HEADER ANTIVIRAL PROTEIN/VIRAL PROTEIN 15-AUG-22 7YTN TITLE CRYSTAL STRUCTURE OF SARS-COV-2 ALPHA RBD IN COMPLEX WITH THE D27LEY TITLE 2 NEUTRALIZING ANTIBODY FAB FRAGMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEAVY CHAIN OF FAB; COMPND 3 CHAIN: H; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: LIGHT CHAIN OF FAB; COMPND 7 CHAIN: L; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: SPIKE PROTEIN S1; COMPND 11 CHAIN: C; COMPND 12 FRAGMENT: RBD; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 8 ORGANISM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 11 MOL_ID: 3; SOURCE 12 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 13 2; SOURCE 14 ORGANISM_TAXID: 2697049; SOURCE 15 GENE: S, 2; SOURCE 16 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 10029 KEYWDS ANTIBODY, ANTIGEN, COMPLEX, SARS-COV-2, RBD, ANTIVIRAL PROTEIN, KEYWDS 2 ANTIVIRAL PROTEIN-VIRAL PROTEIN COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.S.JEONG,J.Y.JEON,B.H.OH REVDAT 3 30-OCT-24 7YTN 1 REMARK REVDAT 2 29-NOV-23 7YTN 1 REMARK REVDAT 1 28-JUN-23 7YTN 0 JRNL AUTH B.S.JEONG,J.Y.JEON,C.J.LAI,H.Y.YUN,J.U.JUNG,B.H.OH JRNL TITL STRUCTURAL BASIS FOR THE BROAD AND POTENT CROSS-REACTIVITY JRNL TITL 2 OF AN N501Y-CENTRIC ANTIBODY AGAINST SARBECOVIRUSES. JRNL REF FRONT IMMUNOL V. 13 49867 2022 JRNL REFN ESSN 1664-3224 JRNL PMID 36466915 JRNL DOI 10.3389/FIMMU.2022.1049867 REMARK 2 REMARK 2 RESOLUTION. 3.51 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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) : 3.51 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.99 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.1 REMARK 3 NUMBER OF REFLECTIONS : 14170 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.240 REMARK 3 R VALUE (WORKING SET) : 0.237 REMARK 3 FREE R VALUE : 0.274 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.930 REMARK 3 FREE R VALUE TEST SET COUNT : 1407 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 38.9900 - 7.5400 0.91 1394 154 0.2108 0.2446 REMARK 3 2 7.5400 - 5.9900 0.94 1343 150 0.2332 0.2736 REMARK 3 3 5.9900 - 5.2400 0.96 1345 150 0.2167 0.2554 REMARK 3 4 5.2300 - 4.7600 0.95 1341 143 0.1979 0.2162 REMARK 3 5 4.7600 - 4.4200 0.95 1319 146 0.2018 0.2412 REMARK 3 6 4.4200 - 4.1600 0.94 1293 146 0.2214 0.2448 REMARK 3 7 4.1600 - 3.9500 0.90 1250 136 0.2410 0.3099 REMARK 3 8 3.9500 - 3.7800 0.88 1194 134 0.2806 0.3258 REMARK 3 9 3.7800 - 3.6300 0.87 1176 129 0.2979 0.3295 REMARK 3 10 3.6300 - 3.5100 0.81 1108 119 0.3223 0.3600 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) : 0.362 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.650 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.96 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.03 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 : 0.002 4753 REMARK 3 ANGLE : 0.472 6469 REMARK 3 CHIRALITY : 0.043 707 REMARK 3 PLANARITY : 0.004 838 REMARK 3 DIHEDRAL : 12.808 656 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 7YTN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-AUG-22. REMARK 100 THE DEPOSITION ID IS D_1300031597. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-APR-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 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) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15579 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.510 REMARK 200 RESOLUTION RANGE LOW (A) : 38.990 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.8 REMARK 200 DATA REDUNDANCY : 21.60 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.51 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.63 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 7VYR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200 MM AMMONIUM CITRATE TRIBASIC (PH REMARK 280 7.0), 20% (V/V) POLYETHYLENEGLYCOL 3350, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 55.56000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 111.12000 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 83.34000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 138.90000 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 27.78000 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 55.56000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 111.12000 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 138.90000 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 83.34000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 27.78000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5680 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27030 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -30.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: H, L, 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET H -18 REMARK 465 GLU H -17 REMARK 465 TRP H -16 REMARK 465 SER H -15 REMARK 465 TRP H -14 REMARK 465 VAL H -13 REMARK 465 PHE H -12 REMARK 465 LEU H -11 REMARK 465 PHE H -10 REMARK 465 PHE H -9 REMARK 465 LEU H -8 REMARK 465 SER H -7 REMARK 465 VAL H -6 REMARK 465 THR H -5 REMARK 465 THR H -4 REMARK 465 GLY H -3 REMARK 465 VAL H -2 REMARK 465 LEU H -1 REMARK 465 SER H 0 REMARK 465 GLN H 1 REMARK 465 SER H 134 REMARK 465 SER H 135 REMARK 465 LYS H 136 REMARK 465 SER H 137 REMARK 465 THR H 138 REMARK 465 SER H 139 REMARK 465 GLY H 140 REMARK 465 MET L -23 REMARK 465 GLY L -22 REMARK 465 ILE L -21 REMARK 465 LYS L -20 REMARK 465 MET L -19 REMARK 465 GLU L -18 REMARK 465 THR L -17 REMARK 465 HIS L -16 REMARK 465 SER L -15 REMARK 465 GLN L -14 REMARK 465 VAL L -13 REMARK 465 PHE L -12 REMARK 465 VAL L -11 REMARK 465 TYR L -10 REMARK 465 MET L -9 REMARK 465 LEU L -8 REMARK 465 LEU L -7 REMARK 465 TRP L -6 REMARK 465 LEU L -5 REMARK 465 SER L -4 REMARK 465 GLY L -3 REMARK 465 VAL L -2 REMARK 465 GLU L -1 REMARK 465 GLY L 0 REMARK 465 SER L 1 REMARK 465 TYR L 2 REMARK 465 GLU L 214 REMARK 465 CYS L 215 REMARK 465 MET C 280 REMARK 465 VAL C 281 REMARK 465 LEU C 282 REMARK 465 VAL C 283 REMARK 465 ASN C 284 REMARK 465 GLN C 285 REMARK 465 SER C 286 REMARK 465 HIS C 287 REMARK 465 GLN C 288 REMARK 465 GLY C 289 REMARK 465 PHE C 290 REMARK 465 ASN C 291 REMARK 465 LYS C 292 REMARK 465 GLU C 293 REMARK 465 HIS C 294 REMARK 465 THR C 295 REMARK 465 SER C 296 REMARK 465 LYS C 297 REMARK 465 MET C 298 REMARK 465 VAL C 299 REMARK 465 SER C 300 REMARK 465 ALA C 301 REMARK 465 ILE C 302 REMARK 465 VAL C 303 REMARK 465 LEU C 304 REMARK 465 TYR C 305 REMARK 465 VAL C 306 REMARK 465 LEU C 307 REMARK 465 LEU C 308 REMARK 465 ALA C 309 REMARK 465 ALA C 310 REMARK 465 ALA C 311 REMARK 465 ALA C 312 REMARK 465 HIS C 313 REMARK 465 SER C 314 REMARK 465 ALA C 315 REMARK 465 PHE C 316 REMARK 465 ALA C 317 REMARK 465 ALA C 318 REMARK 465 ARG C 319 REMARK 465 VAL C 320 REMARK 465 GLN C 321 REMARK 465 PRO C 322 REMARK 465 THR C 323 REMARK 465 GLU C 324 REMARK 465 SER C 325 REMARK 465 ILE C 326 REMARK 465 VAL C 327 REMARK 465 ARG C 328 REMARK 465 PHE C 329 REMARK 465 PRO C 330 REMARK 465 ASN C 331 REMARK 465 ILE C 332 REMARK 465 THR C 333 REMARK 465 ASN C 334 REMARK 465 LEU C 335 REMARK 465 LEU C 517 REMARK 465 LEU C 518 REMARK 465 HIS C 519 REMARK 465 ALA C 520 REMARK 465 PRO C 521 REMARK 465 ALA C 522 REMARK 465 THR C 523 REMARK 465 VAL C 524 REMARK 465 CYS C 525 REMARK 465 GLY C 526 REMARK 465 PRO C 527 REMARK 465 LYS C 528 REMARK 465 LYS C 529 REMARK 465 SER C 530 REMARK 465 THR C 531 REMARK 465 ASN C 532 REMARK 465 LEU C 533 REMARK 465 VAL C 534 REMARK 465 LYS C 535 REMARK 465 ASN C 536 REMARK 465 LYS C 537 REMARK 465 CYS C 538 REMARK 465 VAL C 539 REMARK 465 ASN C 540 REMARK 465 PHE C 541 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 119 OG REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 SER C 359 CA 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 OE2 GLU H 46 NZ LYS H 63 2.17 REMARK 500 OG1 THR H 91 O THR H 117 2.18 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 16 -159.27 -90.47 REMARK 500 ASN H 31 48.82 -106.34 REMARK 500 GLN H 43 -166.31 -126.62 REMARK 500 ASP H 108 -81.68 -84.17 REMARK 500 ASP H 151 82.13 56.67 REMARK 500 PHE H 153 133.37 -170.47 REMARK 500 PRO H 154 -155.57 -87.24 REMARK 500 THR H 167 11.10 -142.51 REMARK 500 LEU H 182 -166.53 -108.17 REMARK 500 LEU L 4 78.51 56.69 REMARK 500 ASP L 50 -62.86 73.44 REMARK 500 ARG L 76 72.33 54.97 REMARK 500 GLU L 78 -169.08 -119.58 REMARK 500 ASN L 139 81.29 54.27 REMARK 500 ASN L 159 52.32 -106.82 REMARK 500 LYS L 170 -62.84 -105.82 REMARK 500 LYS L 191 -56.85 -136.45 REMARK 500 ARG L 212 91.47 -66.81 REMARK 500 PRO C 337 20.45 -73.08 REMARK 500 PHE C 377 87.60 -161.57 REMARK 500 ASP C 389 75.11 -113.38 REMARK 500 THR C 415 -166.89 -115.76 REMARK 500 ALA C 419 15.92 58.47 REMARK 500 ASP C 420 -46.18 -141.74 REMARK 500 ASN C 422 -56.51 -125.82 REMARK 500 ASP C 428 31.04 -96.35 REMARK 500 SER C 438 51.75 -143.20 REMARK 500 PHE C 497 70.69 59.47 REMARK 500 REMARK 500 REMARK: NULL DBREF 7YTN H -18 220 PDB 7YTN 7YTN -18 220 DBREF 7YTN L -23 215 PDB 7YTN 7YTN -23 215 DBREF 7YTN C 319 541 UNP P0DTC2 SPIKE_SARS2 319 541 SEQADV 7YTN MET C 280 UNP P0DTC2 INITIATING METHIONINE SEQADV 7YTN VAL C 281 UNP P0DTC2 EXPRESSION TAG SEQADV 7YTN LEU C 282 UNP P0DTC2 EXPRESSION TAG SEQADV 7YTN VAL C 283 UNP P0DTC2 EXPRESSION TAG SEQADV 7YTN ASN C 284 UNP P0DTC2 EXPRESSION TAG SEQADV 7YTN GLN C 285 UNP P0DTC2 EXPRESSION TAG SEQADV 7YTN SER C 286 UNP P0DTC2 EXPRESSION TAG SEQADV 7YTN HIS C 287 UNP P0DTC2 EXPRESSION TAG SEQADV 7YTN GLN C 288 UNP P0DTC2 EXPRESSION TAG SEQADV 7YTN GLY C 289 UNP P0DTC2 EXPRESSION TAG SEQADV 7YTN PHE C 290 UNP P0DTC2 EXPRESSION TAG SEQADV 7YTN ASN C 291 UNP P0DTC2 EXPRESSION TAG SEQADV 7YTN LYS C 292 UNP P0DTC2 EXPRESSION TAG SEQADV 7YTN GLU C 293 UNP P0DTC2 EXPRESSION TAG SEQADV 7YTN HIS C 294 UNP P0DTC2 EXPRESSION TAG SEQADV 7YTN THR C 295 UNP P0DTC2 EXPRESSION TAG SEQADV 7YTN SER C 296 UNP P0DTC2 EXPRESSION TAG SEQADV 7YTN LYS C 297 UNP P0DTC2 EXPRESSION TAG SEQADV 7YTN MET C 298 UNP P0DTC2 EXPRESSION TAG SEQADV 7YTN VAL C 299 UNP P0DTC2 EXPRESSION TAG SEQADV 7YTN SER C 300 UNP P0DTC2 EXPRESSION TAG SEQADV 7YTN ALA C 301 UNP P0DTC2 EXPRESSION TAG SEQADV 7YTN ILE C 302 UNP P0DTC2 EXPRESSION TAG SEQADV 7YTN VAL C 303 UNP P0DTC2 EXPRESSION TAG SEQADV 7YTN LEU C 304 UNP P0DTC2 EXPRESSION TAG SEQADV 7YTN TYR C 305 UNP P0DTC2 EXPRESSION TAG SEQADV 7YTN VAL C 306 UNP P0DTC2 EXPRESSION TAG SEQADV 7YTN LEU C 307 UNP P0DTC2 EXPRESSION TAG SEQADV 7YTN LEU C 308 UNP P0DTC2 EXPRESSION TAG SEQADV 7YTN ALA C 309 UNP P0DTC2 EXPRESSION TAG SEQADV 7YTN ALA C 310 UNP P0DTC2 EXPRESSION TAG SEQADV 7YTN ALA C 311 UNP P0DTC2 EXPRESSION TAG SEQADV 7YTN ALA C 312 UNP P0DTC2 EXPRESSION TAG SEQADV 7YTN HIS C 313 UNP P0DTC2 EXPRESSION TAG SEQADV 7YTN SER C 314 UNP P0DTC2 EXPRESSION TAG SEQADV 7YTN ALA C 315 UNP P0DTC2 EXPRESSION TAG SEQADV 7YTN PHE C 316 UNP P0DTC2 EXPRESSION TAG SEQADV 7YTN ALA C 317 UNP P0DTC2 EXPRESSION TAG SEQADV 7YTN ALA C 318 UNP P0DTC2 EXPRESSION TAG SEQADV 7YTN TYR C 501 UNP P0DTC2 ASN 501 VARIANT SEQRES 1 H 239 MET GLU TRP SER TRP VAL PHE LEU PHE PHE LEU SER VAL SEQRES 2 H 239 THR THR GLY VAL LEU SER GLN VAL GLN LEU GLN GLN SER SEQRES 3 H 239 GLY ALA GLU VAL LYS LYS PRO GLY SER SER VAL LYS VAL SEQRES 4 H 239 SER CYS LYS ALA SER GLY GLY THR PHE GLY ASN TRP SER SEQRES 5 H 239 ILE SER TRP VAL ARG GLN ALA PRO GLY GLN GLY LEU GLU SEQRES 6 H 239 TRP MET GLY GLY ILE ALA PRO GLY ARG GLY GLU ALA THR SEQRES 7 H 239 TYR ALA GLN LYS PHE GLN GLY ARG VAL THR ILE THR THR SEQRES 8 H 239 ASP GLU SER THR SER THR ALA TYR MET GLU LEU SER SER SEQRES 9 H 239 LEU ARG SER GLU ASP THR ALA VAL TYR TYR CYS ALA ARG SEQRES 10 H 239 GLU THR TRP TYR THR SER GLY GLY MET ASP VAL TRP GLY SEQRES 11 H 239 GLN GLY THR THR VAL THR VAL SER SER ALA SER THR LYS SEQRES 12 H 239 GLY PRO SER VAL PHE PRO LEU ALA PRO SER SER LYS SER SEQRES 13 H 239 THR SER GLY GLY THR ALA ALA LEU GLY CYS LEU VAL LYS SEQRES 14 H 239 ASP TYR PHE PRO GLU PRO VAL THR VAL SER TRP ASN SER SEQRES 15 H 239 GLY ALA LEU THR SER GLY VAL HIS THR PHE PRO ALA VAL SEQRES 16 H 239 LEU GLN SER SER GLY LEU TYR SER LEU SER SER VAL VAL SEQRES 17 H 239 THR VAL PRO SER SER SER LEU GLY THR GLN THR TYR ILE SEQRES 18 H 239 CYS ASN VAL ASN HIS LYS PRO SER ASN THR LYS VAL ASP SEQRES 19 H 239 LYS LYS VAL GLU PRO SEQRES 1 L 239 MET GLY ILE LYS MET GLU THR HIS SER GLN VAL PHE VAL SEQRES 2 L 239 TYR MET LEU LEU TRP LEU SER GLY VAL GLU GLY SER TYR SEQRES 3 L 239 GLU LEU THR GLN PRO PRO SER VAL SER VAL ALA PRO GLY SEQRES 4 L 239 LYS THR ALA ARG ILE THR CYS GLY GLY ASN ASN ILE GLY SEQRES 5 L 239 ARG LYS SER VAL HIS TRP TYR GLN GLN LYS PRO GLY GLN SEQRES 6 L 239 ALA PRO VAL LEU VAL VAL TYR ASP ASP SER ASP ARG PRO SEQRES 7 L 239 SER GLY ILE PRO GLU ARG PHE SER GLY SER ASN SER GLY SEQRES 8 L 239 ASN THR ALA THR LEU THR ILE SER ARG VAL GLU ALA GLY SEQRES 9 L 239 ASP GLU ALA ASP TYR TYR CYS GLN VAL TYR ASP LEU TRP SEQRES 10 L 239 SER SER ASP TYR VAL PHE GLY THR GLY THR LYS VAL GLU SEQRES 11 L 239 ILE LYS ARG THR VAL ALA ALA PRO SER VAL PHE ILE PHE SEQRES 12 L 239 PRO PRO SER ASP GLU GLN LEU LYS SER GLY THR ALA SER SEQRES 13 L 239 VAL VAL CYS LEU LEU ASN ASN PHE TYR PRO ARG GLU ALA SEQRES 14 L 239 LYS VAL GLN TRP LYS VAL ASP ASN ALA LEU GLN SER GLY SEQRES 15 L 239 ASN SER GLN GLU SER VAL THR GLU GLN ASP SER LYS ASP SEQRES 16 L 239 SER THR TYR SER LEU SER SER THR LEU THR LEU SER LYS SEQRES 17 L 239 ALA ASP TYR GLU LYS HIS LYS VAL TYR ALA CYS GLU VAL SEQRES 18 L 239 THR HIS GLN GLY LEU SER SER PRO VAL THR LYS SER PHE SEQRES 19 L 239 ASN ARG GLY GLU CYS SEQRES 1 C 262 MET VAL LEU VAL ASN GLN SER HIS GLN GLY PHE ASN LYS SEQRES 2 C 262 GLU HIS THR SER LYS MET VAL SER ALA ILE VAL LEU TYR SEQRES 3 C 262 VAL LEU LEU ALA ALA ALA ALA HIS SER ALA PHE ALA ALA SEQRES 4 C 262 ARG VAL GLN PRO THR GLU SER ILE VAL ARG PHE PRO ASN SEQRES 5 C 262 ILE THR ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN ALA SEQRES 6 C 262 THR ARG PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG SEQRES 7 C 262 ILE SER ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SEQRES 8 C 262 SER ALA SER PHE SER THR PHE LYS CYS TYR GLY VAL SER SEQRES 9 C 262 PRO THR LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR SEQRES 10 C 262 ALA ASP SER PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN SEQRES 11 C 262 ILE ALA PRO GLY GLN THR GLY LYS ILE ALA ASP TYR ASN SEQRES 12 C 262 TYR LYS LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA SEQRES 13 C 262 TRP ASN SER ASN ASN LEU ASP SER LYS VAL GLY GLY ASN SEQRES 14 C 262 TYR ASN TYR LEU TYR ARG LEU PHE ARG LYS SER ASN LEU SEQRES 15 C 262 LYS PRO PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN SEQRES 16 C 262 ALA GLY SER THR PRO CYS ASN GLY VAL GLU GLY PHE ASN SEQRES 17 C 262 CYS TYR PHE PRO LEU GLN SER TYR GLY PHE GLN PRO THR SEQRES 18 C 262 TYR GLY VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL LEU SEQRES 19 C 262 SER PHE GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY SEQRES 20 C 262 PRO LYS LYS SER THR ASN LEU VAL LYS ASN LYS CYS VAL SEQRES 21 C 262 ASN PHE HELIX 1 AA1 ARG H 87 THR H 91 5 5 HELIX 2 AA2 SER H 194 LEU H 196 5 3 HELIX 3 AA3 LYS H 208 ASN H 211 5 4 HELIX 4 AA4 GLN L 125 SER L 128 5 4 HELIX 5 AA5 LYS L 184 GLU L 188 1 5 HELIX 6 AA6 PHE C 338 ASN C 343 1 6 HELIX 7 AA7 SER C 349 TRP C 353 5 5 HELIX 8 AA8 SER C 366 SER C 371 1 6 HELIX 9 AA9 GLU C 406 ILE C 410 5 5 HELIX 10 AB1 GLY C 502 TYR C 505 5 4 SHEET 1 AA1 4 LEU H 4 GLN H 6 0 SHEET 2 AA1 4 SER H 17 ALA H 24 -1 O LYS H 23 N GLN H 5 SHEET 3 AA1 4 THR H 78 SER H 84 -1 O ALA H 79 N CYS H 22 SHEET 4 AA1 4 VAL H 68 ASP H 73 -1 N THR H 71 O TYR H 80 SHEET 1 AA2 5 ALA H 58 TYR H 60 0 SHEET 2 AA2 5 LEU H 45 ILE H 51 -1 N GLY H 50 O THR H 59 SHEET 3 AA2 5 ILE H 34 GLN H 39 -1 N ILE H 34 O ILE H 51 SHEET 4 AA2 5 ALA H 92 GLU H 99 -1 O TYR H 95 N VAL H 37 SHEET 5 AA2 5 MET H 107 TRP H 110 -1 O ASP H 108 N ARG H 98 SHEET 1 AA3 5 ALA H 58 TYR H 60 0 SHEET 2 AA3 5 LEU H 45 ILE H 51 -1 N GLY H 50 O THR H 59 SHEET 3 AA3 5 ILE H 34 GLN H 39 -1 N ILE H 34 O ILE H 51 SHEET 4 AA3 5 ALA H 92 GLU H 99 -1 O TYR H 95 N VAL H 37 SHEET 5 AA3 5 THR H 114 VAL H 116 -1 O THR H 114 N TYR H 94 SHEET 1 AA4 4 SER H 127 LEU H 131 0 SHEET 2 AA4 4 THR H 142 TYR H 152 -1 O LEU H 148 N PHE H 129 SHEET 3 AA4 4 TYR H 183 PRO H 192 -1 O LEU H 185 N VAL H 149 SHEET 4 AA4 4 VAL H 170 THR H 172 -1 N HIS H 171 O VAL H 188 SHEET 1 AA5 4 SER H 127 LEU H 131 0 SHEET 2 AA5 4 THR H 142 TYR H 152 -1 O LEU H 148 N PHE H 129 SHEET 3 AA5 4 TYR H 183 PRO H 192 -1 O LEU H 185 N VAL H 149 SHEET 4 AA5 4 VAL H 176 LEU H 177 -1 N VAL H 176 O SER H 184 SHEET 1 AA6 3 THR H 158 TRP H 161 0 SHEET 2 AA6 3 TYR H 201 HIS H 207 -1 O ASN H 204 N SER H 160 SHEET 3 AA6 3 THR H 212 VAL H 218 -1 O VAL H 218 N TYR H 201 SHEET 1 AA7 5 SER L 9 VAL L 12 0 SHEET 2 AA7 5 THR L 103 ILE L 107 1 O LYS L 104 N VAL L 10 SHEET 3 AA7 5 ASP L 84 TYR L 90 -1 N TYR L 85 O THR L 103 SHEET 4 AA7 5 HIS L 33 GLN L 37 -1 N GLN L 37 O ASP L 84 SHEET 5 AA7 5 VAL L 44 VAL L 47 -1 O VAL L 47 N TRP L 34 SHEET 1 AA8 4 SER L 9 VAL L 12 0 SHEET 2 AA8 4 THR L 103 ILE L 107 1 O LYS L 104 N VAL L 10 SHEET 3 AA8 4 ASP L 84 TYR L 90 -1 N TYR L 85 O THR L 103 SHEET 4 AA8 4 TYR L 97 VAL L 98 -1 O VAL L 98 N VAL L 89 SHEET 1 AA9 3 ALA L 18 GLY L 23 0 SHEET 2 AA9 3 THR L 69 ILE L 74 -1 O ALA L 70 N CYS L 22 SHEET 3 AA9 3 PHE L 61 ASN L 65 -1 N SER L 62 O THR L 73 SHEET 1 AB1 4 SER L 115 PHE L 119 0 SHEET 2 AB1 4 THR L 130 PHE L 140 -1 O VAL L 134 N PHE L 119 SHEET 3 AB1 4 TYR L 174 SER L 183 -1 O LEU L 176 N LEU L 137 SHEET 4 AB1 4 SER L 160 VAL L 164 -1 N GLN L 161 O THR L 179 SHEET 1 AB2 4 ALA L 154 LEU L 155 0 SHEET 2 AB2 4 LYS L 146 VAL L 151 -1 N VAL L 151 O ALA L 154 SHEET 3 AB2 4 VAL L 192 THR L 198 -1 O ALA L 194 N LYS L 150 SHEET 4 AB2 4 VAL L 206 THR L 207 -1 O VAL L 206 N VAL L 197 SHEET 1 AB3 4 ALA L 154 LEU L 155 0 SHEET 2 AB3 4 LYS L 146 VAL L 151 -1 N VAL L 151 O ALA L 154 SHEET 3 AB3 4 VAL L 192 THR L 198 -1 O ALA L 194 N LYS L 150 SHEET 4 AB3 4 PHE L 210 ASN L 211 -1 O PHE L 210 N TYR L 193 SHEET 1 AB4 5 ASN C 354 ILE C 358 0 SHEET 2 AB4 5 VAL C 395 ARG C 403 -1 O VAL C 395 N ILE C 358 SHEET 3 AB4 5 PRO C 507 PHE C 515 -1 O TYR C 508 N ILE C 402 SHEET 4 AB4 5 GLY C 431 ASN C 437 -1 N ILE C 434 O VAL C 511 SHEET 5 AB4 5 THR C 376 TYR C 380 -1 N TYR C 380 O GLY C 431 SHEET 1 AB5 2 LEU C 452 ARG C 454 0 SHEET 2 AB5 2 LEU C 492 SER C 494 -1 O GLN C 493 N TYR C 453 SHEET 1 AB6 2 TYR C 473 GLN C 474 0 SHEET 2 AB6 2 CYS C 488 TYR C 489 -1 O TYR C 489 N TYR C 473 SSBOND 1 CYS H 22 CYS H 96 1555 1555 2.03 SSBOND 2 CYS H 147 CYS H 203 1555 1555 2.04 SSBOND 3 CYS L 22 CYS L 87 1555 1555 2.03 SSBOND 4 CYS L 135 CYS L 195 1555 1555 2.03 SSBOND 5 CYS C 379 CYS C 432 1555 1555 2.03 SSBOND 6 CYS C 480 CYS C 488 1555 1555 2.03 CISPEP 1 PHE H 153 PRO H 154 0 -0.02 CISPEP 2 TYR L 141 PRO L 142 0 1.94 CRYST1 155.957 155.957 166.680 90.00 90.00 120.00 P 61 2 2 12 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 0.006412 0.003702 0.000000 0.00000 SCALE2 0.000000 0.007404 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006000 0.00000