HEADER ANTIVIRAL PROTEIN 21-JAN-25 9MY8 TITLE D7 HERPES VIRUS SIMPLEX NEUTRALIZING NANOBODY BOUND TO HSV TITLE 2 GLYCOPROTEIN GD COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANTI-NB FAB HEAVY CHAIN; COMPND 3 CHAIN: H; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: IG-LIKE DOMAIN-CONTAINING PROTEIN; COMPND 7 CHAIN: L; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: D7 NEUTRALIZING NANOBODY AGAINST HSV GLYCOPROTEIN D; COMPND 11 CHAIN: A; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 4; COMPND 14 MOLECULE: GLYCOPROTEIN D; COMPND 15 CHAIN: B; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LAMA GLAMA; SOURCE 3 ORGANISM_COMMON: LLAMA; SOURCE 4 ORGANISM_TAXID: 9844; SOURCE 5 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 6 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: HEK293; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: LAMA GLAMA; SOURCE 11 ORGANISM_COMMON: LLAMA; SOURCE 12 ORGANISM_TAXID: 9844; SOURCE 13 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 14 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 16 EXPRESSION_SYSTEM_CELL_LINE: HEK293; SOURCE 17 MOL_ID: 3; SOURCE 18 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 19 ORGANISM_COMMON: HUMAN; SOURCE 20 ORGANISM_TAXID: 9606; SOURCE 21 CELL_LINE: HEK293; SOURCE 22 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 23 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 24 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 25 MOL_ID: 4; SOURCE 26 ORGANISM_SCIENTIFIC: HUMAN HERPESVIRUS 2; SOURCE 27 ORGANISM_COMMON: HHV-2, HUMAN HERPES SIMPLEX VIRUS 2; SOURCE 28 ORGANISM_TAXID: 10310; SOURCE 29 GENE: US6; SOURCE 30 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 31 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 32 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 33 EXPRESSION_SYSTEM_CELL_LINE: HEK293 KEYWDS NEUTRALIZING ANTIBODY, ANTIVIRAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR H.VIADIU,E.ABERNATHY,C.V.LEE,M.HUNG,Y.YU,W.XING,X.YU REVDAT 1 13-AUG-25 9MY8 0 JRNL AUTH C.V.LEE,H.VIADIU,A.KALAMKAR,D.I.BERNSTEIN,A.PAE,X.YU,S.WONG, JRNL AUTH 2 F.J.BRAVO,S.DING,E.SETO,M.HUNG,Y.YU,W.XING,G.A.PAPALIA, JRNL AUTH 3 W.KAN,B.CARR,M.THOMAS,L.TONG,P.DESAI,N.JARROUSSE,A.MERCIER, JRNL AUTH 4 M.M.HOLDORF,S.P.FLETCHER,E.ABERNATHY JRNL TITL IDENTIFICATION AND ENGINEERING OF POTENT BISPECIFIC JRNL TITL 2 ANTIBODIES THAT PROTECT AGAINST HERPES SIMPLEX VIRUS JRNL TITL 3 RECURRENT DISEASE. JRNL REF CELL REP V. 44 16063 2025 JRNL REFN ESSN 2211-1247 JRNL PMID 40716063 JRNL DOI 10.1016/J.CELREP.2025.116063 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, PHENIX, EPU, CRYOSPARC, REMARK 3 CRYOSPARC, CRYOSPARC, CRYOSPARC, REMARK 3 CRYOSPARC REMARK 3 RECONSTRUCTION SCHEMA : FOURIER SPACE REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : NULL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 2.300 REMARK 3 NUMBER OF PARTICLES : 228770 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 9MY8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-JAN-25. REMARK 100 THE DEPOSITION ID IS D_1000291989. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : D7 NEUTRALIZING NANOBODY BOUND REMARK 245 TO THE HSV GLYCOPROTEIN D REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 2.00 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.40 REMARK 245 SAMPLE DETAILS : THERE ARE 4 MOLECULES IN THE REMARK 245 COMPLEX. A HSV GLYCOPROTEIN D MONOMER NEUTRILIZED BY THE D7 REMARK 245 NANOBODY AND ONE TOOL FAB TO ENABLE CRYOEM STUDIES (LIGHT AND REMARK 245 HEAVY CHAINS). REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS KRIOS REMARK 245 DETECTOR TYPE : TFS FALCON 4I (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 600.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1500.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5200.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 165000 REMARK 245 CALIBRATED MAGNIFICATION : 165000 REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: H, L, A, 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 GLU H 1 REMARK 465 LYS H 229 REMARK 465 SER H 230 REMARK 465 CYS H 231 REMARK 465 ASP H 232 REMARK 465 LYS H 233 REMARK 465 THR H 234 REMARK 465 HIS H 235 REMARK 465 THR H 236 REMARK 465 GLY H 237 REMARK 465 SER H 238 REMARK 465 HIS H 239 REMARK 465 HIS H 240 REMARK 465 HIS H 241 REMARK 465 HIS H 242 REMARK 465 HIS H 243 REMARK 465 HIS H 244 REMARK 465 ASP L 1 REMARK 465 ILE L 2 REMARK 465 GLN L 3 REMARK 465 GLY L 212 REMARK 465 GLU L 213 REMARK 465 CYS L 214 REMARK 465 HIS A 120 REMARK 465 HIS A 121 REMARK 465 HIS A 122 REMARK 465 HIS A 123 REMARK 465 HIS A 124 REMARK 465 HIS A 125 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 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 VAL B 286 REMARK 465 SER B 287 REMARK 465 SER B 288 REMARK 465 GLN B 289 REMARK 465 ILE B 290 REMARK 465 PRO B 291 REMARK 465 PRO B 292 REMARK 465 ASN B 293 REMARK 465 TRP B 294 REMARK 465 HIS B 295 REMARK 465 ILE B 296 REMARK 465 PRO B 297 REMARK 465 SER B 298 REMARK 465 ILE B 299 REMARK 465 GLN B 300 REMARK 465 ASP B 301 REMARK 465 VAL B 302 REMARK 465 ALA B 303 REMARK 465 PRO B 304 REMARK 465 HIS B 305 REMARK 465 GLY B 306 REMARK 465 GLY B 307 REMARK 465 GLY B 308 REMARK 465 SER B 309 REMARK 465 HIS B 310 REMARK 465 HIS B 311 REMARK 465 HIS B 312 REMARK 465 HIS B 313 REMARK 465 HIS B 314 REMARK 465 HIS B 315 REMARK 465 HIS B 316 REMARK 465 HIS B 317 REMARK 465 GLY B 318 REMARK 465 SER B 319 REMARK 465 ASP B 320 REMARK 465 TYR B 321 REMARK 465 LYS B 322 REMARK 465 ASP B 323 REMARK 465 ASP B 324 REMARK 465 ASP B 325 REMARK 465 ASP B 326 REMARK 465 LYS B 327 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 SER H 128 OG 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 LEU H 81 O HOH H 301 2.17 REMARK 500 O ALA B 200 O HOH B 401 2.17 REMARK 500 NZ LYS L 45 O HOH L 301 2.18 REMARK 500 O LEU H 115 O HOH H 302 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 CYS A 22 CA - CB - SG ANGL. DEV. = 6.8 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 SER H 54 -64.31 154.87 REMARK 500 TYR H 102 39.80 -99.61 REMARK 500 LEU H 115 148.70 -173.60 REMARK 500 SER H 130 -176.91 61.58 REMARK 500 SER H 147 -136.45 50.75 REMARK 500 ASP H 159 61.91 63.20 REMARK 500 SER L 26 -104.04 52.63 REMARK 500 SER L 31 143.90 -172.04 REMARK 500 TYR L 36 169.60 61.94 REMARK 500 LEU L 47 -33.66 -130.34 REMARK 500 SER L 50 12.65 59.81 REMARK 500 ALA L 51 -7.24 71.84 REMARK 500 ALA L 84 -149.13 54.64 REMARK 500 SER L 93 -55.54 -123.09 REMARK 500 SER L 94 10.53 -141.24 REMARK 500 ALA L 144 11.86 -142.08 REMARK 500 THR L 180 -3.49 67.60 REMARK 500 ASN L 210 -166.98 -117.96 REMARK 500 SER A 25 -85.71 56.35 REMARK 500 TRP A 32 -99.78 39.29 REMARK 500 TYR A 108 -60.32 -96.55 REMARK 500 ILE B 40 -51.64 -122.49 REMARK 500 TYR B 137 -6.20 72.35 REMARK 500 ASN B 171 -96.08 55.13 REMARK 500 HIS B 183 154.27 65.21 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 PHE H 181 PRO H 182 146.84 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH H 679 DISTANCE = 5.82 ANGSTROMS REMARK 525 HOH H 680 DISTANCE = 5.83 ANGSTROMS REMARK 525 HOH H 681 DISTANCE = 5.86 ANGSTROMS REMARK 525 HOH H 682 DISTANCE = 5.87 ANGSTROMS REMARK 525 HOH H 683 DISTANCE = 5.91 ANGSTROMS REMARK 525 HOH H 684 DISTANCE = 5.98 ANGSTROMS REMARK 525 HOH H 685 DISTANCE = 6.07 ANGSTROMS REMARK 525 HOH L 684 DISTANCE = 5.81 ANGSTROMS REMARK 525 HOH L 685 DISTANCE = 5.85 ANGSTROMS REMARK 525 HOH L 686 DISTANCE = 5.89 ANGSTROMS REMARK 525 HOH L 687 DISTANCE = 5.90 ANGSTROMS REMARK 525 HOH L 688 DISTANCE = 5.93 ANGSTROMS REMARK 525 HOH L 689 DISTANCE = 5.96 ANGSTROMS REMARK 525 HOH L 690 DISTANCE = 5.97 ANGSTROMS REMARK 525 HOH L 691 DISTANCE = 5.97 ANGSTROMS REMARK 525 HOH L 692 DISTANCE = 6.03 ANGSTROMS REMARK 525 HOH L 693 DISTANCE = 6.07 ANGSTROMS REMARK 525 HOH L 694 DISTANCE = 6.16 ANGSTROMS REMARK 525 HOH L 695 DISTANCE = 6.23 ANGSTROMS REMARK 525 HOH L 696 DISTANCE = 6.26 ANGSTROMS REMARK 525 HOH L 697 DISTANCE = 6.37 ANGSTROMS REMARK 525 HOH L 698 DISTANCE = 6.50 ANGSTROMS REMARK 525 HOH L 699 DISTANCE = 6.61 ANGSTROMS REMARK 525 HOH L 700 DISTANCE = 7.30 ANGSTROMS REMARK 525 HOH A 383 DISTANCE = 5.85 ANGSTROMS REMARK 525 HOH A 384 DISTANCE = 6.03 ANGSTROMS REMARK 525 HOH B 906 DISTANCE = 5.84 ANGSTROMS REMARK 525 HOH B 907 DISTANCE = 5.85 ANGSTROMS REMARK 525 HOH B 908 DISTANCE = 5.86 ANGSTROMS REMARK 525 HOH B 909 DISTANCE = 5.87 ANGSTROMS REMARK 525 HOH B 910 DISTANCE = 5.88 ANGSTROMS REMARK 525 HOH B 911 DISTANCE = 5.88 ANGSTROMS REMARK 525 HOH B 912 DISTANCE = 5.91 ANGSTROMS REMARK 525 HOH B 913 DISTANCE = 5.97 ANGSTROMS REMARK 525 HOH B 914 DISTANCE = 6.00 ANGSTROMS REMARK 525 HOH B 915 DISTANCE = 6.07 ANGSTROMS REMARK 525 HOH B 916 DISTANCE = 6.15 ANGSTROMS REMARK 525 HOH B 917 DISTANCE = 6.18 ANGSTROMS REMARK 525 HOH B 918 DISTANCE = 6.28 ANGSTROMS REMARK 525 HOH B 919 DISTANCE = 6.36 ANGSTROMS REMARK 525 HOH B 920 DISTANCE = 6.82 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-48730 RELATED DB: EMDB REMARK 900 D7 HERPES VIRUS SIMPLEX NEUTRALIZING NANOBODY BOUND TO HSV REMARK 900 GLYCOPROTEIN GD DBREF 9MY8 H 1 244 PDB 9MY8 9MY8 1 244 DBREF 9MY8 L 1 214 UNP Q7Z3Y4 Q7Z3Y4_HUMAN 23 236 DBREF 9MY8 A 1 125 PDB 9MY8 9MY8 1 125 DBREF 9MY8 B 1 305 UNP Q5ICU7 Q5ICU7_HHV2 26 330 SEQADV 9MY8 ARG L 18 UNP Q7Z3Y4 THR 40 CONFLICT SEQADV 9MY8 SER L 28 UNP Q7Z3Y4 ASP 50 CONFLICT SEQADV 9MY8 VAL L 29 UNP Q7Z3Y4 ILE 51 CONFLICT SEQADV 9MY8 SER L 31 UNP Q7Z3Y4 ASN 53 CONFLICT SEQADV 9MY8 ALA L 32 UNP Q7Z3Y4 TYR 54 CONFLICT SEQADV 9MY8 VAL L 33 UNP Q7Z3Y4 LEU 55 CONFLICT SEQADV 9MY8 TYR L 36 UNP Q7Z3Y4 PHE 58 CONFLICT SEQADV 9MY8 LEU L 46 UNP Q7Z3Y4 SER 68 CONFLICT SEQADV 9MY8 SER L 50 UNP Q7Z3Y4 GLY 72 CONFLICT SEQADV 9MY8 TYR L 55 UNP Q7Z3Y4 GLN 77 CONFLICT SEQADV 9MY8 PRO L 59 UNP Q7Z3Y4 GLN 81 CONFLICT SEQADV 9MY8 ARG L 61 UNP Q7Z3Y4 LYS 83 CONFLICT SEQADV 9MY8 ARG L 66 UNP Q7Z3Y4 GLY 88 CONFLICT SEQADV 9MY8 SER L 91 UNP Q7Z3Y4 TYR 113 CONFLICT SEQADV 9MY8 SER L 92 UNP Q7Z3Y4 LYS 114 CONFLICT SEQADV 9MY8 SER L 94 UNP Q7Z3Y4 TYR 116 CONFLICT SEQADV 9MY8 LEU L 95 UNP Q7Z3Y4 PRO 117 CONFLICT SEQADV 9MY8 ILE L 96 UNP Q7Z3Y4 VAL 118 CONFLICT SEQADV 9MY8 VAL L 104 UNP Q7Z3Y4 LEU 126 CONFLICT SEQADV 9MY8 SER L 123 UNP Q7Z3Y4 GLU 145 CONFLICT SEQADV 9MY8 GLY B 306 UNP Q5ICU7 EXPRESSION TAG SEQADV 9MY8 GLY B 307 UNP Q5ICU7 EXPRESSION TAG SEQADV 9MY8 GLY B 308 UNP Q5ICU7 EXPRESSION TAG SEQADV 9MY8 SER B 309 UNP Q5ICU7 EXPRESSION TAG SEQADV 9MY8 HIS B 310 UNP Q5ICU7 EXPRESSION TAG SEQADV 9MY8 HIS B 311 UNP Q5ICU7 EXPRESSION TAG SEQADV 9MY8 HIS B 312 UNP Q5ICU7 EXPRESSION TAG SEQADV 9MY8 HIS B 313 UNP Q5ICU7 EXPRESSION TAG SEQADV 9MY8 HIS B 314 UNP Q5ICU7 EXPRESSION TAG SEQADV 9MY8 HIS B 315 UNP Q5ICU7 EXPRESSION TAG SEQADV 9MY8 HIS B 316 UNP Q5ICU7 EXPRESSION TAG SEQADV 9MY8 HIS B 317 UNP Q5ICU7 EXPRESSION TAG SEQADV 9MY8 GLY B 318 UNP Q5ICU7 EXPRESSION TAG SEQADV 9MY8 SER B 319 UNP Q5ICU7 EXPRESSION TAG SEQADV 9MY8 ASP B 320 UNP Q5ICU7 EXPRESSION TAG SEQADV 9MY8 TYR B 321 UNP Q5ICU7 EXPRESSION TAG SEQADV 9MY8 LYS B 322 UNP Q5ICU7 EXPRESSION TAG SEQADV 9MY8 ASP B 323 UNP Q5ICU7 EXPRESSION TAG SEQADV 9MY8 ASP B 324 UNP Q5ICU7 EXPRESSION TAG SEQADV 9MY8 ASP B 325 UNP Q5ICU7 EXPRESSION TAG SEQADV 9MY8 ASP B 326 UNP Q5ICU7 EXPRESSION TAG SEQADV 9MY8 LYS B 327 UNP Q5ICU7 EXPRESSION TAG SEQRES 1 H 244 GLU VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 H 244 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 H 244 PHE ASN PHE SER TYR TYR SER ILE HIS TRP VAL ARG GLN SEQRES 4 H 244 ALA PRO GLY LYS GLY LEU GLU TRP VAL ALA TYR ILE SER SEQRES 5 H 244 SER SER SER SER TYR THR SER TYR ALA ASP SER VAL LYS SEQRES 6 H 244 GLY ARG PHE THR ILE SER ALA ASP THR SER LYS ASN THR SEQRES 7 H 244 ALA TYR LEU GLN MET ASN SER LEU ARG ALA GLU ASP THR SEQRES 8 H 244 ALA VAL TYR TYR CYS ALA ARG GLY TYR GLN TYR TRP GLN SEQRES 9 H 244 TYR HIS ALA SER TRP TYR TRP ASN GLY GLY LEU ASP TYR SEQRES 10 H 244 TRP GLY GLN GLY THR LEU VAL THR VAL SER SER ALA SER SEQRES 11 H 244 THR LYS GLY PRO SER VAL PHE PRO LEU ALA PRO SER SER SEQRES 12 H 244 LYS SER THR SER GLY GLY THR ALA ALA LEU GLY CYS LEU SEQRES 13 H 244 VAL LYS ASP TYR PHE PRO GLU PRO VAL THR VAL SER TRP SEQRES 14 H 244 ASN SER GLY ALA LEU THR SER GLY VAL HIS THR PHE PRO SEQRES 15 H 244 ALA VAL LEU GLN SER SER GLY LEU TYR SER LEU SER SER SEQRES 16 H 244 VAL VAL THR VAL PRO SER SER SER LEU GLY THR GLN THR SEQRES 17 H 244 TYR ILE CYS ASN VAL ASN HIS LYS PRO SER ASN THR LYS SEQRES 18 H 244 VAL ASP LYS LYS VAL GLU PRO LYS SER CYS ASP LYS THR SEQRES 19 H 244 HIS THR GLY SER HIS HIS HIS HIS HIS HIS SEQRES 1 L 214 ASP ILE GLN MET THR GLN SER PRO SER SER LEU SER ALA SEQRES 2 L 214 SER VAL GLY ASP ARG VAL THR ILE THR CYS ARG ALA SER SEQRES 3 L 214 GLN SER VAL SER SER ALA VAL ALA TRP TYR GLN GLN LYS SEQRES 4 L 214 PRO GLY LYS ALA PRO LYS LEU LEU ILE TYR SER ALA SER SEQRES 5 L 214 SER LEU TYR SER GLY VAL PRO SER ARG PHE SER GLY SER SEQRES 6 L 214 ARG SER GLY THR ASP PHE THR LEU THR ILE SER SER LEU SEQRES 7 L 214 GLN PRO GLU ASP PHE ALA THR TYR TYR CYS GLN GLN SER SEQRES 8 L 214 SER SER SER LEU ILE THR PHE GLY GLN GLY THR LYS VAL SEQRES 9 L 214 GLU ILE LYS ARG THR VAL ALA ALA PRO SER VAL PHE ILE SEQRES 10 L 214 PHE PRO PRO SER ASP SER GLN LEU LYS SER GLY THR ALA SEQRES 11 L 214 SER VAL VAL CYS LEU LEU ASN ASN PHE TYR PRO ARG GLU SEQRES 12 L 214 ALA LYS VAL GLN TRP LYS VAL ASP ASN ALA LEU GLN SER SEQRES 13 L 214 GLY ASN SER GLN GLU SER VAL THR GLU GLN ASP SER LYS SEQRES 14 L 214 ASP SER THR TYR SER LEU SER SER THR LEU THR LEU SER SEQRES 15 L 214 LYS ALA ASP TYR GLU LYS HIS LYS VAL TYR ALA CYS GLU SEQRES 16 L 214 VAL THR HIS GLN GLY LEU SER SER PRO VAL THR LYS SER SEQRES 17 L 214 PHE ASN ARG GLY GLU CYS SEQRES 1 A 125 GLU VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 A 125 PRO GLY GLY SER LEU ARG LEU SER CYS SER ALA SER GLY SEQRES 3 A 125 SER ILE PRO SER ILE TRP ILE MET TYR TRP TYR ARG GLN SEQRES 4 A 125 ALA PRO GLY LYS GLY ARG GLU LEU VAL ALA GLN ILE THR SEQRES 5 A 125 ASN PHE GLY THR THR VAL TYR ALA ASP SER VAL LYS GLY SEQRES 6 A 125 ARG PHE THR ILE SER SER ASP ALA SER LYS ASN THR VAL SEQRES 7 A 125 TYR LEU GLN MET ASN SER LEU ARG ALA GLU ASP THR ALA SEQRES 8 A 125 VAL TYR TYR CYS ASN LEU ASP VAL THR LEU GLY PRO SER SEQRES 9 A 125 ARG GLY ALA TYR TRP GLY LYS GLY THR PRO VAL THR VAL SEQRES 10 A 125 SER SER HIS HIS HIS HIS HIS HIS SEQRES 1 B 327 LYS TYR ALA LEU ALA ASP PRO SER LEU LYS MET ALA ASP SEQRES 2 B 327 PRO ASN ARG PHE ARG GLY LYS ASN LEU PRO VAL LEU ASP SEQRES 3 B 327 GLN LEU THR ASP PRO PRO GLY VAL LYS ARG VAL TYR HIS SEQRES 4 B 327 ILE GLN PRO SER LEU GLU ASP PRO PHE GLN PRO PRO SER SEQRES 5 B 327 ILE PRO ILE THR VAL TYR TYR ALA VAL LEU GLU ARG ALA SEQRES 6 B 327 CYS ARG SER VAL LEU LEU HIS ALA PRO SER GLU ALA PRO SEQRES 7 B 327 GLN ILE VAL ARG GLY ALA SER ASP GLU ALA ARG LYS HIS SEQRES 8 B 327 THR TYR ASN LEU THR ILE ALA TRP TYR ARG MET GLY ASP SEQRES 9 B 327 ASN CYS ALA ILE PRO ILE THR VAL MET GLU TYR THR GLU SEQRES 10 B 327 CYS PRO TYR ASN LYS SER LEU GLY VAL CYS PRO ILE ARG SEQRES 11 B 327 THR GLN PRO ARG TRP SER TYR TYR ASP SER PHE SER ALA SEQRES 12 B 327 VAL SER GLU ASP ASN LEU GLY PHE LEU MET HIS ALA PRO SEQRES 13 B 327 ALA PHE GLU THR ALA GLY THR TYR LEU ARG LEU VAL LYS SEQRES 14 B 327 ILE ASN ASP TRP THR GLU ILE THR GLN PHE ILE LEU GLU SEQRES 15 B 327 HIS ARG ALA ARG ALA SER CYS LYS TYR ALA LEU PRO LEU SEQRES 16 B 327 ARG ILE PRO PRO ALA ALA CYS LEU THR SER LYS ALA TYR SEQRES 17 B 327 GLN GLN GLY VAL THR VAL ASP SER ILE GLY MET LEU PRO SEQRES 18 B 327 ARG PHE ILE PRO GLU ASN GLN ARG THR VAL ALA LEU TYR SEQRES 19 B 327 SER LEU LYS ILE ALA GLY TRP HIS GLY PRO LYS PRO PRO SEQRES 20 B 327 TYR THR SER THR LEU LEU PRO PRO GLU LEU SER ASP THR SEQRES 21 B 327 THR ASN ALA THR GLN PRO GLU LEU VAL PRO GLU ASP PRO SEQRES 22 B 327 GLU ASP SER ALA LEU LEU GLU ASP PRO ALA GLY THR VAL SEQRES 23 B 327 SER SER GLN ILE PRO PRO ASN TRP HIS ILE PRO SER ILE SEQRES 24 B 327 GLN ASP VAL ALA PRO HIS GLY GLY GLY SER HIS HIS HIS SEQRES 25 B 327 HIS HIS HIS HIS HIS GLY SER ASP TYR LYS ASP ASP ASP SEQRES 26 B 327 ASP LYS FORMUL 5 HOH *1489(H2 O) HELIX 1 AA1 ASN H 28 SER H 30 5 3 HELIX 2 AA2 ARG H 87 THR H 91 5 5 HELIX 3 AA3 SER H 201 GLN H 207 1 7 HELIX 4 AA4 ASP L 122 SER L 127 1 6 HELIX 5 AA5 SER L 182 HIS L 189 1 8 HELIX 6 AA6 ARG A 86 THR A 90 5 5 HELIX 7 AA7 GLU B 76 GLY B 83 1 8 HELIX 8 AA8 SER B 85 LYS B 90 1 6 HELIX 9 AA9 ALA B 157 ALA B 161 5 5 HELIX 10 AB1 PRO B 198 CYS B 202 5 5 HELIX 11 AB2 THR B 204 GLY B 211 1 8 HELIX 12 AB3 ILE B 224 GLY B 240 1 17 SHEET 1 AA1 4 GLN H 3 SER H 7 0 SHEET 2 AA1 4 ARG H 19 SER H 25 -1 O SER H 21 N SER H 7 SHEET 3 AA1 4 THR H 78 GLN H 82 -1 O ALA H 79 N CYS H 22 SHEET 4 AA1 4 THR H 69 ASP H 73 -1 N SER H 71 O TYR H 80 SHEET 1 AA2 6 LEU H 11 VAL H 12 0 SHEET 2 AA2 6 THR H 122 VAL H 126 1 O THR H 125 N VAL H 12 SHEET 3 AA2 6 ALA H 92 TYR H 100 -1 N TYR H 94 O THR H 122 SHEET 4 AA2 6 TYR H 32 GLN H 39 -1 N VAL H 37 O TYR H 95 SHEET 5 AA2 6 LEU H 45 SER H 52 -1 O GLU H 46 N ARG H 38 SHEET 6 AA2 6 TYR H 57 TYR H 60 -1 O TYR H 57 N SER H 52 SHEET 1 AA3 4 LEU H 11 VAL H 12 0 SHEET 2 AA3 4 THR H 122 VAL H 126 1 O THR H 125 N VAL H 12 SHEET 3 AA3 4 ALA H 92 TYR H 100 -1 N TYR H 94 O THR H 122 SHEET 4 AA3 4 TYR H 117 TRP H 118 -1 O TYR H 117 N ARG H 98 SHEET 1 AA4 3 SER H 135 PHE H 137 0 SHEET 2 AA4 3 ALA H 152 TYR H 160 -1 O LYS H 158 N SER H 135 SHEET 3 AA4 3 TYR H 191 THR H 198 -1 O TYR H 191 N TYR H 160 SHEET 1 AA5 4 THR L 5 GLN L 6 0 SHEET 2 AA5 4 VAL L 19 ARG L 24 -1 O ARG L 24 N THR L 5 SHEET 3 AA5 4 ASP L 70 ILE L 75 -1 O PHE L 71 N CYS L 23 SHEET 4 AA5 4 PHE L 62 SER L 67 -1 N SER L 65 O THR L 72 SHEET 1 AA6 2 ILE L 48 TYR L 49 0 SHEET 2 AA6 2 SER L 53 LEU L 54 -1 O SER L 53 N TYR L 49 SHEET 1 AA7 2 GLN L 89 SER L 91 0 SHEET 2 AA7 2 ILE L 96 PHE L 98 -1 O THR L 97 N GLN L 90 SHEET 1 AA8 3 VAL L 115 PHE L 118 0 SHEET 2 AA8 3 VAL L 133 PHE L 139 -1 O LEU L 135 N PHE L 116 SHEET 3 AA8 3 TYR L 173 THR L 178 -1 O TYR L 173 N PHE L 139 SHEET 1 AA9 4 LEU L 154 GLN L 155 0 SHEET 2 AA9 4 GLN L 147 VAL L 150 -1 N TRP L 148 O GLN L 155 SHEET 3 AA9 4 TYR L 192 GLU L 195 -1 O GLU L 195 N GLN L 147 SHEET 4 AA9 4 LYS L 207 PHE L 209 -1 O PHE L 209 N TYR L 192 SHEET 1 AB1 4 VAL A 5 SER A 7 0 SHEET 2 AB1 4 LEU A 18 SER A 23 -1 O SER A 21 N SER A 7 SHEET 3 AB1 4 TYR A 79 MET A 82 -1 O LEU A 80 N LEU A 20 SHEET 4 AB1 4 PHE A 67 SER A 70 -1 N THR A 68 O GLN A 81 SHEET 1 AB2 6 LEU A 11 VAL A 12 0 SHEET 2 AB2 6 THR A 113 VAL A 117 1 O THR A 116 N VAL A 12 SHEET 3 AB2 6 ALA A 91 ASP A 98 -1 N TYR A 93 O THR A 113 SHEET 4 AB2 6 ILE A 33 GLN A 39 -1 N GLN A 39 O VAL A 92 SHEET 5 AB2 6 GLU A 46 THR A 52 -1 O GLU A 46 N ARG A 38 SHEET 6 AB2 6 THR A 57 TYR A 59 -1 O VAL A 58 N GLN A 50 SHEET 1 AB3 7 LYS B 35 VAL B 37 0 SHEET 2 AB3 7 ILE B 129 THR B 131 1 O ARG B 130 N LYS B 35 SHEET 3 AB3 7 CYS B 106 PRO B 119 -1 N GLU B 114 O THR B 131 SHEET 4 AB3 7 THR B 92 GLY B 103 -1 N ARG B 101 O ILE B 108 SHEET 5 AB3 7 GLY B 162 ILE B 170 -1 O LEU B 167 N ALA B 98 SHEET 6 AB3 7 TRP B 173 LEU B 181 -1 O LEU B 181 N GLY B 162 SHEET 7 AB3 7 THR B 56 ALA B 60 1 N THR B 56 O GLN B 178 SHEET 1 AB4 5 LYS B 35 VAL B 37 0 SHEET 2 AB4 5 ILE B 129 THR B 131 1 O ARG B 130 N LYS B 35 SHEET 3 AB4 5 CYS B 106 PRO B 119 -1 N GLU B 114 O THR B 131 SHEET 4 AB4 5 ARG B 134 TRP B 135 -1 O ARG B 134 N VAL B 112 SHEET 5 AB4 5 LEU B 220 PRO B 221 -1 O LEU B 220 N TRP B 135 SHEET 1 AB5 3 VAL B 69 LEU B 71 0 SHEET 2 AB5 3 PHE B 151 MET B 153 -1 O PHE B 151 N LEU B 71 SHEET 3 AB5 3 SER B 142 VAL B 144 -1 N ALA B 143 O LEU B 152 SSBOND 1 CYS H 22 CYS H 96 1555 1555 2.03 SSBOND 2 CYS H 155 CYS H 211 1555 1555 2.04 SSBOND 3 CYS L 134 CYS L 194 1555 1555 2.04 SSBOND 4 CYS A 22 CYS A 95 1555 1555 2.04 SSBOND 5 CYS B 118 CYS B 127 1555 1555 2.03 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000