HEADER VIRAL PROTEIN 24-JUL-20 7CM4 TITLE CRYSTAL STRUCTURE OF COVID-19 VIRUS SPIKE RECEPTOR-BINDING DOMAIN TITLE 2 COMPLEXED WITH A NEUTRALIZING ANTIBODY CT-P59 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE GLYCOPROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: S GLYCOPROTEIN,E2,PEPLOMER PROTEIN; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: IGG HEAVY CHAIN; COMPND 8 CHAIN: H; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: IGG LIGHT CHAIN; COMPND 12 CHAIN: L; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 3 2; SOURCE 4 ORGANISM_COMMON: 2019-NCOV; SOURCE 5 ORGANISM_TAXID: 2697049; SOURCE 6 GENE: S, 2; SOURCE 7 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 14 MOL_ID: 3; SOURCE 15 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 16 ORGANISM_TAXID: 9606; SOURCE 17 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 18 EXPRESSION_SYSTEM_TAXID: 10029 KEYWDS SARS-COV-2, SPIKE, RECEPTOR BINDING DOMAIN, RBD, IGG, FAB, VIRAL KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.G.KIM,J.H.JEONG,J.S.BAE,J.LEE REVDAT 3 29-NOV-23 7CM4 1 REMARK REVDAT 2 03-FEB-21 7CM4 1 AUTHOR JRNL REVDAT 1 20-JAN-21 7CM4 0 JRNL AUTH C.KIM,D.K.RYU,J.LEE,Y.I.KIM,J.M.SEO,Y.G.KIM,J.H.JEONG,M.KIM, JRNL AUTH 2 J.I.KIM,P.KIM,J.S.BAE,E.Y.SHIM,M.S.LEE,M.S.KIM,H.NOH, JRNL AUTH 3 G.S.PARK,J.S.PARK,D.SON,Y.AN,J.N.LEE,K.S.KWON,J.Y.LEE,H.LEE, JRNL AUTH 4 J.S.YANG,K.C.KIM,S.S.KIM,H.M.WOO,J.W.KIM,M.S.PARK,K.M.YU, JRNL AUTH 5 S.M.KIM,E.H.KIM,S.J.PARK,S.T.JEONG,C.H.YU,Y.SONG,S.H.GU, JRNL AUTH 6 H.OH,B.S.KOO,J.J.HONG,C.M.RYU,W.B.PARK,M.D.OH,Y.K.CHOI, JRNL AUTH 7 S.Y.LEE JRNL TITL A THERAPEUTIC NEUTRALIZING ANTIBODY TARGETING RECEPTOR JRNL TITL 2 BINDING DOMAIN OF SARS-COV-2 SPIKE PROTEIN. JRNL REF NAT COMMUN V. 12 288 2021 JRNL REFN ESSN 2041-1723 JRNL PMID 33436577 JRNL DOI 10.1038/S41467-020-20602-5 REMARK 2 REMARK 2 RESOLUTION. 2.71 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.71 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.76 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 25735 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.790 REMARK 3 FREE R VALUE TEST SET COUNT : 2006 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 29.7600 - 6.5100 1.00 1803 150 0.2067 0.2361 REMARK 3 2 6.5100 - 5.1800 1.00 1737 147 0.1969 0.2081 REMARK 3 3 5.1800 - 4.5200 1.00 1718 145 0.1650 0.1916 REMARK 3 4 4.5200 - 4.1100 1.00 1680 146 0.1714 0.1697 REMARK 3 5 4.1100 - 3.8200 1.00 1713 142 0.2049 0.2096 REMARK 3 6 3.8200 - 3.5900 1.00 1690 139 0.2129 0.2560 REMARK 3 7 3.5900 - 3.4100 1.00 1689 141 0.2406 0.3040 REMARK 3 8 3.4100 - 3.2700 1.00 1676 143 0.2521 0.2905 REMARK 3 9 3.2700 - 3.1400 1.00 1678 147 0.2470 0.2296 REMARK 3 10 3.1400 - 3.0300 1.00 1676 141 0.2707 0.3075 REMARK 3 11 3.0300 - 2.9400 1.00 1660 140 0.2761 0.3058 REMARK 3 12 2.9400 - 2.8500 1.00 1676 139 0.2986 0.3610 REMARK 3 13 2.8500 - 2.7800 1.00 1683 143 0.3002 0.3452 REMARK 3 14 2.7800 - 2.7100 1.00 1650 143 0.3087 0.3941 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) : 0.390 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.401 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 58.06 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 65.14 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 : 0.003 5041 REMARK 3 ANGLE : 0.588 6876 REMARK 3 CHIRALITY : 0.044 788 REMARK 3 PLANARITY : 0.005 871 REMARK 3 DIHEDRAL : 13.646 1811 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 7CM4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-JUL-20. REMARK 100 THE DEPOSITION ID IS D_1300017816. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JUL-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 5C (4A) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9796 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25744 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.710 REMARK 200 RESOLUTION RANGE LOW (A) : 29.760 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 13.60 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.4400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.71 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.81 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 99.88 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.630 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.18.2_3874 REMARK 200 STARTING MODEL: 6LZG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM TRIS-CL PH 8.0 16% (W/V) REMARK 280 POLYETHYLENE GLYCOL MONOMETHYL ETHER 2,000 10 MM NICKEL(II) REMARK 280 CHLORIDE HEXAHYDRATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 32.77500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 83.80000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 84.52500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 32.77500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 83.80000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 84.52500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 32.77500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 83.80000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 84.52500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 32.77500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 83.80000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 84.52500 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, H, L, 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 ARG A 319 REMARK 465 VAL A 320 REMARK 465 GLN A 321 REMARK 465 PRO A 322 REMARK 465 THR A 323 REMARK 465 GLU A 324 REMARK 465 SER A 325 REMARK 465 ILE A 326 REMARK 465 VAL A 327 REMARK 465 ARG A 328 REMARK 465 PHE A 329 REMARK 465 PRO A 330 REMARK 465 ASN A 331 REMARK 465 LYS A 528 REMARK 465 LYS A 529 REMARK 465 SER A 530 REMARK 465 THR A 531 REMARK 465 ASN A 532 REMARK 465 LEU A 533 REMARK 465 VAL A 534 REMARK 465 LYS A 535 REMARK 465 ASN A 536 REMARK 465 HIS A 537 REMARK 465 HIS A 538 REMARK 465 HIS A 539 REMARK 465 HIS A 540 REMARK 465 HIS A 541 REMARK 465 HIS A 542 REMARK 465 HIS A 543 REMARK 465 HIS A 544 REMARK 465 LYS H 144 REMARK 465 SER H 145 REMARK 465 THR H 146 REMARK 465 SER H 147 REMARK 465 GLY H 148 REMARK 465 GLY H 149 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 CYS H 237 REMARK 465 PRO H 238 REMARK 465 PRO H 239 REMARK 465 CYS H 240 REMARK 465 PRO H 241 REMARK 465 ALA H 242 REMARK 465 PRO H 243 REMARK 465 GLU H 244 REMARK 465 LEU H 245 REMARK 465 LEU H 246 REMARK 465 GLY H 247 REMARK 465 GLY H 248 REMARK 465 PRO H 249 REMARK 465 SER H 250 REMARK 465 VAL H 251 REMARK 465 PHE H 252 REMARK 465 LEU H 253 REMARK 465 PHE H 254 REMARK 465 PRO H 255 REMARK 465 PRO H 256 REMARK 465 LYS H 257 REMARK 465 PRO H 258 REMARK 465 LYS H 259 REMARK 465 ASP H 260 REMARK 465 THR H 261 REMARK 465 LEU H 262 REMARK 465 MET H 263 REMARK 465 ILE H 264 REMARK 465 SER H 265 REMARK 465 ARG H 266 REMARK 465 THR H 267 REMARK 465 PRO H 268 REMARK 465 GLU H 269 REMARK 465 VAL H 270 REMARK 465 THR H 271 REMARK 465 CYS H 272 REMARK 465 VAL H 273 REMARK 465 VAL H 274 REMARK 465 VAL H 275 REMARK 465 ASP H 276 REMARK 465 VAL H 277 REMARK 465 SER H 278 REMARK 465 HIS H 279 REMARK 465 GLU H 280 REMARK 465 ASP H 281 REMARK 465 PRO H 282 REMARK 465 GLU H 283 REMARK 465 VAL H 284 REMARK 465 LYS H 285 REMARK 465 PHE H 286 REMARK 465 ASN H 287 REMARK 465 TRP H 288 REMARK 465 TYR H 289 REMARK 465 VAL H 290 REMARK 465 ASP H 291 REMARK 465 GLY H 292 REMARK 465 VAL H 293 REMARK 465 GLU H 294 REMARK 465 VAL H 295 REMARK 465 HIS H 296 REMARK 465 ASN H 297 REMARK 465 ALA H 298 REMARK 465 LYS H 299 REMARK 465 THR H 300 REMARK 465 LYS H 301 REMARK 465 PRO H 302 REMARK 465 ARG H 303 REMARK 465 GLU H 304 REMARK 465 GLU H 305 REMARK 465 GLN H 306 REMARK 465 TYR H 307 REMARK 465 ASN H 308 REMARK 465 SER H 309 REMARK 465 THR H 310 REMARK 465 TYR H 311 REMARK 465 ARG H 312 REMARK 465 VAL H 313 REMARK 465 VAL H 314 REMARK 465 SER H 315 REMARK 465 VAL H 316 REMARK 465 LEU H 317 REMARK 465 THR H 318 REMARK 465 VAL H 319 REMARK 465 LEU H 320 REMARK 465 HIS H 321 REMARK 465 GLN H 322 REMARK 465 ASP H 323 REMARK 465 TRP H 324 REMARK 465 LEU H 325 REMARK 465 ASN H 326 REMARK 465 GLY H 327 REMARK 465 LYS H 328 REMARK 465 GLU H 329 REMARK 465 TYR H 330 REMARK 465 LYS H 331 REMARK 465 CYS H 332 REMARK 465 LYS H 333 REMARK 465 VAL H 334 REMARK 465 SER H 335 REMARK 465 ASN H 336 REMARK 465 LYS H 337 REMARK 465 ALA H 338 REMARK 465 LEU H 339 REMARK 465 PRO H 340 REMARK 465 ALA H 341 REMARK 465 PRO H 342 REMARK 465 ILE H 343 REMARK 465 GLU H 344 REMARK 465 LYS H 345 REMARK 465 THR H 346 REMARK 465 ILE H 347 REMARK 465 SER H 348 REMARK 465 LYS H 349 REMARK 465 ALA H 350 REMARK 465 LYS H 351 REMARK 465 GLY H 352 REMARK 465 GLN H 353 REMARK 465 PRO H 354 REMARK 465 ARG H 355 REMARK 465 GLU H 356 REMARK 465 PRO H 357 REMARK 465 GLN H 358 REMARK 465 VAL H 359 REMARK 465 TYR H 360 REMARK 465 THR H 361 REMARK 465 LEU H 362 REMARK 465 PRO H 363 REMARK 465 PRO H 364 REMARK 465 SER H 365 REMARK 465 ARG H 366 REMARK 465 ASP H 367 REMARK 465 GLU H 368 REMARK 465 LEU H 369 REMARK 465 THR H 370 REMARK 465 LYS H 371 REMARK 465 ASN H 372 REMARK 465 GLN H 373 REMARK 465 VAL H 374 REMARK 465 SER H 375 REMARK 465 LEU H 376 REMARK 465 THR H 377 REMARK 465 CYS H 378 REMARK 465 LEU H 379 REMARK 465 VAL H 380 REMARK 465 LYS H 381 REMARK 465 GLY H 382 REMARK 465 PHE H 383 REMARK 465 TYR H 384 REMARK 465 PRO H 385 REMARK 465 SER H 386 REMARK 465 ASP H 387 REMARK 465 ILE H 388 REMARK 465 ALA H 389 REMARK 465 VAL H 390 REMARK 465 GLU H 391 REMARK 465 TRP H 392 REMARK 465 GLU H 393 REMARK 465 SER H 394 REMARK 465 ASN H 395 REMARK 465 GLY H 396 REMARK 465 GLN H 397 REMARK 465 PRO H 398 REMARK 465 GLU H 399 REMARK 465 ASN H 400 REMARK 465 ASN H 401 REMARK 465 TYR H 402 REMARK 465 LYS H 403 REMARK 465 THR H 404 REMARK 465 THR H 405 REMARK 465 PRO H 406 REMARK 465 PRO H 407 REMARK 465 VAL H 408 REMARK 465 LEU H 409 REMARK 465 ASP H 410 REMARK 465 SER H 411 REMARK 465 ASP H 412 REMARK 465 GLY H 413 REMARK 465 SER H 414 REMARK 465 PHE H 415 REMARK 465 PHE H 416 REMARK 465 LEU H 417 REMARK 465 TYR H 418 REMARK 465 SER H 419 REMARK 465 LYS H 420 REMARK 465 LEU H 421 REMARK 465 THR H 422 REMARK 465 VAL H 423 REMARK 465 ASP H 424 REMARK 465 LYS H 425 REMARK 465 SER H 426 REMARK 465 ARG H 427 REMARK 465 TRP H 428 REMARK 465 GLN H 429 REMARK 465 GLN H 430 REMARK 465 GLY H 431 REMARK 465 ASN H 432 REMARK 465 VAL H 433 REMARK 465 PHE H 434 REMARK 465 SER H 435 REMARK 465 CYS H 436 REMARK 465 SER H 437 REMARK 465 VAL H 438 REMARK 465 MET H 439 REMARK 465 HIS H 440 REMARK 465 GLU H 441 REMARK 465 ALA H 442 REMARK 465 LEU H 443 REMARK 465 HIS H 444 REMARK 465 ASN H 445 REMARK 465 HIS H 446 REMARK 465 TYR H 447 REMARK 465 THR H 448 REMARK 465 GLN H 449 REMARK 465 LYS H 450 REMARK 465 SER H 451 REMARK 465 LEU H 452 REMARK 465 SER H 453 REMARK 465 LEU H 454 REMARK 465 SER H 455 REMARK 465 PRO H 456 REMARK 465 GLY H 457 REMARK 465 LYS H 458 REMARK 465 CYS L 215 REMARK 465 SER L 216 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 PHE A 400 -179.74 -170.10 REMARK 500 ASN A 422 -56.75 -126.65 REMARK 500 ASP A 428 31.94 -89.53 REMARK 500 ASN A 487 16.39 59.40 REMARK 500 THR A 523 -42.74 -130.54 REMARK 500 THR H 15 -11.53 80.76 REMARK 500 LEU H 50 -70.85 -111.81 REMARK 500 ARG H 107 -100.36 55.58 REMARK 500 ASN L 28 -89.97 -119.60 REMARK 500 ASN L 52 -43.85 72.97 REMARK 500 ASN L 174 -0.59 69.57 REMARK 500 REMARK 500 REMARK: NULL DBREF 7CM4 A 319 536 UNP P0DTC2 SPIKE_SARS2 319 536 DBREF 7CM4 H 1 458 PDB 7CM4 7CM4 1 458 DBREF 7CM4 L 1 216 PDB 7CM4 7CM4 1 216 SEQADV 7CM4 HIS A 537 UNP P0DTC2 EXPRESSION TAG SEQADV 7CM4 HIS A 538 UNP P0DTC2 EXPRESSION TAG SEQADV 7CM4 HIS A 539 UNP P0DTC2 EXPRESSION TAG SEQADV 7CM4 HIS A 540 UNP P0DTC2 EXPRESSION TAG SEQADV 7CM4 HIS A 541 UNP P0DTC2 EXPRESSION TAG SEQADV 7CM4 HIS A 542 UNP P0DTC2 EXPRESSION TAG SEQADV 7CM4 HIS A 543 UNP P0DTC2 EXPRESSION TAG SEQADV 7CM4 HIS A 544 UNP P0DTC2 EXPRESSION TAG SEQRES 1 A 226 ARG VAL GLN PRO THR GLU SER ILE VAL ARG PHE PRO ASN SEQRES 2 A 226 ILE THR ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN ALA SEQRES 3 A 226 THR ARG PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG SEQRES 4 A 226 ILE SER ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SEQRES 5 A 226 SER ALA SER PHE SER THR PHE LYS CYS TYR GLY VAL SER SEQRES 6 A 226 PRO THR LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR SEQRES 7 A 226 ALA ASP SER PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN SEQRES 8 A 226 ILE ALA PRO GLY GLN THR GLY LYS ILE ALA ASP TYR ASN SEQRES 9 A 226 TYR LYS LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA SEQRES 10 A 226 TRP ASN SER ASN ASN LEU ASP SER LYS VAL GLY GLY ASN SEQRES 11 A 226 TYR ASN TYR LEU TYR ARG LEU PHE ARG LYS SER ASN LEU SEQRES 12 A 226 LYS PRO PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN SEQRES 13 A 226 ALA GLY SER THR PRO CYS ASN GLY VAL GLU GLY PHE ASN SEQRES 14 A 226 CYS TYR PHE PRO LEU GLN SER TYR GLY PHE GLN PRO THR SEQRES 15 A 226 ASN GLY VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL LEU SEQRES 16 A 226 SER PHE GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY SEQRES 17 A 226 PRO LYS LYS SER THR ASN LEU VAL LYS ASN HIS HIS HIS SEQRES 18 A 226 HIS HIS HIS HIS HIS SEQRES 1 H 458 GLN ILE THR LEU LYS GLU SER GLY PRO THR LEU VAL LYS SEQRES 2 H 458 PRO THR GLN THR LEU THR LEU THR CYS SER PHE SER GLY SEQRES 3 H 458 PHE SER LEU SER THR SER GLY VAL GLY VAL GLY TRP ILE SEQRES 4 H 458 ARG GLN PRO PRO GLY LYS ALA LEU GLU TRP LEU ALA LEU SEQRES 5 H 458 ILE ASP TRP ASP ASP ASN LYS TYR HIS THR THR SER LEU SEQRES 6 H 458 LYS THR ARG LEU THR ILE SER LYS ASP THR SER LYS ASN SEQRES 7 H 458 GLN VAL VAL LEU THR MET THR ASN MET ASP PRO VAL ASP SEQRES 8 H 458 THR ALA THR TYR TYR CYS ALA ARG ILE PRO GLY PHE LEU SEQRES 9 H 458 ARG TYR ARG ASN ARG TYR TYR TYR TYR GLY MET ASP VAL SEQRES 10 H 458 TRP GLY GLN GLY THR THR VAL THR VAL SER SER ALA SER SEQRES 11 H 458 THR LYS GLY PRO SER VAL PHE PRO LEU ALA PRO SER SER SEQRES 12 H 458 LYS SER THR SER GLY GLY THR ALA ALA LEU GLY CYS LEU SEQRES 13 H 458 VAL LYS ASP TYR PHE PRO GLU PRO VAL THR VAL SER TRP SEQRES 14 H 458 ASN SER GLY ALA LEU THR SER GLY VAL HIS THR PHE PRO SEQRES 15 H 458 ALA VAL LEU GLN SER SER GLY LEU TYR SER LEU SER SER SEQRES 16 H 458 VAL VAL THR VAL PRO SER SER SER LEU GLY THR GLN THR SEQRES 17 H 458 TYR ILE CYS ASN VAL ASN HIS LYS PRO SER ASN THR LYS SEQRES 18 H 458 VAL ASP LYS ARG VAL GLU PRO LYS SER CYS ASP LYS THR SEQRES 19 H 458 HIS THR CYS PRO PRO CYS PRO ALA PRO GLU LEU LEU GLY SEQRES 20 H 458 GLY PRO SER VAL PHE LEU PHE PRO PRO LYS PRO LYS ASP SEQRES 21 H 458 THR LEU MET ILE SER ARG THR PRO GLU VAL THR CYS VAL SEQRES 22 H 458 VAL VAL ASP VAL SER HIS GLU ASP PRO GLU VAL LYS PHE SEQRES 23 H 458 ASN TRP TYR VAL ASP GLY VAL GLU VAL HIS ASN ALA LYS SEQRES 24 H 458 THR LYS PRO ARG GLU GLU GLN TYR ASN SER THR TYR ARG SEQRES 25 H 458 VAL VAL SER VAL LEU THR VAL LEU HIS GLN ASP TRP LEU SEQRES 26 H 458 ASN GLY LYS GLU TYR LYS CYS LYS VAL SER ASN LYS ALA SEQRES 27 H 458 LEU PRO ALA PRO ILE GLU LYS THR ILE SER LYS ALA LYS SEQRES 28 H 458 GLY GLN PRO ARG GLU PRO GLN VAL TYR THR LEU PRO PRO SEQRES 29 H 458 SER ARG ASP GLU LEU THR LYS ASN GLN VAL SER LEU THR SEQRES 30 H 458 CYS LEU VAL LYS GLY PHE TYR PRO SER ASP ILE ALA VAL SEQRES 31 H 458 GLU TRP GLU SER ASN GLY GLN PRO GLU ASN ASN TYR LYS SEQRES 32 H 458 THR THR PRO PRO VAL LEU ASP SER ASP GLY SER PHE PHE SEQRES 33 H 458 LEU TYR SER LYS LEU THR VAL ASP LYS SER ARG TRP GLN SEQRES 34 H 458 GLN GLY ASN VAL PHE SER CYS SER VAL MET HIS GLU ALA SEQRES 35 H 458 LEU HIS ASN HIS TYR THR GLN LYS SER LEU SER LEU SER SEQRES 36 H 458 PRO GLY LYS SEQRES 1 L 216 GLU LEU VAL LEU THR GLN PRO PRO SER VAL SER ALA ALA SEQRES 2 L 216 PRO GLY GLN LYS VAL THR ILE SER CYS SER GLY SER SER SEQRES 3 L 216 SER ASN ILE GLY ASN ASN TYR VAL SER TRP TYR GLN GLN SEQRES 4 L 216 LEU PRO GLY THR ALA PRO LYS LEU LEU ILE TYR ASP ASN SEQRES 5 L 216 ASN LYS ARG PRO SER GLY ILE PRO ASP ARG PHE SER GLY SEQRES 6 L 216 SER LYS SER GLY THR SER ALA THR LEU GLY ILE THR GLY SEQRES 7 L 216 LEU GLN THR GLY ASP GLU ALA ASP TYR TYR CYS GLY THR SEQRES 8 L 216 TRP ASP SER SER LEU SER ALA GLY VAL PHE GLY GLY GLY SEQRES 9 L 216 THR GLU LEU THR VAL LEU GLY GLN PRO LYS ALA ALA PRO SEQRES 10 L 216 SER VAL THR LEU PHE PRO PRO SER SER GLU GLU LEU GLN SEQRES 11 L 216 ALA ASN LYS ALA THR LEU VAL CYS LEU ILE SER ASP PHE SEQRES 12 L 216 TYR PRO GLY ALA VAL THR VAL ALA TRP LYS ALA ASP GLY SEQRES 13 L 216 SER PRO VAL LYS ALA GLY VAL GLU THR THR LYS PRO SER SEQRES 14 L 216 LYS GLN SER ASN ASN LYS TYR ALA ALA SER SER TYR LEU SEQRES 15 L 216 SER LEU THR PRO GLU GLN TRP LYS SER HIS ARG SER TYR SEQRES 16 L 216 SER CYS GLN VAL THR HIS GLU GLY SER THR VAL GLU LYS SEQRES 17 L 216 THR VAL ALA PRO THR GLU CYS SER HET NAG B 1 14 HET NAG B 2 14 HET MAN B 3 11 HET MAN B 4 11 HET FUC B 5 10 HET NI H 501 1 HET EDO L 301 4 HET EDO L 302 4 HET NI L 303 1 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM FUC ALPHA-L-FUCOPYRANOSE HETNAM NI NICKEL (II) ION HETNAM EDO 1,2-ETHANEDIOL 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 HETSYN MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN FUC ALPHA-L-FUCOSE; 6-DEOXY-ALPHA-L-GALACTOPYRANOSE; L- HETSYN 2 FUC FUCOSE; FUCOSE HETSYN EDO ETHYLENE GLYCOL FORMUL 4 NAG 2(C8 H15 N O6) FORMUL 4 MAN 2(C6 H12 O6) FORMUL 4 FUC C6 H12 O5 FORMUL 5 NI 2(NI 2+) FORMUL 6 EDO 2(C2 H6 O2) FORMUL 9 HOH *65(H2 O) HELIX 1 AA1 PHE A 338 ASN A 343 1 6 HELIX 2 AA2 SER A 349 TRP A 353 5 5 HELIX 3 AA3 TYR A 365 SER A 371 1 7 HELIX 4 AA4 SER A 383 LEU A 387 5 5 HELIX 5 AA5 ASP A 405 ILE A 410 5 6 HELIX 6 AA6 GLY A 416 ASN A 422 1 7 HELIX 7 AA7 SER A 438 SER A 443 1 6 HELIX 8 AA8 GLY A 502 TYR A 505 5 4 HELIX 9 AA9 THR H 63 THR H 67 5 5 HELIX 10 AB1 ASP H 88 THR H 92 5 5 HELIX 11 AB2 SER H 171 ALA H 173 5 3 HELIX 12 AB3 PRO H 200 LEU H 204 5 5 HELIX 13 AB4 GLN L 80 GLU L 84 5 5 HELIX 14 AB5 SER L 125 ALA L 131 1 7 HELIX 15 AB6 THR L 185 HIS L 192 1 8 SHEET 1 AA1 5 ASN A 354 ILE A 358 0 SHEET 2 AA1 5 VAL A 395 ARG A 403 -1 O ALA A 397 N LYS A 356 SHEET 3 AA1 5 PRO A 507 PHE A 515 -1 O VAL A 512 N ASP A 398 SHEET 4 AA1 5 GLY A 431 ASN A 437 -1 N ILE A 434 O VAL A 511 SHEET 5 AA1 5 THR A 376 TYR A 380 -1 N LYS A 378 O VAL A 433 SHEET 1 AA2 3 CYS A 361 VAL A 362 0 SHEET 2 AA2 3 VAL A 524 CYS A 525 1 O CYS A 525 N CYS A 361 SHEET 3 AA2 3 CYS A 391 PHE A 392 -1 N PHE A 392 O VAL A 524 SHEET 1 AA3 2 LEU A 452 ARG A 454 0 SHEET 2 AA3 2 LEU A 492 SER A 494 -1 O GLN A 493 N TYR A 453 SHEET 1 AA4 2 TYR A 473 GLN A 474 0 SHEET 2 AA4 2 CYS A 488 TYR A 489 -1 O TYR A 489 N TYR A 473 SHEET 1 AA5 4 THR H 3 SER H 7 0 SHEET 2 AA5 4 LEU H 18 SER H 25 -1 O SER H 23 N LYS H 5 SHEET 3 AA5 4 GLN H 79 MET H 84 -1 O LEU H 82 N LEU H 20 SHEET 4 AA5 4 LEU H 69 ASP H 74 -1 N THR H 70 O THR H 83 SHEET 1 AA6 6 LEU H 11 VAL H 12 0 SHEET 2 AA6 6 THR H 122 VAL H 126 1 O THR H 125 N VAL H 12 SHEET 3 AA6 6 ALA H 93 ILE H 100 -1 N TYR H 95 O THR H 122 SHEET 4 AA6 6 GLY H 35 GLN H 41 -1 N ILE H 39 O TYR H 96 SHEET 5 AA6 6 GLU H 48 ASP H 54 -1 O GLU H 48 N ARG H 40 SHEET 6 AA6 6 LYS H 59 HIS H 61 -1 O TYR H 60 N LEU H 52 SHEET 1 AA7 4 LEU H 11 VAL H 12 0 SHEET 2 AA7 4 THR H 122 VAL H 126 1 O THR H 125 N VAL H 12 SHEET 3 AA7 4 ALA H 93 ILE H 100 -1 N TYR H 95 O THR H 122 SHEET 4 AA7 4 VAL H 117 TRP H 118 -1 O VAL H 117 N ARG H 99 SHEET 1 AA8 2 PHE H 103 TYR H 106 0 SHEET 2 AA8 2 ARG H 109 TYR H 112 -1 O TYR H 111 N LEU H 104 SHEET 1 AA9 4 SER H 135 LEU H 139 0 SHEET 2 AA9 4 ALA H 151 TYR H 160 -1 O GLY H 154 N LEU H 139 SHEET 3 AA9 4 TYR H 191 VAL H 199 -1 O VAL H 197 N LEU H 153 SHEET 4 AA9 4 VAL H 178 THR H 180 -1 N HIS H 179 O VAL H 196 SHEET 1 AB1 4 SER H 135 LEU H 139 0 SHEET 2 AB1 4 ALA H 151 TYR H 160 -1 O GLY H 154 N LEU H 139 SHEET 3 AB1 4 TYR H 191 VAL H 199 -1 O VAL H 197 N LEU H 153 SHEET 4 AB1 4 VAL H 184 LEU H 185 -1 N VAL H 184 O SER H 192 SHEET 1 AB2 3 THR H 166 TRP H 169 0 SHEET 2 AB2 3 TYR H 209 HIS H 215 -1 O ASN H 212 N SER H 168 SHEET 3 AB2 3 THR H 220 VAL H 226 -1 O THR H 220 N HIS H 215 SHEET 1 AB3 5 SER L 9 ALA L 12 0 SHEET 2 AB3 5 THR L 105 VAL L 109 1 O THR L 108 N VAL L 10 SHEET 3 AB3 5 ASP L 86 ASP L 93 -1 N TYR L 87 O THR L 105 SHEET 4 AB3 5 SER L 35 GLN L 39 -1 N SER L 35 O GLY L 90 SHEET 5 AB3 5 LYS L 46 ILE L 49 -1 O LEU L 48 N TRP L 36 SHEET 1 AB4 4 SER L 9 ALA L 12 0 SHEET 2 AB4 4 THR L 105 VAL L 109 1 O THR L 108 N VAL L 10 SHEET 3 AB4 4 ASP L 86 ASP L 93 -1 N TYR L 87 O THR L 105 SHEET 4 AB4 4 ALA L 98 PHE L 101 -1 O ALA L 98 N ASP L 93 SHEET 1 AB5 3 VAL L 18 SER L 23 0 SHEET 2 AB5 3 SER L 71 ILE L 76 -1 O LEU L 74 N ILE L 20 SHEET 3 AB5 3 PHE L 63 SER L 68 -1 N SER L 68 O SER L 71 SHEET 1 AB6 4 SER L 118 PHE L 122 0 SHEET 2 AB6 4 ALA L 134 PHE L 143 -1 O VAL L 137 N PHE L 122 SHEET 3 AB6 4 TYR L 176 LEU L 184 -1 O SER L 180 N CYS L 138 SHEET 4 AB6 4 VAL L 163 THR L 165 -1 N GLU L 164 O TYR L 181 SHEET 1 AB7 4 SER L 118 PHE L 122 0 SHEET 2 AB7 4 ALA L 134 PHE L 143 -1 O VAL L 137 N PHE L 122 SHEET 3 AB7 4 TYR L 176 LEU L 184 -1 O SER L 180 N CYS L 138 SHEET 4 AB7 4 SER L 169 LYS L 170 -1 N SER L 169 O ALA L 177 SHEET 1 AB8 4 SER L 157 VAL L 159 0 SHEET 2 AB8 4 THR L 149 ALA L 154 -1 N TRP L 152 O VAL L 159 SHEET 3 AB8 4 TYR L 195 HIS L 201 -1 O GLN L 198 N ALA L 151 SHEET 4 AB8 4 SER L 204 VAL L 210 -1 O VAL L 206 N VAL L 199 SSBOND 1 CYS A 336 CYS A 361 1555 1555 2.03 SSBOND 2 CYS A 391 CYS A 525 1555 1555 2.03 SSBOND 3 CYS A 480 CYS A 488 1555 1555 2.04 SSBOND 4 CYS H 22 CYS H 97 1555 1555 2.05 SSBOND 5 CYS H 155 CYS H 211 1555 1555 2.04 SSBOND 6 CYS L 22 CYS L 89 1555 1555 2.03 SSBOND 7 CYS L 138 CYS L 197 1555 1555 2.03 LINK ND2 ASN A 343 C1 NAG B 1 1555 1555 1.44 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.46 LINK O6 NAG B 1 C1 FUC B 5 1555 1555 1.44 LINK O4 NAG B 2 C1 MAN B 3 1555 1555 1.45 LINK O6 MAN B 3 C1 MAN B 4 1555 1555 1.41 LINK NE2 HIS L 192 NI NI L 303 1555 1555 2.19 CISPEP 1 PHE H 161 PRO H 162 0 -4.10 CISPEP 2 GLU H 163 PRO H 164 0 -3.56 CISPEP 3 TYR L 144 PRO L 145 0 -2.30 CRYST1 65.550 167.600 169.050 90.00 90.00 90.00 I 2 2 2 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 0.015256 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005967 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005915 0.00000