HEADER VIRAL PROTEIN/IMMUNE SYSTEM 02-NOV-20 7KM5 TITLE CRYSTAL STRUCTURE OF SARS-COV-2 RBD COMPLEXED WITH NANOSOTA-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE PROTEIN S1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RECEPTOR-BINDING DOMAIN; COMPND 5 SYNONYM: S GLYCOPROTEIN,E2,PEPLOMER PROTEIN,SPIKE GLYCOPROTEIN; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: NANOBODY; COMPND 9 CHAIN: C, D; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 3 2; SOURCE 4 ORGANISM_COMMON: 2019-NCOV, SARS-COV-2, COVID-19 VIRUS; 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: LAMA GLAMA; SOURCE 11 ORGANISM_TAXID: 9844; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RBD, NANOBODY, VIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR G.YE,K.SHI,H.AIHARA,F.LI REVDAT 3 18-OCT-23 7KM5 1 REMARK REVDAT 2 29-DEC-21 7KM5 1 JRNL REVDAT 1 04-AUG-21 7KM5 0 JRNL AUTH G.YE,J.GALLANT,J.ZHENG,C.MASSEY,K.SHI,W.TAI,A.ODLE, JRNL AUTH 2 M.VICKERS,J.SHANG,Y.WAN,L.DU,H.AIHARA,S.PERLMAN,A.LEBEAU, JRNL AUTH 3 F.LI JRNL TITL THE DEVELOPMENT OF NANOSOTA - 1 AS ANTI-SARS-COV-2 NANOBODY JRNL TITL 2 DRUG CANDIDATES. JRNL REF ELIFE V. 10 2021 JRNL REFN ESSN 2050-084X JRNL PMID 34338634 JRNL DOI 10.7554/ELIFE.64815 REMARK 2 REMARK 2 RESOLUTION. 3.19 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) : 3.19 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.89 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 3 NUMBER OF REFLECTIONS : 13567 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.249 REMARK 3 R VALUE (WORKING SET) : 0.247 REMARK 3 FREE R VALUE : 0.294 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 1182 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 48.8900 - 6.3800 0.93 2733 139 0.2229 0.2611 REMARK 3 2 6.3700 - 5.0600 0.96 2777 132 0.2281 0.2624 REMARK 3 3 5.0600 - 4.4200 0.93 2730 173 0.2108 0.2675 REMARK 3 4 4.4200 - 4.0200 0.96 2790 137 0.2265 0.2795 REMARK 3 5 4.0200 - 3.7300 0.98 2840 171 0.2797 0.3074 REMARK 3 6 3.7300 - 3.5100 0.98 2882 147 0.2823 0.3624 REMARK 3 7 3.5100 - 3.3300 0.98 2857 145 0.3045 0.3724 REMARK 3 8 3.3300 - 3.1900 0.95 2762 138 0.3597 0.4245 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) : 0.512 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 36.080 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 83.25 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 89.68 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 5012 REMARK 3 ANGLE : 0.448 6810 REMARK 3 CHIRALITY : 0.044 733 REMARK 3 PLANARITY : 0.003 886 REMARK 3 DIHEDRAL : 15.493 1779 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 : 2 REMARK 3 NCS GROUP : ens_1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: NULL REMARK 3 SELECTION : (chain "A" and (resid 333 through 525 or REMARK 3 (resid 526 and (name N or name CA or name REMARK 3 C or name O )) or resid 601)) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 NCS OPERATOR : 2 REMARK 3 REFERENCE SELECTION: NULL REMARK 3 SELECTION : (chain "B" and (resid 333 through 526 or REMARK 3 resid 601)) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 NCS GROUP : ens_2 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: NULL REMARK 3 SELECTION : (chain "C" and (resid 1 through 98 or REMARK 3 resid 111 through 115)) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 NCS OPERATOR : 2 REMARK 3 REFERENCE SELECTION: NULL REMARK 3 SELECTION : (chain "D" and (resid 1 through 98 or REMARK 3 resid 111 through 115)) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7KM5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-NOV-20. REMARK 100 THE DEPOSITION ID IS D_1000251941. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-SEP-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 : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 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 : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13567 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.190 REMARK 200 RESOLUTION RANGE LOW (A) : 48.890 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : 0.14500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.19 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.41 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : 0.75400 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: PHASER REMARK 200 STARTING MODEL: 7C01 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM MNCL2, 50 MM MES (PH 6.0), 20% REMARK 280 (W/V) PEG 4000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 205.35050 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 30.42450 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 30.42450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 308.02575 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 30.42450 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 30.42450 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 102.67525 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 30.42450 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 30.42450 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 308.02575 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 30.42450 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 30.42450 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 102.67525 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 205.35050 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15160 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D, E REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15010 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C, F 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 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 HIS 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 ARG B 319 REMARK 465 VAL B 320 REMARK 465 GLN B 321 REMARK 465 PRO B 322 REMARK 465 THR B 323 REMARK 465 GLU B 324 REMARK 465 SER B 325 REMARK 465 ILE B 326 REMARK 465 VAL B 327 REMARK 465 ARG B 328 REMARK 465 PHE B 329 REMARK 465 PRO B 330 REMARK 465 ASN B 331 REMARK 465 ILE B 332 REMARK 465 LYS B 528 REMARK 465 LYS B 529 REMARK 465 SER B 530 REMARK 465 THR B 531 REMARK 465 ASN B 532 REMARK 465 LEU B 533 REMARK 465 VAL B 534 REMARK 465 LYS B 535 REMARK 465 HIS B 536 REMARK 465 HIS B 537 REMARK 465 HIS B 538 REMARK 465 HIS B 539 REMARK 465 HIS B 540 REMARK 465 HIS B 541 REMARK 465 HIS B 542 REMARK 465 HIS B 543 REMARK 465 SER C 99 REMARK 465 LYS C 100 REMARK 465 SER C 101 REMARK 465 GLY C 102 REMARK 465 HIS C 103 REMARK 465 HIS C 119 REMARK 465 HIS C 120 REMARK 465 HIS C 121 REMARK 465 HIS C 122 REMARK 465 HIS C 123 REMARK 465 HIS C 124 REMARK 465 HIS D 119 REMARK 465 HIS D 120 REMARK 465 HIS D 121 REMARK 465 HIS D 122 REMARK 465 HIS D 123 REMARK 465 HIS D 124 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 ASN A 334 42.77 -88.92 REMARK 500 SER A 371 -39.09 -137.53 REMARK 500 ALA A 372 17.40 57.61 REMARK 500 ASN A 422 -54.08 -126.36 REMARK 500 ASP A 428 33.97 -90.10 REMARK 500 CYS A 525 -141.05 -127.26 REMARK 500 ASN B 334 44.02 -84.86 REMARK 500 ALA B 352 58.37 -119.06 REMARK 500 ASN B 370 49.43 -76.03 REMARK 500 ALA B 372 8.40 58.90 REMARK 500 LYS B 386 -77.32 -84.35 REMARK 500 LEU B 387 -57.01 65.11 REMARK 500 ASN B 422 -57.48 -122.88 REMARK 500 ASP B 428 31.28 -86.57 REMARK 500 LEU B 441 -50.42 -123.97 REMARK 500 ASP B 442 32.91 -98.35 REMARK 500 LEU B 518 -158.74 -99.13 REMARK 500 CYS B 525 -121.04 -121.29 REMARK 500 ASN C 31 56.73 -119.47 REMARK 500 PRO C 41 108.36 -57.14 REMARK 500 ALA C 97 -108.82 -105.91 REMARK 500 PRO D 41 108.16 -57.15 REMARK 500 SER D 99 -166.71 74.97 REMARK 500 LYS D 100 -21.48 82.51 REMARK 500 HIS D 103 39.29 -73.53 REMARK 500 REMARK 500 REMARK: NULL DBREF 7KM5 A 319 535 UNP P0DTC2 SPIKE_SARS2 319 535 DBREF 7KM5 B 319 535 UNP P0DTC2 SPIKE_SARS2 319 535 DBREF 7KM5 C 1 124 PDB 7KM5 7KM5 1 124 DBREF 7KM5 D 1 124 PDB 7KM5 7KM5 1 124 SEQADV 7KM5 HIS A 536 UNP P0DTC2 EXPRESSION TAG SEQADV 7KM5 HIS A 537 UNP P0DTC2 EXPRESSION TAG SEQADV 7KM5 HIS A 538 UNP P0DTC2 EXPRESSION TAG SEQADV 7KM5 HIS A 539 UNP P0DTC2 EXPRESSION TAG SEQADV 7KM5 HIS A 540 UNP P0DTC2 EXPRESSION TAG SEQADV 7KM5 HIS A 541 UNP P0DTC2 EXPRESSION TAG SEQADV 7KM5 HIS A 542 UNP P0DTC2 EXPRESSION TAG SEQADV 7KM5 HIS A 543 UNP P0DTC2 EXPRESSION TAG SEQADV 7KM5 HIS B 536 UNP P0DTC2 EXPRESSION TAG SEQADV 7KM5 HIS B 537 UNP P0DTC2 EXPRESSION TAG SEQADV 7KM5 HIS B 538 UNP P0DTC2 EXPRESSION TAG SEQADV 7KM5 HIS B 539 UNP P0DTC2 EXPRESSION TAG SEQADV 7KM5 HIS B 540 UNP P0DTC2 EXPRESSION TAG SEQADV 7KM5 HIS B 541 UNP P0DTC2 EXPRESSION TAG SEQADV 7KM5 HIS B 542 UNP P0DTC2 EXPRESSION TAG SEQADV 7KM5 HIS B 543 UNP P0DTC2 EXPRESSION TAG SEQRES 1 A 225 ARG VAL GLN PRO THR GLU SER ILE VAL ARG PHE PRO ASN SEQRES 2 A 225 ILE THR ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN ALA SEQRES 3 A 225 THR ARG PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG SEQRES 4 A 225 ILE SER ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SEQRES 5 A 225 SER ALA SER PHE SER THR PHE LYS CYS TYR GLY VAL SER SEQRES 6 A 225 PRO THR LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR SEQRES 7 A 225 ALA ASP SER PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN SEQRES 8 A 225 ILE ALA PRO GLY GLN THR GLY LYS ILE ALA ASP TYR ASN SEQRES 9 A 225 TYR LYS LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA SEQRES 10 A 225 TRP ASN SER ASN ASN LEU ASP SER LYS VAL GLY GLY ASN SEQRES 11 A 225 TYR ASN TYR LEU TYR ARG LEU PHE ARG LYS SER ASN LEU SEQRES 12 A 225 LYS PRO PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN SEQRES 13 A 225 ALA GLY SER THR PRO CYS ASN GLY VAL GLU GLY PHE ASN SEQRES 14 A 225 CYS TYR PHE PRO LEU GLN SER TYR GLY PHE GLN PRO THR SEQRES 15 A 225 ASN GLY VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL LEU SEQRES 16 A 225 SER PHE GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY SEQRES 17 A 225 PRO LYS LYS SER THR ASN LEU VAL LYS HIS HIS HIS HIS SEQRES 18 A 225 HIS HIS HIS HIS SEQRES 1 B 225 ARG VAL GLN PRO THR GLU SER ILE VAL ARG PHE PRO ASN SEQRES 2 B 225 ILE THR ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN ALA SEQRES 3 B 225 THR ARG PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG SEQRES 4 B 225 ILE SER ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SEQRES 5 B 225 SER ALA SER PHE SER THR PHE LYS CYS TYR GLY VAL SER SEQRES 6 B 225 PRO THR LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR SEQRES 7 B 225 ALA ASP SER PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN SEQRES 8 B 225 ILE ALA PRO GLY GLN THR GLY LYS ILE ALA ASP TYR ASN SEQRES 9 B 225 TYR LYS LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA SEQRES 10 B 225 TRP ASN SER ASN ASN LEU ASP SER LYS VAL GLY GLY ASN SEQRES 11 B 225 TYR ASN TYR LEU TYR ARG LEU PHE ARG LYS SER ASN LEU SEQRES 12 B 225 LYS PRO PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN SEQRES 13 B 225 ALA GLY SER THR PRO CYS ASN GLY VAL GLU GLY PHE ASN SEQRES 14 B 225 CYS TYR PHE PRO LEU GLN SER TYR GLY PHE GLN PRO THR SEQRES 15 B 225 ASN GLY VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL LEU SEQRES 16 B 225 SER PHE GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY SEQRES 17 B 225 PRO LYS LYS SER THR ASN LEU VAL LYS HIS HIS HIS HIS SEQRES 18 B 225 HIS HIS HIS HIS SEQRES 1 C 124 GLN VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 C 124 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 C 124 PHE THR PHE LYS ASN ALA ASP MET ASN TRP TYR ARG GLN SEQRES 4 C 124 VAL PRO GLY GLN GLY LEU GLU TRP VAL THR SER ILE TYR SEQRES 5 C 124 SER ASP GLY ARG THR VAL TYR ALA ASP SER VAL LYS GLY SEQRES 6 C 124 ARG PHE THR VAL SER ARG ASP ASN PRO LYS SER THR VAL SEQRES 7 C 124 SER LEU GLN MET ASN SER LEU LYS PRO GLU ASP THR GLY SEQRES 8 C 124 VAL TYR TYR CYS MET ALA GLY SER LYS SER GLY HIS GLU SEQRES 9 C 124 LEU ASP HIS TRP GLY GLN GLY THR GLN VAL THR VAL SER SEQRES 10 C 124 SER HIS HIS HIS HIS HIS HIS SEQRES 1 D 124 GLN VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 D 124 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 D 124 PHE THR PHE LYS ASN ALA ASP MET ASN TRP TYR ARG GLN SEQRES 4 D 124 VAL PRO GLY GLN GLY LEU GLU TRP VAL THR SER ILE TYR SEQRES 5 D 124 SER ASP GLY ARG THR VAL TYR ALA ASP SER VAL LYS GLY SEQRES 6 D 124 ARG PHE THR VAL SER ARG ASP ASN PRO LYS SER THR VAL SEQRES 7 D 124 SER LEU GLN MET ASN SER LEU LYS PRO GLU ASP THR GLY SEQRES 8 D 124 VAL TYR TYR CYS MET ALA GLY SER LYS SER GLY HIS GLU SEQRES 9 D 124 LEU ASP HIS TRP GLY GLN GLY THR GLN VAL THR VAL SER SEQRES 10 D 124 SER HIS HIS HIS HIS HIS HIS HET NAG E 1 14 HET NAG E 2 14 HET NAG F 1 14 HET NAG F 2 14 HET CL B 601 1 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM CL CHLORIDE ION 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 4(C8 H15 N O6) FORMUL 7 CL CL 1- HELIX 1 AA1 TYR A 365 ASN A 370 1 6 HELIX 2 AA2 ASP A 405 ILE A 410 5 6 HELIX 3 AA3 GLY A 416 ASN A 422 1 7 HELIX 4 AA4 PHE B 338 ASN B 343 1 6 HELIX 5 AA5 TYR B 365 ASN B 370 1 6 HELIX 6 AA6 ASP B 405 ILE B 410 5 6 HELIX 7 AA7 GLY B 416 ASN B 422 1 7 HELIX 8 AA8 THR C 28 ALA C 32 5 5 HELIX 9 AA9 LYS C 86 THR C 90 5 5 HELIX 10 AB1 THR D 28 ALA D 32 5 5 HELIX 11 AB2 LYS D 86 THR D 90 5 5 SHEET 1 AA1 5 ASN A 354 ILE A 358 0 SHEET 2 AA1 5 ASN A 394 ARG A 403 -1 O SER A 399 N ASN A 354 SHEET 3 AA1 5 PRO A 507 GLU A 516 -1 O TYR A 508 N ILE A 402 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 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 AA511 ASN B 354 ILE B 358 0 SHEET 2 AA511 ASN B 394 ARG B 403 -1 O SER B 399 N ASN B 354 SHEET 3 AA511 PRO B 507 GLU B 516 -1 O TYR B 508 N ILE B 402 SHEET 4 AA511 GLY B 431 ASN B 437 -1 N ILE B 434 O VAL B 511 SHEET 5 AA511 THR B 376 TYR B 380 -1 N LYS B 378 O VAL B 433 SHEET 6 AA511 GLY D 10 VAL D 12 -1 O LEU D 11 N PHE B 377 SHEET 7 AA511 THR D 112 VAL D 116 1 O GLN D 113 N GLY D 10 SHEET 8 AA511 GLY D 91 GLY D 98 -1 N GLY D 91 O VAL D 114 SHEET 9 AA511 ASP D 33 GLN D 39 -1 N TYR D 37 O TYR D 94 SHEET 10 AA511 LEU D 45 ILE D 51 -1 O VAL D 48 N TRP D 36 SHEET 11 AA511 THR D 57 TYR D 59 -1 O VAL D 58 N SER D 50 SHEET 1 AA6 9 ASN B 354 ILE B 358 0 SHEET 2 AA6 9 ASN B 394 ARG B 403 -1 O SER B 399 N ASN B 354 SHEET 3 AA6 9 PRO B 507 GLU B 516 -1 O TYR B 508 N ILE B 402 SHEET 4 AA6 9 GLY B 431 ASN B 437 -1 N ILE B 434 O VAL B 511 SHEET 5 AA6 9 THR B 376 TYR B 380 -1 N LYS B 378 O VAL B 433 SHEET 6 AA6 9 GLY D 10 VAL D 12 -1 O LEU D 11 N PHE B 377 SHEET 7 AA6 9 THR D 112 VAL D 116 1 O GLN D 113 N GLY D 10 SHEET 8 AA6 9 GLY D 91 GLY D 98 -1 N GLY D 91 O VAL D 114 SHEET 9 AA6 9 HIS D 107 TRP D 108 -1 O HIS D 107 N ALA D 97 SHEET 1 AA7 2 CYS B 361 VAL B 362 0 SHEET 2 AA7 2 VAL B 524 CYS B 525 1 O CYS B 525 N CYS B 361 SHEET 1 AA8 2 LEU B 452 ARG B 454 0 SHEET 2 AA8 2 LEU B 492 SER B 494 -1 O GLN B 493 N TYR B 453 SHEET 1 AA9 2 TYR B 473 GLN B 474 0 SHEET 2 AA9 2 CYS B 488 TYR B 489 -1 O TYR B 489 N TYR B 473 SHEET 1 AB1 4 GLN C 3 SER C 7 0 SHEET 2 AB1 4 SER C 17 SER C 25 -1 O SER C 21 N SER C 7 SHEET 3 AB1 4 THR C 77 ASN C 83 -1 O MET C 82 N LEU C 18 SHEET 4 AB1 4 PHE C 67 ASP C 72 -1 N SER C 70 O SER C 79 SHEET 1 AB2 6 GLY C 10 VAL C 12 0 SHEET 2 AB2 6 THR C 112 VAL C 116 1 O GLN C 113 N GLY C 10 SHEET 3 AB2 6 GLY C 91 MET C 96 -1 N GLY C 91 O VAL C 114 SHEET 4 AB2 6 MET C 34 GLN C 39 -1 N TYR C 37 O TYR C 94 SHEET 5 AB2 6 GLU C 46 ILE C 51 -1 O VAL C 48 N TRP C 36 SHEET 6 AB2 6 THR C 57 TYR C 59 -1 O VAL C 58 N SER C 50 SHEET 1 AB3 4 GLN D 3 SER D 7 0 SHEET 2 AB3 4 SER D 17 SER D 25 -1 O SER D 21 N SER D 7 SHEET 3 AB3 4 THR D 77 ASN D 83 -1 O MET D 82 N LEU D 18 SHEET 4 AB3 4 PHE D 67 ASP D 72 -1 N SER D 70 O SER D 79 SSBOND 1 CYS A 336 CYS A 361 1555 1555 2.03 SSBOND 2 CYS A 379 CYS A 432 1555 1555 2.03 SSBOND 3 CYS A 391 CYS A 525 1555 1555 2.03 SSBOND 4 CYS A 480 CYS A 488 1555 1555 2.03 SSBOND 5 CYS B 336 CYS B 361 1555 1555 2.03 SSBOND 6 CYS B 379 CYS B 432 1555 1555 2.03 SSBOND 7 CYS B 391 CYS B 525 1555 1555 2.04 SSBOND 8 CYS B 480 CYS B 488 1555 1555 2.03 SSBOND 9 CYS C 22 CYS C 95 1555 1555 2.03 SSBOND 10 CYS D 22 CYS D 95 1555 1555 2.03 LINK ND2 ASN A 343 C1 NAG E 1 1555 1555 1.45 LINK ND2 ASN B 343 C1 NAG F 1 1555 1555 1.45 LINK O4 NAG E 1 C1 NAG E 2 1555 1555 1.46 LINK O4 NAG F 1 C1 NAG F 2 1555 1555 1.46 CRYST1 60.849 60.849 410.701 90.00 90.00 90.00 P 43 21 2 16 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 0.016434 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016434 0.000000 0.00000 SCALE3 0.000000 0.000000 0.002435 0.00000