HEADER VIRAL PROTEIN/IMMUNE SYSTEM 04-NOV-20 7KN6 TITLE CRYSTAL STRUCTURE OF SARS-COV-2 RECEPTOR BINDING DOMAIN COMPLEXED WITH TITLE 2 NANOBODY VHH V AND ANTIBODY FAB CC12.3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE PROTEIN S1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: S GLYCOPROTEIN,E2,PEPLOMER PROTEIN; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: VHH V; COMPND 8 CHAIN: C; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: CC12.3 FAB HEAVY CHAIN; COMPND 12 CHAIN: H; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 4; COMPND 15 MOLECULE: CC12.3 FAB LIGHT CHAIN; COMPND 16 CHAIN: L; COMPND 17 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: TRICHOPLUSIA NI; SOURCE 8 EXPRESSION_SYSTEM_COMMON: CABBAGE LOOPER; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 7111; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: VICUGNA PACOS; SOURCE 13 ORGANISM_TAXID: 30538; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 16 EXPRESSION_SYSTEM_STRAIN: WK6; SOURCE 17 MOL_ID: 3; SOURCE 18 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 19 ORGANISM_COMMON: HUMAN; SOURCE 20 ORGANISM_TAXID: 9606; SOURCE 21 EXPRESSION_SYSTEM: MUS MUSCULUS; SOURCE 22 EXPRESSION_SYSTEM_COMMON: MOUSE; SOURCE 23 EXPRESSION_SYSTEM_TAXID: 10090; SOURCE 24 MOL_ID: 4; SOURCE 25 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 26 ORGANISM_COMMON: HUMAN; SOURCE 27 ORGANISM_TAXID: 9606; SOURCE 28 EXPRESSION_SYSTEM: MUS MUSCULUS; SOURCE 29 EXPRESSION_SYSTEM_COMMON: MOUSE; SOURCE 30 EXPRESSION_SYSTEM_TAXID: 10090 KEYWDS SARS-COV-2, NANOBODY, SPIKE, CORONAVIRUS, COVID-19, IMMUNE SYSTEM, KEYWDS 2 NANOBODY-ANTIGEN COMPLEX, SINGLE-DOMAIN ANTIBODY, ANTIBODY, VIRAL KEYWDS 3 PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.LIU,M.YUAN,X.ZHU,N.C.WU,I.A.WILSON REVDAT 5 06-NOV-24 7KN6 1 REMARK REVDAT 4 18-OCT-23 7KN6 1 REMARK REVDAT 3 24-FEB-21 7KN6 1 JRNL REVDAT 2 27-JAN-21 7KN6 1 JRNL REVDAT 1 20-JAN-21 7KN6 0 JRNL AUTH P.A.KOENIG,H.DAS,H.LIU,B.M.KUMMERER,F.N.GOHR,L.M.JENSTER, JRNL AUTH 2 L.D.J.SCHIFFELERS,Y.M.TESFAMARIAM,M.UCHIMA,J.D.WUERTH, JRNL AUTH 3 K.GATTERDAM,N.RUETALO,M.H.CHRISTENSEN,C.I.FANDREY,S.NORMANN, JRNL AUTH 4 J.M.P.TODTMANN,S.PRITZL,L.HANKE,J.BOOS,M.YUAN,X.ZHU, JRNL AUTH 5 J.L.SCHMID-BURGK,H.KATO,M.SCHINDLER,I.A.WILSON,M.GEYER, JRNL AUTH 6 K.U.LUDWIG,B.M.HALLBERG,N.C.WU,F.I.SCHMIDT JRNL TITL STRUCTURE-GUIDED MULTIVALENT NANOBODIES BLOCK SARS-COV-2 JRNL TITL 2 INFECTION AND SUPPRESS MUTATIONAL ESCAPE. JRNL REF SCIENCE V. 371 2021 JRNL REFN ESSN 1095-9203 JRNL PMID 33436526 JRNL DOI 10.1126/SCIENCE.ABE6230 REMARK 2 REMARK 2 RESOLUTION. 2.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 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) : 2.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.27 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 84.0 REMARK 3 NUMBER OF REFLECTIONS : 25466 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1276 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 48.2700 - 5.3000 0.97 3181 176 0.1666 0.1838 REMARK 3 2 5.3000 - 4.2100 0.96 3107 174 0.1346 0.1783 REMARK 3 3 4.2100 - 3.6700 0.98 3131 155 0.1705 0.2548 REMARK 3 4 3.6700 - 3.3400 0.99 3158 150 0.2046 0.2382 REMARK 3 5 3.3400 - 3.1000 0.96 3078 158 0.2446 0.2995 REMARK 3 6 3.1000 - 2.9200 0.87 2785 141 0.2663 0.3185 REMARK 3 7 2.9200 - 2.7700 0.77 2459 137 0.2960 0.3503 REMARK 3 8 2.7700 - 2.6500 0.60 1903 105 0.2964 0.3650 REMARK 3 9 2.6500 - 2.5500 0.44 1388 80 0.3206 0.3737 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) : 0.371 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.904 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 49.12 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.57 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 : 0.004 5674 REMARK 3 ANGLE : 0.803 7723 REMARK 3 CHIRALITY : 0.048 849 REMARK 3 PLANARITY : 0.004 1000 REMARK 3 DIHEDRAL : 9.968 3295 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -43.7126 -15.9730 -1.7568 REMARK 3 T TENSOR REMARK 3 T11: 0.2222 T22: 0.2290 REMARK 3 T33: 0.2431 T12: 0.0081 REMARK 3 T13: 0.0318 T23: 0.0022 REMARK 3 L TENSOR REMARK 3 L11: 0.2877 L22: 0.4029 REMARK 3 L33: 0.4301 L12: -0.1139 REMARK 3 L13: 0.2567 L23: -0.1037 REMARK 3 S TENSOR REMARK 3 S11: -0.0081 S12: -0.0370 S13: -0.0303 REMARK 3 S21: -0.0170 S22: 0.0406 S23: 0.0704 REMARK 3 S31: -0.0288 S32: -0.0134 S33: 0.0000 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 7KN6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-NOV-20. REMARK 100 THE DEPOSITION ID IS D_1000252736. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUL-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL12-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97946 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25515 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.550 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.16400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.76500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.3 REMARK 200 STARTING MODEL: 6XC7, 7JMW, 6WAQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, 0.2 M NA2HPO4, PH 9.1, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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+1/2,Y+1/2,Z 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 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 93.67850 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 45.07300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 93.67850 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 45.07300 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, H, L 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 ILE A 332 REMARK 465 THR A 333 REMARK 465 LEU A 517 REMARK 465 LEU A 518 REMARK 465 HIS A 519 REMARK 465 ALA A 520 REMARK 465 PRO A 521 REMARK 465 GLY A 526 REMARK 465 PRO A 527 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 LYS A 537 REMARK 465 CYS A 538 REMARK 465 VAL A 539 REMARK 465 ASN A 540 REMARK 465 PHE A 541 REMARK 465 SER A 542 REMARK 465 GLY A 543 REMARK 465 HIS A 544 REMARK 465 HIS A 545 REMARK 465 HIS A 546 REMARK 465 HIS A 547 REMARK 465 HIS A 548 REMARK 465 HIS A 549 REMARK 465 GLY C 114 REMARK 465 GLY C 115 REMARK 465 LEU C 116 REMARK 465 PRO C 117 REMARK 465 GLU C 118 REMARK 465 THR C 119 REMARK 465 GLY C 120 REMARK 465 GLY C 121 REMARK 465 HIS C 122 REMARK 465 HIS C 123 REMARK 465 HIS C 124 REMARK 465 HIS C 125 REMARK 465 HIS C 126 REMARK 465 HIS C 127 REMARK 465 SER H 128 REMARK 465 LYS H 129 REMARK 465 SER H 130 REMARK 465 THR H 131 REMARK 465 SER H 132 REMARK 465 LYS H 214 REMARK 465 SER H 215 REMARK 465 CYS H 216 REMARK 465 CYS L 214 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 334 CG OD1 ND2 REMARK 470 LEU A 335 CG CD1 CD2 REMARK 470 ARG A 346 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 357 CG CD NE CZ NH1 NH2 REMARK 470 VAL A 362 CG1 CG2 REMARK 470 VAL A 382 CG1 CG2 REMARK 470 LYS A 386 CD CE NZ REMARK 470 ASP A 389 CG OD1 OD2 REMARK 470 LEU A 390 CG CD1 CD2 REMARK 470 THR A 393 OG1 CG2 REMARK 470 LYS A 458 CD CE NZ REMARK 470 LYS A 462 CE NZ REMARK 470 GLU A 471 CD OE1 OE2 REMARK 470 GLU A 516 CG CD OE1 OE2 REMARK 470 THR A 523 OG1 CG2 REMARK 470 VAL A 524 CG1 CG2 REMARK 470 GLN C 1 CG CD OE1 NE2 REMARK 470 LYS C 43 CD CE NZ REMARK 470 ASP C 54 CG OD1 OD2 REMARK 470 LYS C 64 CG CD CE NZ REMARK 470 ASP C 72 CG OD1 OD2 REMARK 470 LYS C 83 CD CE NZ REMARK 470 GLU C 85 CG CD OE1 OE2 REMARK 470 GLN C 105 CG CD OE1 NE2 REMARK 470 GLN H 1 CG CD OE1 NE2 REMARK 470 LYS H 201 CG CD CE NZ REMARK 470 ARG L 24 CD NE CZ NH1 NH2 REMARK 470 LYS L 126 CD CE NZ REMARK 470 LYS L 169 CG CD CE NZ REMARK 470 LYS L 190 CE NZ 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 391 CA - CB - SG ANGL. DEV. = 13.9 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 ALA A 352 55.12 -113.78 REMARK 500 PHE A 377 81.25 -157.03 REMARK 500 ILE A 402 -165.80 -118.89 REMARK 500 ASN A 422 -58.84 -131.76 REMARK 500 PHE A 497 79.00 51.57 REMARK 500 THR A 523 -67.84 -95.69 REMARK 500 SER C 25 149.12 -171.51 REMARK 500 ALA C 88 -179.63 -174.72 REMARK 500 PHE H 99 -71.33 -106.20 REMARK 500 ASP H 144 71.81 61.09 REMARK 500 SER L 30 -116.83 54.52 REMARK 500 ALA L 51 -45.76 65.72 REMARK 500 ASN L 138 77.59 45.09 REMARK 500 ASN L 158 35.82 -150.21 REMARK 500 REMARK 500 REMARK: NULL DBREF 7KN6 A 319 541 UNP P0DTC2 SPIKE_SARS2 319 541 DBREF 7KN6 C 1 127 PDB 7KN6 7KN6 1 127 DBREF 7KN6 H 1 216 PDB 7KN6 7KN6 1 216 DBREF 7KN6 L 1 214 PDB 7KN6 7KN6 1 214 SEQADV 7KN6 SER A 542 UNP P0DTC2 EXPRESSION TAG SEQADV 7KN6 GLY A 543 UNP P0DTC2 EXPRESSION TAG SEQADV 7KN6 HIS A 544 UNP P0DTC2 EXPRESSION TAG SEQADV 7KN6 HIS A 545 UNP P0DTC2 EXPRESSION TAG SEQADV 7KN6 HIS A 546 UNP P0DTC2 EXPRESSION TAG SEQADV 7KN6 HIS A 547 UNP P0DTC2 EXPRESSION TAG SEQADV 7KN6 HIS A 548 UNP P0DTC2 EXPRESSION TAG SEQADV 7KN6 HIS A 549 UNP P0DTC2 EXPRESSION TAG SEQRES 1 A 231 ARG VAL GLN PRO THR GLU SER ILE VAL ARG PHE PRO ASN SEQRES 2 A 231 ILE THR ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN ALA SEQRES 3 A 231 THR ARG PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG SEQRES 4 A 231 ILE SER ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SEQRES 5 A 231 SER ALA SER PHE SER THR PHE LYS CYS TYR GLY VAL SER SEQRES 6 A 231 PRO THR LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR SEQRES 7 A 231 ALA ASP SER PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN SEQRES 8 A 231 ILE ALA PRO GLY GLN THR GLY LYS ILE ALA ASP TYR ASN SEQRES 9 A 231 TYR LYS LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA SEQRES 10 A 231 TRP ASN SER ASN ASN LEU ASP SER LYS VAL GLY GLY ASN SEQRES 11 A 231 TYR ASN TYR LEU TYR ARG LEU PHE ARG LYS SER ASN LEU SEQRES 12 A 231 LYS PRO PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN SEQRES 13 A 231 ALA GLY SER THR PRO CYS ASN GLY VAL GLU GLY PHE ASN SEQRES 14 A 231 CYS TYR PHE PRO LEU GLN SER TYR GLY PHE GLN PRO THR SEQRES 15 A 231 ASN GLY VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL LEU SEQRES 16 A 231 SER PHE GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY SEQRES 17 A 231 PRO LYS LYS SER THR ASN LEU VAL LYS ASN LYS CYS VAL SEQRES 18 A 231 ASN PHE SER GLY HIS HIS HIS HIS HIS HIS SEQRES 1 C 135 GLN VAL GLN LEU VAL GLU THR GLY GLY GLY LEU VAL GLN SEQRES 2 C 135 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 C 135 PHE THR PHE SER SER TYR ALA MET GLY TRP ALA ARG GLN SEQRES 4 C 135 VAL PRO GLY LYS GLY LEU GLU TRP VAL SER TYR ILE TYR SEQRES 5 C 135 SER ASP GLY SER THR GLU TYR GLN ASP SER VAL LYS GLY SEQRES 6 C 135 ARG PHE THR ILE SER ARG ASP ASN ALA LYS SER THR VAL SEQRES 7 C 135 TYR LEU GLN MET ASN SER LEU LYS PRO GLU ASP THR ALA SEQRES 8 C 135 VAL TYR TYR CYS ALA THR GLU GLY SER LEU GLY GLY TRP SEQRES 9 C 135 GLY ARG ASP PHE GLY SER TRP GLY GLN GLY THR GLN VAL SEQRES 10 C 135 THR VAL SER SER GLY GLY LEU PRO GLU THR GLY GLY HIS SEQRES 11 C 135 HIS HIS HIS HIS HIS SEQRES 1 H 220 GLN VAL GLN LEU VAL GLU SER GLY GLY GLY LEU ILE GLN SEQRES 2 H 220 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 H 220 PHE THR VAL SER SER ASN TYR MET SER TRP VAL ARG GLN SEQRES 4 H 220 ALA PRO GLY LYS GLY LEU GLU TRP VAL SER VAL ILE TYR SEQRES 5 H 220 SER GLY GLY SER THR PHE TYR ALA ASP SER VAL LYS GLY SEQRES 6 H 220 ARG PHE THR ILE SER ARG ASP ASN SER LYS SER THR LEU SEQRES 7 H 220 TYR LEU GLN MET ASN SER LEU ARG VAL GLU ASP THR ALA SEQRES 8 H 220 VAL TYR TYR CYS ALA ARG ASP PHE GLY ASP PHE TYR PHE SEQRES 9 H 220 ASP TYR TRP GLY GLN GLY THR LEU VAL THR VAL SER SER SEQRES 10 H 220 ALA SER THR LYS GLY PRO SER VAL PHE PRO LEU ALA PRO SEQRES 11 H 220 SER SER LYS SER THR SER GLY GLY THR ALA ALA LEU GLY SEQRES 12 H 220 CYS LEU VAL LYS ASP TYR PHE PRO GLU PRO VAL THR VAL SEQRES 13 H 220 SER TRP ASN SER GLY ALA LEU THR SER GLY VAL HIS THR SEQRES 14 H 220 PHE PRO ALA VAL LEU GLN SER SER GLY LEU TYR SER LEU SEQRES 15 H 220 SER SER VAL VAL THR VAL PRO SER SER SER LEU GLY THR SEQRES 16 H 220 GLN THR TYR ILE CYS ASN VAL ASN HIS LYS PRO SER ASN SEQRES 17 H 220 THR LYS VAL ASP LYS LYS VAL GLU PRO LYS SER CYS SEQRES 1 L 214 GLU ILE VAL LEU THR GLN SER PRO GLY THR LEU SER LEU SEQRES 2 L 214 SER PRO GLY GLU ARG ALA THR LEU SER CYS ARG ALA SER SEQRES 3 L 214 GLN SER VAL SER SER TYR LEU ALA TRP TYR GLN GLN LYS SEQRES 4 L 214 PRO GLY GLN ALA PRO ARG LEU LEU ILE TYR GLY ALA SER SEQRES 5 L 214 SER ARG ALA THR GLY ILE PRO ASP ARG PHE SER GLY SER SEQRES 6 L 214 GLY SER GLY THR ASP PHE THR LEU THR ILE SER ARG LEU SEQRES 7 L 214 GLU PRO GLU ASP PHE ALA VAL TYR TYR CYS GLN GLN TYR SEQRES 8 L 214 GLY SER SER PRO ARG THR PHE GLY GLN GLY THR LYS LEU 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 GLU 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 HET NAG A1001 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 5 NAG C8 H15 N O6 HELIX 1 AA1 PRO A 337 ASN A 343 1 7 HELIX 2 AA2 SER A 349 TRP A 353 5 5 HELIX 3 AA3 ASP A 364 ASN A 370 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 ASP C 61 LYS C 64 5 4 HELIX 10 AB1 LYS C 83 THR C 87 5 5 HELIX 11 AB2 THR H 28 ASN H 32 5 5 HELIX 12 AB3 ARG H 83 THR H 87 5 5 HELIX 13 AB4 SER H 156 ALA H 158 5 3 HELIX 14 AB5 SER H 187 LEU H 189 5 3 HELIX 15 AB6 LYS H 201 ASN H 204 5 4 HELIX 16 AB7 GLU L 79 PHE L 83 5 5 HELIX 17 AB8 SER L 121 SER L 127 1 7 HELIX 18 AB9 LYS L 183 HIS L 189 1 7 SHEET 1 AA1 6 ASN A 354 ILE A 358 0 SHEET 2 AA1 6 VAL A 395 ARG A 403 -1 O ALA A 397 N LYS A 356 SHEET 3 AA1 6 PRO A 507 PHE A 515 -1 O VAL A 510 N PHE A 400 SHEET 4 AA1 6 GLY A 431 ASN A 437 -1 N ILE A 434 O VAL A 511 SHEET 5 AA1 6 THR A 376 TYR A 380 -1 N TYR A 380 O GLY A 431 SHEET 6 AA1 6 TRP C 100A ARG C 100C-1 O TRP C 100A N CYS A 379 SHEET 1 AA2 2 CYS A 361 VAL A 362 0 SHEET 2 AA2 2 VAL A 524 CYS A 525 1 O CYS A 525 N CYS A 361 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 GLN C 3 THR C 7 0 SHEET 2 AA5 4 LEU C 18 SER C 25 -1 O ALA C 23 N VAL C 5 SHEET 3 AA5 4 THR C 77 MET C 82 -1 O MET C 82 N LEU C 18 SHEET 4 AA5 4 PHE C 67 ASP C 72 -1 N SER C 70 O TYR C 79 SHEET 1 AA6 6 LEU C 11 VAL C 12 0 SHEET 2 AA6 6 THR C 107 VAL C 111 1 O THR C 110 N VAL C 12 SHEET 3 AA6 6 ALA C 88 THR C 94 -1 N TYR C 90 O THR C 107 SHEET 4 AA6 6 MET C 34 GLN C 39 -1 N GLN C 39 O VAL C 89 SHEET 5 AA6 6 GLU C 46 ILE C 51 -1 O GLU C 46 N ARG C 38 SHEET 6 AA6 6 THR C 57 TYR C 59 -1 O GLU C 58 N TYR C 50 SHEET 1 AA7 4 LEU C 11 VAL C 12 0 SHEET 2 AA7 4 THR C 107 VAL C 111 1 O THR C 110 N VAL C 12 SHEET 3 AA7 4 ALA C 88 THR C 94 -1 N TYR C 90 O THR C 107 SHEET 4 AA7 4 SER C 102 TRP C 103 -1 O SER C 102 N THR C 94 SHEET 1 AA8 4 GLN H 3 SER H 7 0 SHEET 2 AA8 4 LEU H 18 SER H 25 -1 O SER H 25 N GLN H 3 SHEET 3 AA8 4 THR H 77 MET H 82 -1 O LEU H 80 N LEU H 20 SHEET 4 AA8 4 PHE H 67 ASP H 72 -1 N THR H 68 O GLN H 81 SHEET 1 AA9 6 LEU H 11 ILE H 12 0 SHEET 2 AA9 6 THR H 107 VAL H 111 1 O THR H 110 N ILE H 12 SHEET 3 AA9 6 ALA H 88 ASP H 95 -1 N TYR H 90 O THR H 107 SHEET 4 AA9 6 TYR H 33 GLN H 39 -1 N VAL H 37 O TYR H 91 SHEET 5 AA9 6 LEU H 45 ILE H 51 -1 O VAL H 48 N TRP H 36 SHEET 6 AA9 6 THR H 57 TYR H 59 -1 O PHE H 58 N VAL H 50 SHEET 1 AB1 4 LEU H 11 ILE H 12 0 SHEET 2 AB1 4 THR H 107 VAL H 111 1 O THR H 110 N ILE H 12 SHEET 3 AB1 4 ALA H 88 ASP H 95 -1 N TYR H 90 O THR H 107 SHEET 4 AB1 4 PHE H 100A TRP H 103 -1 O TYR H 102 N ARG H 94 SHEET 1 AB2 4 SER H 120 LEU H 124 0 SHEET 2 AB2 4 THR H 135 TYR H 145 -1 O LYS H 143 N SER H 120 SHEET 3 AB2 4 TYR H 176 PRO H 185 -1 O TYR H 176 N TYR H 145 SHEET 4 AB2 4 VAL H 163 THR H 165 -1 N HIS H 164 O VAL H 181 SHEET 1 AB3 4 SER H 120 LEU H 124 0 SHEET 2 AB3 4 THR H 135 TYR H 145 -1 O LYS H 143 N SER H 120 SHEET 3 AB3 4 TYR H 176 PRO H 185 -1 O TYR H 176 N TYR H 145 SHEET 4 AB3 4 VAL H 169 LEU H 170 -1 N VAL H 169 O SER H 177 SHEET 1 AB4 3 THR H 151 TRP H 154 0 SHEET 2 AB4 3 ILE H 195 HIS H 200 -1 O ASN H 197 N SER H 153 SHEET 3 AB4 3 THR H 205 LYS H 210 -1 O VAL H 207 N VAL H 198 SHEET 1 AB5 4 LEU L 4 SER L 7 0 SHEET 2 AB5 4 ALA L 19 ALA L 25 -1 O ARG L 24 N THR L 5 SHEET 3 AB5 4 ASP L 70 ILE L 75 -1 O LEU L 73 N LEU L 21 SHEET 4 AB5 4 PHE L 62 SER L 67 -1 N SER L 65 O THR L 72 SHEET 1 AB6 6 THR L 10 LEU L 13 0 SHEET 2 AB6 6 THR L 102 ILE L 106 1 O GLU L 105 N LEU L 11 SHEET 3 AB6 6 VAL L 85 GLN L 90 -1 N TYR L 86 O THR L 102 SHEET 4 AB6 6 LEU L 33 GLN L 38 -1 N GLN L 38 O VAL L 85 SHEET 5 AB6 6 ARG L 45 TYR L 49 -1 O LEU L 47 N TRP L 35 SHEET 6 AB6 6 SER L 53 ARG L 54 -1 O SER L 53 N TYR L 49 SHEET 1 AB7 4 THR L 10 LEU L 13 0 SHEET 2 AB7 4 THR L 102 ILE L 106 1 O GLU L 105 N LEU L 11 SHEET 3 AB7 4 VAL L 85 GLN L 90 -1 N TYR L 86 O THR L 102 SHEET 4 AB7 4 THR L 97 PHE L 98 -1 O THR L 97 N GLN L 90 SHEET 1 AB8 4 SER L 114 PHE L 118 0 SHEET 2 AB8 4 THR L 129 PHE L 139 -1 O VAL L 133 N PHE L 118 SHEET 3 AB8 4 TYR L 173 SER L 182 -1 O TYR L 173 N PHE L 139 SHEET 4 AB8 4 SER L 159 VAL L 163 -1 N GLN L 160 O THR L 178 SHEET 1 AB9 4 ALA L 153 GLN L 155 0 SHEET 2 AB9 4 LYS L 145 VAL L 150 -1 N VAL L 150 O ALA L 153 SHEET 3 AB9 4 VAL L 191 THR L 197 -1 O ALA L 193 N LYS L 149 SHEET 4 AB9 4 VAL L 205 ASN L 210 -1 O VAL L 205 N VAL L 196 SSBOND 1 CYS A 336 CYS A 361 1555 1555 2.09 SSBOND 2 CYS A 379 CYS A 432 1555 1555 2.05 SSBOND 3 CYS A 391 CYS A 525 1555 1555 2.28 SSBOND 4 CYS A 480 CYS A 488 1555 1555 2.03 SSBOND 5 CYS C 22 CYS C 92 1555 1555 2.04 SSBOND 6 CYS H 22 CYS H 92 1555 1555 2.03 SSBOND 7 CYS H 140 CYS H 196 1555 1555 2.03 SSBOND 8 CYS L 23 CYS L 88 1555 1555 2.04 SSBOND 9 CYS L 134 CYS L 194 1555 1555 2.03 LINK ND2 ASN A 343 C1 NAG A1001 1555 1555 1.45 CISPEP 1 PHE H 146 PRO H 147 0 1.20 CISPEP 2 GLU H 148 PRO H 149 0 -8.40 CISPEP 3 SER L 7 PRO L 8 0 -6.90 CISPEP 4 SER L 94 PRO L 95 0 -0.16 CISPEP 5 TYR L 140 PRO L 141 0 2.76 CRYST1 187.357 90.146 57.261 90.00 104.36 90.00 C 1 2 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.005337 0.000000 0.001367 0.00000 SCALE2 0.000000 0.011093 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018027 0.00000