HEADER VIRAL PROTEIN 13-OCT-22 8H5U TITLE CRYSTAL STRUCTURE OF SARS-COV-2 SPIKE RECEPTOR-BINDING DOMAIN IN TITLE 2 COMPLEX WITH NEUTRALIZING NANOBODY NB-021 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE PROTEIN S1; COMPND 3 CHAIN: A, C; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: NANOBODY NB-021; COMPND 7 CHAIN: B, D; COMPND 8 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; SOURCE 5 ORGANISM_TAXID: 2697049; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: VICUGNA PACOS; SOURCE 10 ORGANISM_TAXID: 30538; SOURCE 11 EXPRESSION_SYSTEM: BREVIBACILLUS CHOSHINENSIS; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 54911 KEYWDS VIRAL PROTEIN, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR J.YANG,S.LIN,G.W.LU REVDAT 2 13-DEC-23 8H5U 1 JRNL REVDAT 1 18-OCT-23 8H5U 0 JRNL AUTH J.YANG,S.LIN,Z.CHEN,F.YANG,L.GUO,L.WANG,Y.DUAN,X.ZHANG, JRNL AUTH 2 Y.DAI,K.YIN,C.YU,X.YUAN,H.SUN,B.HE,Y.CAO,H.YE,H.DONG,X.LIU, JRNL AUTH 3 B.CHEN,J.LI,Q.ZHAO,G.LU JRNL TITL DEVELOPMENT OF A BISPECIFIC NANOBODY CONJUGATE BROADLY JRNL TITL 2 NEUTRALIZES DIVERSE SARS-COV-2 VARIANTS AND STRUCTURAL BASIS JRNL TITL 3 FOR ITS BROAD NEUTRALIZATION. JRNL REF PLOS PATHOG. V. 19 11804 2023 JRNL REFN ESSN 1553-7374 JRNL PMID 38033141 JRNL DOI 10.1371/JOURNAL.PPAT.1011804 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1_2155 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.69 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 3 NUMBER OF REFLECTIONS : 33843 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.226 REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.710 REMARK 3 FREE R VALUE TEST SET COUNT : 1595 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 40.6860 - 5.3363 0.99 3179 166 0.2332 0.2510 REMARK 3 2 5.3363 - 4.2370 0.99 3065 150 0.1830 0.1680 REMARK 3 3 4.2370 - 3.7018 0.99 3019 144 0.2010 0.2315 REMARK 3 4 3.7018 - 3.3635 0.99 3006 141 0.2199 0.2600 REMARK 3 5 3.3635 - 3.1225 0.99 2976 132 0.2364 0.2589 REMARK 3 6 3.1225 - 2.9385 0.98 2913 176 0.2492 0.2758 REMARK 3 7 2.9385 - 2.7914 0.98 2914 164 0.2455 0.2853 REMARK 3 8 2.7914 - 2.6699 0.98 2904 147 0.2527 0.2647 REMARK 3 9 2.6699 - 2.5671 0.97 2896 150 0.2536 0.2845 REMARK 3 10 2.5671 - 2.4786 0.97 2882 136 0.2615 0.2904 REMARK 3 11 2.4786 - 2.4011 0.82 2494 89 0.2779 0.3034 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) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.730 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.71 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 4979 REMARK 3 ANGLE : 0.725 6778 REMARK 3 CHIRALITY : 0.050 728 REMARK 3 PLANARITY : 0.004 884 REMARK 3 DIHEDRAL : 14.248 2912 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 : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: (CHAIN A AND (RESSEQ 334:350 OR (RESID REMARK 3 351 AND (NAME N OR NAME CA OR NAME C OR REMARK 3 NAME O OR NAME CB OR NAME CG OR NAME CD2 REMARK 3 OR NAME CE2 OR NAME CZ OR NAME OH )) OR REMARK 3 RESSEQ 352:356 OR RESSEQ 358:422 OR REMARK 3 (RESID 423 AND (NAME N OR NAME CA OR NAME REMARK 3 C OR NAME O OR NAME CB OR NAME CG OR NAME REMARK 3 CD2 OR NAME CE2 OR NAME CZ OR NAME OH )) REMARK 3 OR RESSEQ 424:485 OR (RESID 486 AND (NAME REMARK 3 N OR NAME CA OR NAME C OR NAME O OR NAME REMARK 3 CB OR NAME CG OR NAME CD1 OR NAME CE1 OR REMARK 3 NAME CZ )) OR RESSEQ 487:518 OR RESSEQ REMARK 3 520:527)) REMARK 3 SELECTION : (CHAIN C AND (RESSEQ 334:350 OR (RESID REMARK 3 351 AND (NAME N OR NAME CA OR NAME C OR REMARK 3 NAME O OR NAME CB OR NAME CG OR NAME CD2 REMARK 3 OR NAME CE2 OR NAME CZ OR NAME OH )) OR REMARK 3 RESSEQ 352:356 OR RESSEQ 358:422 OR REMARK 3 (RESID 423 AND (NAME N OR NAME CA OR NAME REMARK 3 C OR NAME O OR NAME CB OR NAME CG OR NAME REMARK 3 CD2 OR NAME CE2 OR NAME CZ OR NAME OH )) REMARK 3 OR RESSEQ 424:485 OR (RESID 486 AND (NAME REMARK 3 N OR NAME CA OR NAME C OR NAME O OR NAME REMARK 3 CB OR NAME CG OR NAME CD1 OR NAME CE1 OR REMARK 3 NAME CZ )) OR RESSEQ 487:518 OR RESSEQ REMARK 3 520:527)) REMARK 3 ATOM PAIRS NUMBER : 1777 REMARK 3 RMSD : NULL REMARK 3 NCS GROUP : 2 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: (CHAIN D AND (RESSEQ 1:12 OR RESSEQ 14:30 REMARK 3 OR (RESID 31 AND (NAME N OR NAME CA OR REMARK 3 NAME C OR NAME O OR NAME CB OR NAME CG OR REMARK 3 NAME CD2 OR NAME CE2 OR NAME CZ )) OR REMARK 3 RESSEQ 32:43 OR (RESID 44 AND (NAME N OR REMARK 3 NAME CA OR NAME C )) OR (RESID 45 AND REMARK 3 (NAME N OR NAME CA OR NAME C OR NAME CB REMARK 3 OR NAME CG OR NAME ND2)) OR RESSEQ 46:80 REMARK 3 OR (RESID 81 AND (NAME N OR NAME CA OR REMARK 3 NAME C OR NAME O OR NAME CB OR NAME CG OR REMARK 3 NAME CD1 OR NAME CE1 OR NAME CZ OR NAME REMARK 3 OH )) OR RESSEQ 82:113)) REMARK 3 SELECTION : (CHAIN B AND (RESSEQ 1:12 OR RESSEQ 14:30 REMARK 3 OR (RESID 31 AND (NAME N OR NAME CA OR REMARK 3 NAME C OR NAME O OR NAME CB OR NAME CG OR REMARK 3 NAME CD2 OR NAME CE2 OR NAME CZ )) OR REMARK 3 RESSEQ 32:43 OR (RESID 44 AND (NAME O OR REMARK 3 NAME N OR NAME CA )) OR (RESID 45 AND REMARK 3 (NAME O OR NAME N OR NAME CA OR NAME C OR REMARK 3 NAME CB OR NAME OD1)) OR RESSEQ 46:80 OR REMARK 3 (RESID 81 AND (NAME N OR NAME CA OR NAME REMARK 3 C OR NAME O OR NAME CB OR NAME CG OR NAME REMARK 3 CD1 OR NAME CE1 OR NAME CZ OR NAME OH )) REMARK 3 OR RESSEQ 82:113)) REMARK 3 ATOM PAIRS NUMBER : 981 REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8H5U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 19-OCT-22. REMARK 100 THE DEPOSITION ID IS D_1300032861. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUL-21 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 : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97852 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33895 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 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 (%) : 97.9 REMARK 200 DATA REDUNDANCY : 11.90 REMARK 200 R MERGE (I) : 0.17300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.6920 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.72200 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: 6YZ5, 6B20 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CITRATE TRIBASIC REMARK 280 DIHYDRATE, PH 5.0, 18% W/V POLYETHYLENE GLYCOL 20000, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 39.03600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.52650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 52.41350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 53.52650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 39.03600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 52.41350 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 APPLY THE FOLLOWING TO CHAINS: A, B, 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 APPLY THE FOLLOWING TO CHAINS: C, D 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 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 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 HIS B 114 REMARK 465 HIS B 115 REMARK 465 HIS B 116 REMARK 465 HIS B 117 REMARK 465 HIS B 118 REMARK 465 HIS B 119 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 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 HIS D 114 REMARK 465 HIS D 115 REMARK 465 HIS D 116 REMARK 465 HIS D 117 REMARK 465 HIS D 118 REMARK 465 HIS D 119 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 693 O HOH A 701 1.88 REMARK 500 OG1 THR A 376 O HOH A 601 1.91 REMARK 500 O HOH B 240 O HOH B 244 1.94 REMARK 500 OE1 GLU D 48 O HOH D 201 1.95 REMARK 500 ND2 ASN C 360 O HOH C 701 1.96 REMARK 500 OD1 ASN D 85 O HOH D 202 1.98 REMARK 500 O HOH A 702 O HOH A 712 2.02 REMARK 500 O HOH C 726 O HOH C 753 2.03 REMARK 500 O HOH C 790 O HOH C 791 2.05 REMARK 500 OD1 ASN C 440 O HOH C 702 2.06 REMARK 500 O HOH B 248 O HOH B 255 2.13 REMARK 500 NE2 GLN D 83 O HOH D 202 2.14 REMARK 500 O PRO A 384 O HOH A 602 2.15 REMARK 500 O HOH C 760 O HOH C 798 2.16 REMARK 500 O HOH A 703 O HOH A 713 2.17 REMARK 500 O LEU C 518 O HOH C 703 2.18 REMARK 500 O HOH A 714 O HOH A 715 2.18 REMARK 500 O HOH C 756 O HOH C 795 2.18 REMARK 500 O HIS C 519 O HOH C 704 2.19 REMARK 500 O6 NAG C 601 O HOH C 705 2.19 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 ASP A 405 0.51 -69.12 REMARK 500 ASN A 422 -53.12 -129.98 REMARK 500 HIS A 519 43.90 -94.54 REMARK 500 ALA B 93 168.56 179.05 REMARK 500 ALA C 352 50.13 -111.32 REMARK 500 ASP C 405 0.94 -69.02 REMARK 500 ASN C 422 -54.53 -129.08 REMARK 500 ALA D 93 168.72 179.55 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 717 DISTANCE = 5.98 ANGSTROMS DBREF 8H5U A 320 537 UNP P0DTC2 SPIKE_SARS2 320 537 DBREF 8H5U B 1 119 PDB 8H5U 8H5U 1 119 DBREF 8H5U C 320 537 UNP P0DTC2 SPIKE_SARS2 320 537 DBREF 8H5U D 1 119 PDB 8H5U 8H5U 1 119 SEQRES 1 A 218 VAL GLN PRO THR GLU SER ILE VAL ARG PHE PRO ASN ILE SEQRES 2 A 218 THR ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN ALA THR SEQRES 3 A 218 ARG PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG ILE SEQRES 4 A 218 SER ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SER SEQRES 5 A 218 ALA SER PHE SER THR PHE LYS CYS TYR GLY VAL SER PRO SEQRES 6 A 218 THR LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR ALA SEQRES 7 A 218 ASP SER PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN ILE SEQRES 8 A 218 ALA PRO GLY GLN THR GLY LYS ILE ALA ASP TYR ASN TYR SEQRES 9 A 218 LYS LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA TRP SEQRES 10 A 218 ASN SER ASN ASN LEU ASP SER LYS VAL GLY GLY ASN TYR SEQRES 11 A 218 ASN TYR LEU TYR ARG LEU PHE ARG LYS SER ASN LEU LYS SEQRES 12 A 218 PRO PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN ALA SEQRES 13 A 218 GLY SER THR PRO CYS ASN GLY VAL GLU GLY PHE ASN CYS SEQRES 14 A 218 TYR PHE PRO LEU GLN SER TYR GLY PHE GLN PRO THR ASN SEQRES 15 A 218 GLY VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL LEU SER SEQRES 16 A 218 PHE GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY PRO SEQRES 17 A 218 LYS LYS SER THR ASN LEU VAL LYS ASN LYS SEQRES 1 B 119 GLU VAL GLN VAL VAL GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 B 119 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 B 119 THR GLY SER THR PHE SER THR TYR ALA MET GLY TRP TYR SEQRES 4 B 119 ARG GLN ALA PRO GLY ASN GLN HIS GLU ARG VAL ALA ILE SEQRES 5 B 119 ILE ASP SER VAL GLY ASN THR ASN TYR PRO ASP SER VAL SEQRES 6 B 119 LYS GLY ARG PHE THR ILE SER ARG ASP ASN ALA LYS ASN SEQRES 7 B 119 THR GLY TYR LEU GLN MET ASN SER LEU LYS SER GLU ASP SEQRES 8 B 119 THR ALA VAL TYR TYR CYS ASN LEU GLY THR ILE TRP GLY SEQRES 9 B 119 GLN GLY THR GLN VAL THR VAL SER SER HIS HIS HIS HIS SEQRES 10 B 119 HIS HIS SEQRES 1 C 218 VAL GLN PRO THR GLU SER ILE VAL ARG PHE PRO ASN ILE SEQRES 2 C 218 THR ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN ALA THR SEQRES 3 C 218 ARG PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG ILE SEQRES 4 C 218 SER ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SER SEQRES 5 C 218 ALA SER PHE SER THR PHE LYS CYS TYR GLY VAL SER PRO SEQRES 6 C 218 THR LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR ALA SEQRES 7 C 218 ASP SER PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN ILE SEQRES 8 C 218 ALA PRO GLY GLN THR GLY LYS ILE ALA ASP TYR ASN TYR SEQRES 9 C 218 LYS LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA TRP SEQRES 10 C 218 ASN SER ASN ASN LEU ASP SER LYS VAL GLY GLY ASN TYR SEQRES 11 C 218 ASN TYR LEU TYR ARG LEU PHE ARG LYS SER ASN LEU LYS SEQRES 12 C 218 PRO PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN ALA SEQRES 13 C 218 GLY SER THR PRO CYS ASN GLY VAL GLU GLY PHE ASN CYS SEQRES 14 C 218 TYR PHE PRO LEU GLN SER TYR GLY PHE GLN PRO THR ASN SEQRES 15 C 218 GLY VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL LEU SER SEQRES 16 C 218 PHE GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY PRO SEQRES 17 C 218 LYS LYS SER THR ASN LEU VAL LYS ASN LYS SEQRES 1 D 119 GLU VAL GLN VAL VAL GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 D 119 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 D 119 THR GLY SER THR PHE SER THR TYR ALA MET GLY TRP TYR SEQRES 4 D 119 ARG GLN ALA PRO GLY ASN GLN HIS GLU ARG VAL ALA ILE SEQRES 5 D 119 ILE ASP SER VAL GLY ASN THR ASN TYR PRO ASP SER VAL SEQRES 6 D 119 LYS GLY ARG PHE THR ILE SER ARG ASP ASN ALA LYS ASN SEQRES 7 D 119 THR GLY TYR LEU GLN MET ASN SER LEU LYS SER GLU ASP SEQRES 8 D 119 THR ALA VAL TYR TYR CYS ASN LEU GLY THR ILE TRP GLY SEQRES 9 D 119 GLN GLY THR GLN VAL THR VAL SER SER HIS HIS HIS HIS SEQRES 10 D 119 HIS HIS HET NAG E 1 14 HET NAG E 2 14 HET NAG C 601 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 3(C8 H15 N O6) FORMUL 7 HOH *308(H2 O) HELIX 1 AA1 PRO A 337 ASN A 343 1 7 HELIX 2 AA2 TYR A 365 ASN A 370 1 6 HELIX 3 AA3 SER A 383 ASN A 388 1 6 HELIX 4 AA4 ASP A 405 ILE A 410 5 6 HELIX 5 AA5 GLY A 416 ASN A 422 1 7 HELIX 6 AA6 SER A 438 SER A 443 1 6 HELIX 7 AA7 GLY A 502 TYR A 505 5 4 HELIX 8 AA8 THR B 30 TYR B 34 5 5 HELIX 9 AA9 LYS B 88 THR B 92 5 5 HELIX 10 AB1 PRO C 337 ASN C 343 1 7 HELIX 11 AB2 TYR C 365 ASN C 370 1 6 HELIX 12 AB3 LYS C 386 ASP C 389 5 4 HELIX 13 AB4 ASP C 405 ILE C 410 5 6 HELIX 14 AB5 GLY C 416 ASN C 422 1 7 HELIX 15 AB6 SER C 438 SER C 443 1 6 HELIX 16 AB7 GLY C 502 TYR C 505 5 4 HELIX 17 AB8 PRO C 527 SER C 530 5 4 HELIX 18 AB9 THR D 30 TYR D 34 5 5 HELIX 19 AC1 LYS D 88 THR D 92 5 5 SHEET 1 AA1 9 ASN A 354 ILE A 358 0 SHEET 2 AA1 9 ASN A 394 ARG A 403 -1 O ALA A 397 N LYS A 356 SHEET 3 AA1 9 PRO A 507 GLU A 516 -1 O VAL A 510 N PHE A 400 SHEET 4 AA1 9 GLY A 431 ASN A 437 -1 N CYS A 432 O LEU A 513 SHEET 5 AA1 9 THR A 376 TYR A 380 -1 N TYR A 380 O GLY A 431 SHEET 6 AA1 9 GLN B 46 ILE B 53 -1 O HIS B 47 N CYS A 379 SHEET 7 AA1 9 MET B 36 ALA B 42 -1 N TRP B 38 O VAL B 50 SHEET 8 AA1 9 ALA B 93 LEU B 99 -1 O TYR B 96 N TYR B 39 SHEET 9 AA1 9 THR B 59 ASN B 60 0 SHEET 1 AA2 6 LEU B 11 VAL B 12 0 SHEET 2 AA2 6 THR B 107 VAL B 111 1 O THR B 110 N VAL B 12 SHEET 3 AA2 6 ALA B 93 LEU B 99 -1 N TYR B 95 O THR B 107 SHEET 4 AA2 6 MET B 36 ALA B 42 -1 N TYR B 39 O TYR B 96 SHEET 5 AA2 6 GLN B 46 ILE B 53 -1 O VAL B 50 N TRP B 38 SHEET 6 AA2 6 ILE B 102 TRP B 103 0 SHEET 1 AA3 3 CYS A 361 VAL A 362 0 SHEET 2 AA3 3 VAL A 524 CYS A 525 1 O CYS A 525 N CYS A 361 SHEET 3 AA3 3 CYS A 391 PHE A 392 -1 N PHE A 392 O VAL A 524 SHEET 1 AA4 2 LEU A 452 ARG A 454 0 SHEET 2 AA4 2 LEU A 492 SER A 494 -1 O GLN A 493 N TYR A 453 SHEET 1 AA5 2 TYR A 473 GLN A 474 0 SHEET 2 AA5 2 CYS A 488 TYR A 489 -1 O TYR A 489 N TYR A 473 SHEET 1 AA6 4 GLN B 3 SER B 7 0 SHEET 2 AA6 4 LEU B 18 SER B 25 -1 O ALA B 23 N VAL B 5 SHEET 3 AA6 4 THR B 79 MET B 84 -1 O MET B 84 N LEU B 18 SHEET 4 AA6 4 PHE B 69 ASP B 74 -1 N THR B 70 O GLN B 83 SHEET 1 AA7 9 ASN C 354 ILE C 358 0 SHEET 2 AA7 9 ASN C 394 ARG C 403 -1 O SER C 399 N ASN C 354 SHEET 3 AA7 9 PRO C 507 GLU C 516 -1 O GLU C 516 N ASN C 394 SHEET 4 AA7 9 GLY C 431 ASN C 437 -1 N CYS C 432 O LEU C 513 SHEET 5 AA7 9 THR C 376 TYR C 380 -1 N LYS C 378 O VAL C 433 SHEET 6 AA7 9 GLN D 46 ILE D 53 -1 O HIS D 47 N CYS C 379 SHEET 7 AA7 9 MET D 36 ALA D 42 -1 N TRP D 38 O VAL D 50 SHEET 8 AA7 9 ALA D 93 LEU D 99 -1 O TYR D 96 N TYR D 39 SHEET 9 AA7 9 THR D 59 ASN D 60 0 SHEET 1 AA8 6 LEU D 11 VAL D 12 0 SHEET 2 AA8 6 THR D 107 VAL D 111 1 O THR D 110 N VAL D 12 SHEET 3 AA8 6 ALA D 93 LEU D 99 -1 N TYR D 95 O THR D 107 SHEET 4 AA8 6 MET D 36 ALA D 42 -1 N TYR D 39 O TYR D 96 SHEET 5 AA8 6 GLN D 46 ILE D 53 -1 O VAL D 50 N TRP D 38 SHEET 6 AA8 6 ILE D 102 TRP D 103 0 SHEET 1 AA9 3 CYS C 361 VAL C 362 0 SHEET 2 AA9 3 VAL C 524 CYS C 525 1 O CYS C 525 N CYS C 361 SHEET 3 AA9 3 CYS C 391 PHE C 392 -1 N PHE C 392 O VAL C 524 SHEET 1 AB1 2 LEU C 452 ARG C 454 0 SHEET 2 AB1 2 LEU C 492 SER C 494 -1 O GLN C 493 N TYR C 453 SHEET 1 AB2 2 TYR C 473 GLN C 474 0 SHEET 2 AB2 2 CYS C 488 TYR C 489 -1 O TYR C 489 N TYR C 473 SHEET 1 AB3 4 GLN D 3 SER D 7 0 SHEET 2 AB3 4 LEU D 18 SER D 25 -1 O ALA D 23 N VAL D 5 SHEET 3 AB3 4 THR D 79 MET D 84 -1 O MET D 84 N LEU D 18 SHEET 4 AB3 4 PHE D 69 ASP D 74 -1 N ASP D 74 O THR D 79 SSBOND 1 CYS A 336 CYS A 361 1555 1555 2.04 SSBOND 2 CYS A 379 CYS A 432 1555 1555 2.04 SSBOND 3 CYS A 391 CYS A 525 1555 1555 2.04 SSBOND 4 CYS A 480 CYS A 488 1555 1555 2.03 SSBOND 5 CYS B 22 CYS B 97 1555 1555 2.03 SSBOND 6 CYS C 336 CYS C 361 1555 1555 2.03 SSBOND 7 CYS C 379 CYS C 432 1555 1555 2.05 SSBOND 8 CYS C 391 CYS C 525 1555 1555 2.03 SSBOND 9 CYS C 480 CYS C 488 1555 1555 2.03 SSBOND 10 CYS D 22 CYS D 97 1555 1555 2.04 LINK ND2 ASN A 343 C1 NAG E 1 1555 1555 1.44 LINK ND2 ASN C 343 C1 NAG C 601 1555 1555 1.44 LINK O4 NAG E 1 C1 NAG E 2 1555 1555 1.45 CRYST1 78.072 104.827 107.053 90.00 90.00 90.00 P 21 21 21 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 0.012809 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009540 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009341 0.00000