HEADER VIRAL PROTEIN/IMMUNE SYSTEM 22-APR-22 7URS TITLE CRYSTAL STRUCTURE OF SARS-COV-2 S DELTA VARIANT RECEPTOR-BINDING TITLE 2 DOMAIN (RBD) IN COMPLEX COV11 FAB CRYSTAL FORM 2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE PROTEIN S1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: COV11 FAB HEAVY CHAIN; COMPND 8 CHAIN: H; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: COV11 FAB HEAVY CHAIN; COMPND 12 CHAIN: L; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 3 2; SOURCE 4 ORGANISM_TAXID: 2697049; SOURCE 5 GENE: S, 2; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 EXPRESSION_SYSTEM_CELL: HEK 293 GNT1-; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 14 EXPRESSION_SYSTEM_CELL: HEK 293; SOURCE 15 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 16 MOL_ID: 3; SOURCE 17 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 18 ORGANISM_TAXID: 9606; SOURCE 19 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 20 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 21 EXPRESSION_SYSTEM_CELL: HEK 293; SOURCE 22 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS SARS-COV-2 S RBD FAB COMPLEX, SARS-COV-2 S RECEPTOR-BINDING DOMAIN KEYWDS 2 ANTIBODY FAB COMPLEX, COVID-19 SPIKE PROTEIN ANTIBODY FAB COMPLEX, KEYWDS 3 DELTA VARIANT, VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR W.D.TOLBERT,M.PAZGIER REVDAT 4 30-OCT-24 7URS 1 REMARK REVDAT 3 15-NOV-23 7URS 1 JRNL REVDAT 2 18-OCT-23 7URS 1 REMARK REVDAT 1 04-MAY-22 7URS 0 JRNL AUTH W.D.TOLBERT,Y.CHEN,L.SUN,M.BENLARBI,S.DING,R.MANICKAM, JRNL AUTH 2 E.PANGARO,D.N.NGUYEN,S.GOTTUMUKKALA,M.COTE,F.J.GONZALEZ, JRNL AUTH 3 A.FINZI,Z.R.TEHRANI,M.M.SAJADI,M.PAZGIER JRNL TITL THE MOLECULAR BASIS OF THE NEUTRALIZATION BREADTH OF THE JRNL TITL 2 RBD-SPECIFIC ANTIBODY COV11. JRNL REF FRONT IMMUNOL V. 14 78355 2023 JRNL REFN ESSN 1664-3224 JRNL PMID 37334379 JRNL DOI 10.3389/FIMMU.2023.1178355 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.19.1_4122: ???) 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) : 41.05 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.1 REMARK 3 NUMBER OF REFLECTIONS : 34218 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 1718 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 41.0500 - 5.4800 0.98 2987 137 0.1687 0.1885 REMARK 3 2 5.4800 - 4.3500 0.97 2848 170 0.1298 0.1870 REMARK 3 3 4.3500 - 3.8000 0.99 2937 159 0.1426 0.1833 REMARK 3 4 3.8000 - 3.4600 0.97 2857 146 0.1745 0.2204 REMARK 3 5 3.4600 - 3.2100 0.99 2898 142 0.1923 0.2172 REMARK 3 6 3.2100 - 3.0200 0.99 2931 161 0.2106 0.2959 REMARK 3 7 3.0200 - 2.8700 0.98 2854 158 0.2443 0.2864 REMARK 3 8 2.8700 - 2.7400 0.92 2665 155 0.2351 0.3053 REMARK 3 9 2.7400 - 2.6400 0.90 2666 139 0.2383 0.3016 REMARK 3 10 2.6400 - 2.5500 0.85 2487 132 0.2477 0.2705 REMARK 3 11 2.5500 - 2.4700 0.79 2315 116 0.2529 0.2846 REMARK 3 12 2.4700 - 2.4000 0.70 2055 103 0.2613 0.3335 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) : 0.320 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.860 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.010 4900 REMARK 3 ANGLE : 1.156 6663 REMARK 3 CHIRALITY : 0.066 732 REMARK 3 PLANARITY : 0.008 855 REMARK 3 DIHEDRAL : 7.776 687 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'A' AND RESID 336 THROUGH 526) REMARK 3 ORIGIN FOR THE GROUP (A): -29.9222 -28.3506 16.1113 REMARK 3 T TENSOR REMARK 3 T11: 0.3669 T22: 0.3747 REMARK 3 T33: 0.4765 T12: 0.0198 REMARK 3 T13: 0.0108 T23: 0.0408 REMARK 3 L TENSOR REMARK 3 L11: 3.6971 L22: 3.8178 REMARK 3 L33: 4.0795 L12: -0.3168 REMARK 3 L13: -0.7290 L23: 0.3116 REMARK 3 S TENSOR REMARK 3 S11: -0.0579 S12: -0.0854 S13: 0.2653 REMARK 3 S21: -0.1984 S22: -0.0627 S23: -0.7794 REMARK 3 S31: -0.4203 S32: 0.5924 S33: 0.1042 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN 'H' AND RESID 2 THROUGH 214) REMARK 3 ORIGIN FOR THE GROUP (A): -69.7774 -27.9169 39.5788 REMARK 3 T TENSOR REMARK 3 T11: 0.3891 T22: 0.3757 REMARK 3 T33: 0.2686 T12: 0.0307 REMARK 3 T13: -0.0032 T23: 0.0191 REMARK 3 L TENSOR REMARK 3 L11: 3.1015 L22: 0.9197 REMARK 3 L33: 0.3495 L12: -0.8049 REMARK 3 L13: -0.7956 L23: 0.1403 REMARK 3 S TENSOR REMARK 3 S11: -0.1830 S12: -0.2395 S13: -0.0966 REMARK 3 S21: 0.1894 S22: 0.1244 S23: 0.0290 REMARK 3 S31: 0.1158 S32: -0.0261 S33: 0.0409 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN 'L' AND RESID 1 THROUGH 214) REMARK 3 ORIGIN FOR THE GROUP (A): -76.3881 -17.6857 25.5407 REMARK 3 T TENSOR REMARK 3 T11: 0.3429 T22: 0.4085 REMARK 3 T33: 0.2713 T12: 0.0142 REMARK 3 T13: -0.0272 T23: 0.0376 REMARK 3 L TENSOR REMARK 3 L11: 3.5974 L22: 1.6923 REMARK 3 L33: 0.4162 L12: -1.5580 REMARK 3 L13: -1.0047 L23: 0.4646 REMARK 3 S TENSOR REMARK 3 S11: 0.0792 S12: 0.2935 S13: 0.1193 REMARK 3 S21: -0.1143 S22: -0.0578 S23: -0.0300 REMARK 3 S31: 0.0252 S32: 0.0357 S33: -0.0216 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 7URS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-APR-22. REMARK 100 THE DEPOSITION ID IS D_1000264752. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-MAR-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL12-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : SI (1 1 1) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34224 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 (%) : 92.3 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.12600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.5000 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) : 2.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 72.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : 0.38000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.050 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: 7S4S REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12% PEG 8000 0.1 M SODIUM PHOSPHATE PH REMARK 280 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294K 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 97.23350 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.31300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 97.23350 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 43.31300 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6940 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26740 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -51.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 ASN A 334 REMARK 465 LEU A 335 REMARK 465 HIS A 519 REMARK 465 ALA A 520 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 GLU H 1 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 GLY H 133 REMARK 465 SER H 215 REMARK 465 CYS H 216 REMARK 465 CYS L 215 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 ASN L 153 O HOH L 401 2.14 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 50.58 -111.19 REMARK 500 ALA A 363 -86.79 -82.30 REMARK 500 ASP A 364 110.52 63.42 REMARK 500 PHE A 377 85.12 -154.13 REMARK 500 VAL A 382 -117.59 -130.98 REMARK 500 SER A 383 118.05 166.73 REMARK 500 LYS A 386 46.33 -89.44 REMARK 500 ASP A 389 48.46 -104.63 REMARK 500 ASN A 422 -59.17 -129.45 REMARK 500 ASP A 428 36.84 -96.27 REMARK 500 ARG A 457 128.44 -170.72 REMARK 500 LYS H 43 -164.25 -120.73 REMARK 500 GLU H 97 -135.21 51.84 REMARK 500 ALA H 100A -151.96 55.97 REMARK 500 SER H 112 -54.63 -137.78 REMARK 500 PRO L 45 151.41 -46.48 REMARK 500 ALA L 52 -36.77 63.52 REMARK 500 ARG L 78 74.09 58.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7S4S RELATED DB: PDB REMARK 900 COV11 FAB BOUND TO WILD TYPE SARS-COV-2 RECEPTOR BINDING DOMAIN DBREF 7URS A 319 541 UNP P0DTC2 SPIKE_SARS2 319 541 DBREF 7URS H 1 216 PDB 7URS 7URS 1 216 DBREF 7URS L 1 215 PDB 7URS 7URS 1 215 SEQADV 7URS ARG A 452 UNP P0DTC2 LEU 452 ENGINEERED MUTATION SEQADV 7URS LYS A 478 UNP P0DTC2 THR 478 ENGINEERED MUTATION SEQADV 7URS SER A 542 UNP P0DTC2 EXPRESSION TAG SEQADV 7URS GLY A 543 UNP P0DTC2 EXPRESSION TAG SEQADV 7URS HIS A 544 UNP P0DTC2 EXPRESSION TAG SEQADV 7URS HIS A 545 UNP P0DTC2 EXPRESSION TAG SEQADV 7URS HIS A 546 UNP P0DTC2 EXPRESSION TAG SEQADV 7URS HIS A 547 UNP P0DTC2 EXPRESSION TAG SEQADV 7URS HIS A 548 UNP P0DTC2 EXPRESSION TAG SEQADV 7URS 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 ARG 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 LYS 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 H 221 GLU VAL GLN LEU VAL GLU SER GLY GLY GLY LEU ILE GLN SEQRES 2 H 221 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 H 221 PHE ILE VAL SER ARG ASN TYR MET ILE TRP VAL ARG GLN SEQRES 4 H 221 ALA PRO GLY LYS GLY LEU GLU TRP VAL SER VAL ILE TYR SEQRES 5 H 221 SER GLY GLY SER THR PHE TYR ALA ASP SER VAL LYS GLY SEQRES 6 H 221 ARG PHE THR ILE SER ARG ASP ASN SER LYS ASN THR LEU SEQRES 7 H 221 TYR LEU GLN MET ASN SER LEU ARG ALA GLU ASP THR ALA SEQRES 8 H 221 VAL TYR TYR CYS ALA ARG ASP LEU GLU VAL ALA GLY ALA SEQRES 9 H 221 ILE ASP TYR TRP GLY GLN GLY THR LEU VAL THR VAL SER SEQRES 10 H 221 SER ALA SER THR LYS GLY PRO SER VAL PHE PRO LEU ALA SEQRES 11 H 221 PRO SER SER LYS SER THR SER GLY GLY THR ALA ALA LEU SEQRES 12 H 221 GLY CYS LEU VAL LYS ASP TYR PHE PRO GLU PRO VAL THR SEQRES 13 H 221 VAL SER TRP ASN SER GLY ALA LEU THR SER GLY VAL HIS SEQRES 14 H 221 THR PHE PRO ALA VAL LEU GLN SER SER GLY LEU TYR SER SEQRES 15 H 221 LEU SER SER VAL VAL THR VAL PRO SER SER SER LEU GLY SEQRES 16 H 221 THR GLN THR TYR ILE CYS ASN VAL ASN HIS LYS PRO SER SEQRES 17 H 221 ASN THR LYS VAL ASP LYS LYS VAL GLU PRO LYS SER CYS SEQRES 1 L 216 GLU ILE VAL LEU THR GLN SER PRO GLY THR LEU SER LEU SEQRES 2 L 216 SER PRO GLY GLU ARG ALA THR LEU SER CYS ARG ALA SER SEQRES 3 L 216 GLN SER ILE SER SER SER TYR LEU ALA TRP TYR GLN GLN SEQRES 4 L 216 LYS PRO GLY GLN ALA PRO ARG LEU LEU ILE TYR GLY ALA SEQRES 5 L 216 THR SER ARG ALA THR GLY THR PRO ASP ARG PHE SER GLY SEQRES 6 L 216 SER GLY SER GLY THR ASP PHE THR LEU THR ILE ASN ARG SEQRES 7 L 216 LEU GLU PRO GLU ASP PHE ALA VAL TYR TYR CYS GLN GLN SEQRES 8 L 216 TYR GLY SER SER PRO GLY TYR THR PHE GLY GLN GLY THR SEQRES 9 L 216 LYS LEU GLU ILE LYS ARG THR VAL ALA ALA PRO SER VAL SEQRES 10 L 216 PHE ILE PHE PRO PRO SER ASP GLU GLN LEU LYS SER GLY SEQRES 11 L 216 THR ALA SER VAL VAL CYS LEU LEU ASN ASN PHE TYR PRO SEQRES 12 L 216 ARG GLU ALA LYS VAL GLN TRP LYS VAL ASP ASN ALA LEU SEQRES 13 L 216 GLN SER GLY ASN SER GLN GLU SER VAL THR GLU GLN ASP SEQRES 14 L 216 SER ARG ASP SER THR TYR SER LEU GLY SER THR LEU THR SEQRES 15 L 216 LEU SER LYS ALA ASP TYR GLU LYS HIS LYS VAL TYR ALA SEQRES 16 L 216 CYS GLU VAL THR HIS GLN GLY LEU SER SER PRO VAL THR SEQRES 17 L 216 LYS SER PHE ASN ARG GLY GLU CYS HET NAG A1001 14 HET PO4 A1002 5 HET PO4 A1003 5 HET MPD A1004 8 HET MPD L 301 8 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM PO4 PHOSPHATE ION HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL 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 4 NAG C8 H15 N O6 FORMUL 5 PO4 2(O4 P 3-) FORMUL 7 MPD 2(C6 H14 O2) FORMUL 9 HOH *85(H2 O) HELIX 1 AA1 PHE A 338 ASN A 343 1 6 HELIX 2 AA2 SER A 349 TRP A 353 5 5 HELIX 3 AA3 TYR A 365 ASN A 370 1 6 HELIX 4 AA4 PRO A 384 ASN A 388 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 ILE H 28 ASN H 32 5 5 HELIX 10 AB1 ASP H 61 LYS H 64 5 4 HELIX 11 AB2 ARG H 83 THR H 87 5 5 HELIX 12 AB3 LEU H 96 GLY H 100 5 5 HELIX 13 AB4 SER H 156 ALA H 158 5 3 HELIX 14 AB5 SER H 187 GLY H 190 5 4 HELIX 15 AB6 LYS H 201 ASN H 204 5 4 HELIX 16 AB7 SER L 30 SER L 32 5 3 HELIX 17 AB8 GLU L 80 PHE L 84 5 5 HELIX 18 AB9 SER L 122 SER L 128 1 7 HELIX 19 AC1 LYS L 184 LYS L 189 1 6 SHEET 1 AA1 5 ASN A 354 ILE A 358 0 SHEET 2 AA1 5 ASN A 394 ARG A 403 -1 O VAL A 395 N ILE A 358 SHEET 3 AA1 5 PRO A 507 GLU A 516 -1 O VAL A 510 N PHE A 400 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 TYR A 380 O GLY A 431 SHEET 1 AA2 3 CYS A 361 VAL A 362 0 SHEET 2 AA2 3 VAL A 524 CYS A 525 1 O CYS A 525 N CYS A 361 SHEET 3 AA2 3 CYS A 391 PHE A 392 -1 N PHE A 392 O VAL A 524 SHEET 1 AA3 2 ARG 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 H 3 SER H 7 0 SHEET 2 AA5 4 LEU H 18 SER H 25 -1 O ALA H 23 N VAL H 5 SHEET 3 AA5 4 THR H 77 MET H 82 -1 O MET H 82 N LEU H 18 SHEET 4 AA5 4 PHE H 67 ASP H 72 -1 N THR H 68 O GLN H 81 SHEET 1 AA6 6 GLY H 10 ILE H 12 0 SHEET 2 AA6 6 THR H 107 VAL H 111 1 O THR H 110 N GLY H 10 SHEET 3 AA6 6 ALA H 88 ASP H 95 -1 N TYR H 90 O THR H 107 SHEET 4 AA6 6 TYR H 33 GLN H 39 -1 N VAL H 37 O TYR H 91 SHEET 5 AA6 6 LEU H 45 ILE H 51 -1 O GLU H 46 N ARG H 38 SHEET 6 AA6 6 THR H 57 TYR H 59 -1 O PHE H 58 N VAL H 50 SHEET 1 AA7 4 GLY H 10 ILE H 12 0 SHEET 2 AA7 4 THR H 107 VAL H 111 1 O THR H 110 N GLY H 10 SHEET 3 AA7 4 ALA H 88 ASP H 95 -1 N TYR H 90 O THR H 107 SHEET 4 AA7 4 TYR H 102 TRP H 103 -1 O TYR H 102 N ARG H 94 SHEET 1 AA8 4 SER H 120 LEU H 124 0 SHEET 2 AA8 4 THR H 135 TYR H 145 -1 O LEU H 141 N PHE H 122 SHEET 3 AA8 4 TYR H 176 PRO H 185 -1 O TYR H 176 N TYR H 145 SHEET 4 AA8 4 VAL H 163 THR H 165 -1 N HIS H 164 O VAL H 181 SHEET 1 AA9 4 SER H 120 LEU H 124 0 SHEET 2 AA9 4 THR H 135 TYR H 145 -1 O LEU H 141 N PHE H 122 SHEET 3 AA9 4 TYR H 176 PRO H 185 -1 O TYR H 176 N TYR H 145 SHEET 4 AA9 4 VAL H 169 LEU H 170 -1 N VAL H 169 O SER H 177 SHEET 1 AB1 3 THR H 151 TRP H 154 0 SHEET 2 AB1 3 ILE H 195 HIS H 200 -1 O ASN H 197 N SER H 153 SHEET 3 AB1 3 THR H 205 LYS H 210 -1 O THR H 205 N HIS H 200 SHEET 1 AB2 3 LEU L 4 SER L 7 0 SHEET 2 AB2 3 ALA L 20 ILE L 29 -1 O SER L 23 N SER L 7 SHEET 3 AB2 3 PHE L 63 ILE L 76 -1 O LEU L 74 N LEU L 22 SHEET 1 AB3 6 THR L 10 LEU L 14 0 SHEET 2 AB3 6 THR L 104 ILE L 108 1 O GLU L 107 N LEU L 12 SHEET 3 AB3 6 ALA L 85 GLN L 91 -1 N TYR L 87 O THR L 104 SHEET 4 AB3 6 LEU L 34 GLN L 39 -1 N GLN L 39 O VAL L 86 SHEET 5 AB3 6 ARG L 46 TYR L 50 -1 O LEU L 48 N TRP L 36 SHEET 6 AB3 6 SER L 54 ARG L 55 -1 O SER L 54 N TYR L 50 SHEET 1 AB4 4 THR L 10 LEU L 14 0 SHEET 2 AB4 4 THR L 104 ILE L 108 1 O GLU L 107 N LEU L 12 SHEET 3 AB4 4 ALA L 85 GLN L 91 -1 N TYR L 87 O THR L 104 SHEET 4 AB4 4 THR L 99 PHE L 100 -1 O THR L 99 N GLN L 91 SHEET 1 AB5 4 SER L 115 PHE L 119 0 SHEET 2 AB5 4 THR L 130 PHE L 140 -1 O LEU L 136 N PHE L 117 SHEET 3 AB5 4 TYR L 174 SER L 183 -1 O TYR L 174 N PHE L 140 SHEET 4 AB5 4 SER L 160 VAL L 164 -1 N GLN L 161 O THR L 179 SHEET 1 AB6 4 ALA L 154 GLN L 156 0 SHEET 2 AB6 4 LYS L 146 VAL L 151 -1 N TRP L 149 O GLN L 156 SHEET 3 AB6 4 VAL L 192 THR L 198 -1 O ALA L 194 N LYS L 150 SHEET 4 AB6 4 VAL L 206 ASN L 211 -1 O VAL L 206 N VAL L 197 SSBOND 1 CYS A 336 CYS A 361 1555 1555 2.04 SSBOND 2 CYS A 379 CYS A 432 1555 1555 2.06 SSBOND 3 CYS A 391 CYS A 525 1555 1555 2.04 SSBOND 4 CYS A 480 CYS A 488 1555 1555 2.07 SSBOND 5 CYS H 22 CYS H 92 1555 1555 2.07 SSBOND 6 CYS H 140 CYS H 196 1555 1555 2.02 SSBOND 7 CYS L 24 CYS L 89 1555 1555 2.08 SSBOND 8 CYS L 135 CYS L 195 1555 1555 2.06 LINK ND2 ASN A 343 C1 NAG A1001 1555 1555 1.46 CISPEP 1 PHE H 146 PRO H 147 0 -8.37 CISPEP 2 GLU H 148 PRO H 149 0 -4.64 CISPEP 3 SER L 7 PRO L 8 0 -9.83 CISPEP 4 SER L 95 PRO L 96 0 7.04 CISPEP 5 TYR L 141 PRO L 142 0 0.55 CRYST1 194.467 86.626 57.718 90.00 99.85 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 0.005142 0.000000 0.000892 0.00000 SCALE2 0.000000 0.011544 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017585 0.00000