELIX 7 7 GLU B 76 ILE B 80 5 5 HELIX 8 8 ASP B 87 GLN B 91 5 5 HELIX 9 9 ALA B 157 ALA B 161 5 5 HELIX 10 10 PRO B 198 CYS B 202 5 5 HELIX 11 11 SER B 204 GLN B 210 1 7 HELIX 12 12 ILE B 224 ALA B 239 1 16 SHEET 1 AA 8 ARG A 35 CYS A 37 0 SHEET 2 AA 8 ILE A 129 THR A 131 1 O ARG A 130 N CYS A 37 SHEET 3 AA 8 CYS A 106 CYS A 118 -1 O GLU A 114 N THR A 131 SHEET 4 AA 8 TYR A 93 GLY A 103 -1 O TYR A 93 N CYS A 118 SHEET 5 AA 8 GLY A 162 ILE A 170 -1 O THR A 163 N MET A 102 SHEET 6 AA 8 TRP A 173 HIS A 183 -1 O TRP A 173 N ILE A 170 SHEET 7 AA 8 THR A 56 LEU A 62 1 O THR A 56 N GLN A 178 SHEET 8 AA 8 SER A 250 THR A 251 -1 O THR A 251 N TYR A 59 SHEET 1 AB 5 ARG A 35 CYS A 37 0 SHEET 2 AB 5 ILE A 129 THR A 131 1 O ARG A 130 N CYS A 37 SHEET 3 AB 5 CYS A 106 CYS A 118 -1 O GLU A 114 N THR A 131 SHEET 4 AB 5 ARG A 134 TRP A 135 -1 O ARG A 134 N VAL A 112 SHEET 5 AB 5 LEU A 220 PRO A 221 -1 O LEU A 220 N TRP A 135 SHEET 1 AC 3 SER A 68 LEU A 71 0 SHEET 2 AC 3 PHE A 151 HIS A 154 -1 O PHE A 151 N LEU A 71 SHEET 3 AC 3 SER A 142 VAL A 144 -1 O ALA A 143 N LEU A 152 SHEET 1 BA 7 ARG B 35 CYS B 37 0 SHEET 2 BA 7 ILE B 129 THR B 131 1 O ARG B 130 N CYS B 37 SHEET 3 BA 7 ALA B 107 CYS B 118 -1 O GLU B 114 N THR B 131 SHEET 4 BA 7 TYR B 93 MET B 102 -1 O TYR B 93 N CYS B 118 SHEET 5 BA 7 GLY B 162 ILE B 170 -1 O THR B 163 N MET B 102 SHEET 6 BA 7 TRP B 173 HIS B 183 -1 O TRP B 173 N ILE B 170 SHEET 7 BA 7 THR B 56 LEU B 62 1 O THR B 56 N GLN B 178 SHEET 1 BB 5 ARG B 35 CYS B 37 0 SHEET 2 BB 5 ILE B 129 THR B 131 1 O ARG B 130 N CYS B 37 SHEET 3 BB 5 ALA B 107 CYS B 118 -1 O GLU B 114 N THR B 131 SHEET 4 BB 5 ARG B 134 TRP B 135 -1 O ARG B 134 N VAL B 112 SHEET 5 BB 5 LEU B 220 PRO B 221 -1 O LEU B 220 N TRP B 135 SHEET 1 BC 3 SER B 68 LEU B 71 0 SHEET 2 BC 3 PHE B 151 HIS B 154 -1 O PHE B 151 N LEU B 71 SHEET 3 BC 3 SER B 142 VAL B 144 -1 O ALA B 143 N LEU B 152 SSBOND 1 CYS A 37 CYS A 302 1555 1555 2.03 SSBOND 2 CYS A 66 CYS A 189 1555 1555 2.04 SSBOND 3 CYS A 106 CYS A 202 1555 1555 2.06 SSBOND 4 CYS A 118 CYS A 127 1555 1555 2.06 SSBOND 5 CYS B 37 CYS B 302 1555 1555 1.93 SSBOND 6 CYS B 66 CYS B 189 1555 1555 2.11 SSBOND 7 CYS B 106 CYS B 202 1555 1555 2.08 SSBOND 8 CYS B 118 CYS B 127 1555 1555 2.06 LINK ND2 ASN A 94 C1 NAG C 1 1555 1555 1.44 LINK ND2 ASN B 94 C1 NAG D 1 1555 1555 1.44 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.46 LINK O4 NAG D 1 C1 NAG D 2 1555 1555 1.44 LINK NE2 HIS A 39 ZN ZN B1315 2564 1555 1.86 LINK OD2 ASP A 215 ZN ZN B1315 2564 1555 2.07 LINK OE2 GLU A 226 ZN ZN A1310 1555 1555 2.26 LINK OD1 ASP A 301 ZN ZN B1314 2564 1555 1.91 LINK OD2 ASP A 301 ZN ZN B1314 2564 1555 2.48 LINK NE2 HIS B 39 ZN ZN B1314 1555 1555 1.91 LINK OE1 GLU B 146 NA NA B1311 1555 1555 1.97 LINK OD1 ASP B 147 ZN ZN B1313 1555 1555 2.07 LINK OD2 ASP B 215 ZN ZN B1314 1555 1555 1.81 LINK OE2 GLU B 226 NA NA B1311 1555 1555 2.32 LINK ND1 HIS B 242 ZN ZN B1316 1555 1555 2.46 LINK OD2 ASP B 272 ZN ZN B1316 1555 1555 1.66 LINK OD1 ASP B 281 ZN ZN B1313 4455 1555 2.63 LINK OD2 ASP B 281 ZN ZN B1313 4455 1555 2.00 LINK OD2 ASP B 301 ZN ZN B1315 1555 1555 2.04 LINK OD1 ASP B 301 ZN ZN B1315 1555 1555 2.67 LINK ZN ZN B1315 O HOH B2035 1555 1555 2.35 CISPEP 1 GLY A 243 PRO A 244 0 10.27 CISPEP 2 GLY B 243 PRO B 244 0 -4.85 CRYST1 67.629 79.105 123.563 90.00 90.00 90.00 P 21 21 21 8 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 0.014787 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012641 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008093 0.00000 MTRIX1 1 0.960450 0.276670 0.031550 -10.02013 1 MTRIX2 1 0.277500 -0.960390 -0.025630 73.80945 1 MTRIX3 1 0.023210 0.033370 -0.999170 -3.41714 1 MASTER 494 0 13 12 31 0 0 9 0 0 0 44 END