HEADER VIRAL PROTEIN/IMMUNE SYSTEM 22-APR-22 7URQ TITLE CRYSTAL STRUCTURE OF SARS-COV-2 S DELTA VARIANT RECEPTOR-BINDING TITLE 2 DOMAIN (RBD) IN COMPLEX COV11 FAB CRYSTAL FORM 1 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 LIGHT 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 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 15 EXPRESSION_SYSTEM_CELL: HEK 293; SOURCE 16 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 17 MOL_ID: 3; SOURCE 18 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 19 ORGANISM_TAXID: 9606; SOURCE 20 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 21 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 22 EXPRESSION_SYSTEM_CELL: HEK 293; SOURCE 23 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 3 15-NOV-23 7URQ 1 JRNL REVDAT 2 18-OCT-23 7URQ 1 REMARK REVDAT 1 04-MAY-22 7URQ 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. 2.05 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) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.23 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.8 REMARK 3 NUMBER OF REFLECTIONS : 59746 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.130 REMARK 3 FREE R VALUE TEST SET COUNT : 3067 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 41.2300 - 5.7100 0.99 2944 175 0.1679 0.1832 REMARK 3 2 5.7100 - 4.5300 0.98 2795 150 0.1306 0.1471 REMARK 3 3 4.5300 - 3.9600 1.00 2816 152 0.1304 0.1565 REMARK 3 4 3.9600 - 3.6000 0.98 2770 132 0.1474 0.1980 REMARK 3 5 3.6000 - 3.3400 1.00 2783 148 0.1663 0.1928 REMARK 3 6 3.3400 - 3.1400 1.00 2770 160 0.1759 0.2128 REMARK 3 7 3.1400 - 2.9900 1.00 2772 145 0.1793 0.2168 REMARK 3 8 2.9900 - 2.8600 1.00 2743 163 0.2083 0.2367 REMARK 3 9 2.8600 - 2.7500 0.97 2685 158 0.2147 0.2259 REMARK 3 10 2.7500 - 2.6500 1.00 2777 141 0.2070 0.2227 REMARK 3 11 2.6500 - 2.5700 1.00 2742 149 0.2033 0.2640 REMARK 3 12 2.5700 - 2.5000 1.00 2708 166 0.2068 0.2322 REMARK 3 13 2.5000 - 2.4300 0.99 2728 151 0.2123 0.2687 REMARK 3 14 2.4300 - 2.3700 0.96 2647 142 0.2273 0.3028 REMARK 3 15 2.3700 - 2.3200 0.94 2592 124 0.2517 0.3096 REMARK 3 16 2.3200 - 2.2700 0.88 2432 123 0.2654 0.3298 REMARK 3 17 2.2700 - 2.2200 0.87 2411 120 0.2595 0.2884 REMARK 3 18 2.2200 - 2.1800 0.84 2277 120 0.2521 0.2843 REMARK 3 19 2.1800 - 2.1400 0.81 2204 140 0.2654 0.3081 REMARK 3 20 2.1400 - 2.1000 0.78 2141 103 0.2689 0.2948 REMARK 3 21 2.1000 - 2.0700 0.76 2063 120 0.2819 0.2909 REMARK 3 22 2.0700 - 2.0500 0.68 1879 85 0.2904 0.2868 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.850 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 : 0.008 4968 REMARK 3 ANGLE : 1.010 6755 REMARK 3 CHIRALITY : 0.061 741 REMARK 3 PLANARITY : 0.006 876 REMARK 3 DIHEDRAL : 7.356 700 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 334 THROUGH 529) REMARK 3 ORIGIN FOR THE GROUP (A): 16.4873 31.9571 4.3753 REMARK 3 T TENSOR REMARK 3 T11: 0.3609 T22: 0.3254 REMARK 3 T33: 0.2646 T12: -0.0064 REMARK 3 T13: -0.0332 T23: -0.0069 REMARK 3 L TENSOR REMARK 3 L11: 1.9022 L22: 5.6319 REMARK 3 L33: 3.1822 L12: -0.2902 REMARK 3 L13: -0.0819 L23: 0.9971 REMARK 3 S TENSOR REMARK 3 S11: -0.0140 S12: -0.1378 S13: 0.3542 REMARK 3 S21: -0.1874 S22: 0.0224 S23: -0.0002 REMARK 3 S31: -0.5933 S32: -0.0286 S33: -0.0042 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN 'H' AND RESID 1 THROUGH 214) REMARK 3 ORIGIN FOR THE GROUP (A): 27.0367 -11.1639 16.2037 REMARK 3 T TENSOR REMARK 3 T11: 0.2326 T22: 0.3097 REMARK 3 T33: 0.2493 T12: -0.0010 REMARK 3 T13: 0.0318 T23: -0.0392 REMARK 3 L TENSOR REMARK 3 L11: 0.4618 L22: 3.3453 REMARK 3 L33: 1.7485 L12: -0.4515 REMARK 3 L13: 0.3192 L23: -1.4174 REMARK 3 S TENSOR REMARK 3 S11: -0.0104 S12: 0.0983 S13: -0.1035 REMARK 3 S21: -0.2231 S22: -0.0599 S23: -0.1204 REMARK 3 S31: 0.3321 S32: -0.0113 S33: 0.0778 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN 'L' AND RESID 1 THROUGH 214) REMARK 3 ORIGIN FOR THE GROUP (A): 11.7022 -14.6649 26.7657 REMARK 3 T TENSOR REMARK 3 T11: 0.2548 T22: 0.3197 REMARK 3 T33: 0.2771 T12: -0.0573 REMARK 3 T13: 0.0293 T23: -0.0109 REMARK 3 L TENSOR REMARK 3 L11: 0.7077 L22: 4.0957 REMARK 3 L33: 1.8173 L12: -1.3473 REMARK 3 L13: 0.8996 L23: -1.9660 REMARK 3 S TENSOR REMARK 3 S11: 0.0472 S12: -0.0352 S13: -0.1516 REMARK 3 S21: -0.0562 S22: 0.0823 S23: 0.2856 REMARK 3 S31: 0.2551 S32: -0.2144 S33: -0.1287 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 7URQ 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_1000264750. 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 : 5.5 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 : 59785 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 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 (%) : 93.3 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : 0.12800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.09 REMARK 200 COMPLETENESS FOR SHELL (%) : 74.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.82700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.300 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 (%): 64.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% PEG 4000 0.2 M SODIUM ACETATE 0.1 REMARK 280 M SODIUM CITRATE PH 5.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 2 21 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,-Z+1/2 REMARK 290 4555 -X+1/2,-Y,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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 42.90900 REMARK 290 SMTRY2 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 56.05200 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 42.90900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 56.05200 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: 6270 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26970 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 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 GLY A 317 REMARK 465 SER A 318 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 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 LEU A 538 REMARK 465 GLU A 539 REMARK 465 HIS A 540 REMARK 465 HIS A 541 REMARK 465 HIS A 542 REMARK 465 HIS A 543 REMARK 465 HIS A 544 REMARK 465 HIS A 545 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: 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 363 -76.87 -68.42 REMARK 500 ASP A 364 75.19 64.67 REMARK 500 PHE A 377 85.68 -150.25 REMARK 500 ASN A 422 -51.19 -126.40 REMARK 500 LEU A 518 -115.16 -90.43 REMARK 500 HIS A 519 53.36 -150.82 REMARK 500 LYS A 528 33.97 -88.58 REMARK 500 ALA H 88 169.19 177.62 REMARK 500 GLU H 97 -134.85 53.08 REMARK 500 ALA H 100A -155.27 58.92 REMARK 500 ALA L 52 -39.38 68.90 REMARK 500 ALA L 85 176.43 175.81 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 H 486 DISTANCE = 6.53 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7S4S RELATED DB: PDB REMARK 900 CONTAINS SAME COV11 FAB IN COMPLEX WITH WILD TYPE SARS-COV-2 RBD DBREF 7URQ A 319 537 UNP P0DTC2 SPIKE_SARS2 319 537 DBREF 7URQ H 1 216 PDB 7URQ 7URQ 1 216 DBREF 7URQ L 1 215 PDB 7URQ 7URQ 1 215 SEQADV 7URQ GLY A 317 UNP P0DTC2 EXPRESSION TAG SEQADV 7URQ SER A 318 UNP P0DTC2 EXPRESSION TAG SEQADV 7URQ ARG A 452 UNP P0DTC2 LEU 452 ENGINEERED MUTATION SEQADV 7URQ LYS A 478 UNP P0DTC2 THR 478 ENGINEERED MUTATION SEQADV 7URQ LEU A 538 UNP P0DTC2 EXPRESSION TAG SEQADV 7URQ GLU A 539 UNP P0DTC2 EXPRESSION TAG SEQADV 7URQ HIS A 540 UNP P0DTC2 EXPRESSION TAG SEQADV 7URQ HIS A 541 UNP P0DTC2 EXPRESSION TAG SEQADV 7URQ HIS A 542 UNP P0DTC2 EXPRESSION TAG SEQADV 7URQ HIS A 543 UNP P0DTC2 EXPRESSION TAG SEQADV 7URQ HIS A 544 UNP P0DTC2 EXPRESSION TAG SEQADV 7URQ HIS A 545 UNP P0DTC2 EXPRESSION TAG SEQRES 1 A 229 GLY SER ARG VAL GLN PRO THR GLU SER ILE VAL ARG PHE SEQRES 2 A 229 PRO ASN ILE THR ASN LEU CYS PRO PHE GLY GLU VAL PHE SEQRES 3 A 229 ASN ALA THR ARG PHE ALA SER VAL TYR ALA TRP ASN ARG SEQRES 4 A 229 LYS ARG ILE SER ASN CYS VAL ALA ASP TYR SER VAL LEU SEQRES 5 A 229 TYR ASN SER ALA SER PHE SER THR PHE LYS CYS TYR GLY SEQRES 6 A 229 VAL SER PRO THR LYS LEU ASN ASP LEU CYS PHE THR ASN SEQRES 7 A 229 VAL TYR ALA ASP SER PHE VAL ILE ARG GLY ASP GLU VAL SEQRES 8 A 229 ARG GLN ILE ALA PRO GLY GLN THR GLY LYS ILE ALA ASP SEQRES 9 A 229 TYR ASN TYR LYS LEU PRO ASP ASP PHE THR GLY CYS VAL SEQRES 10 A 229 ILE ALA TRP ASN SER ASN ASN LEU ASP SER LYS VAL GLY SEQRES 11 A 229 GLY ASN TYR ASN TYR ARG TYR ARG LEU PHE ARG LYS SER SEQRES 12 A 229 ASN LEU LYS PRO PHE GLU ARG ASP ILE SER THR GLU ILE SEQRES 13 A 229 TYR GLN ALA GLY SER LYS PRO CYS ASN GLY VAL GLU GLY SEQRES 14 A 229 PHE ASN CYS TYR PHE PRO LEU GLN SER TYR GLY PHE GLN SEQRES 15 A 229 PRO THR ASN GLY VAL GLY TYR GLN PRO TYR ARG VAL VAL SEQRES 16 A 229 VAL LEU SER PHE GLU LEU LEU HIS ALA PRO ALA THR VAL SEQRES 17 A 229 CYS GLY PRO LYS LYS SER THR ASN LEU VAL LYS ASN LYS SEQRES 18 A 229 LEU GLU 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 CIT H 301 13 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM CIT CITRIC ACID 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 CIT C6 H8 O7 FORMUL 6 HOH *243(H2 O) 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 TYR A 365 ASN A 370 1 6 HELIX 4 AA4 LYS A 386 ASP A 389 5 4 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 ARG H 83 THR H 87 5 5 HELIX 11 AB2 GLU H 97 GLY H 100 5 4 HELIX 12 AB3 SER H 156 ALA H 158 5 3 HELIX 13 AB4 SER H 187 GLN H 192 1 6 HELIX 14 AB5 LYS H 201 ASN H 204 5 4 HELIX 15 AB6 SER L 30 SER L 32 5 3 HELIX 16 AB7 GLU L 80 PHE L 84 5 5 HELIX 17 AB8 SER L 122 SER L 128 1 7 HELIX 18 AB9 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 CYS A 432 O LEU A 513 SHEET 5 AA1 5 THR A 376 TYR A 380 -1 N LYS A 378 O VAL A 433 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 SER H 21 N SER H 7 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 SER H 70 O TYR H 79 SHEET 1 AA6 6 LEU H 11 ILE H 12 0 SHEET 2 AA6 6 THR H 107 VAL H 111 1 O THR H 110 N ILE H 12 SHEET 3 AA6 6 ALA H 88 ASP H 95 -1 N ALA H 88 O VAL H 109 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 LEU H 11 ILE H 12 0 SHEET 2 AA7 4 THR H 107 VAL H 111 1 O THR H 110 N ILE H 12 SHEET 3 AA7 4 ALA H 88 ASP H 95 -1 N ALA H 88 O VAL H 109 SHEET 4 AA7 4 ILE H 100B 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 TYR H 194 HIS H 200 -1 O ASN H 197 N SER H 153 SHEET 3 AB1 3 THR H 205 VAL H 211 -1 O VAL H 207 N VAL H 198 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 ALA L 85 O LEU L 106 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 ALA L 85 O LEU L 106 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 LEU L 176 N LEU L 137 SHEET 4 AB5 4 SER L 160 VAL L 164 -1 N SER L 163 O GLY L 177 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 2.07 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 2.08 SSBOND 6 CYS H 140 CYS H 196 1555 1555 2.04 SSBOND 7 CYS L 24 CYS L 89 1555 1555 2.12 SSBOND 8 CYS L 135 CYS L 195 1555 1555 2.06 LINK ND2 ASN A 343 C1 NAG A1001 1555 1555 1.45 CISPEP 1 PHE H 146 PRO H 147 0 -5.63 CISPEP 2 GLU H 148 PRO H 149 0 -7.20 CISPEP 3 SER L 7 PRO L 8 0 -2.35 CISPEP 4 SER L 95 PRO L 96 0 10.64 CISPEP 5 TYR L 141 PRO L 142 0 2.18 CRYST1 85.818 103.551 112.104 90.00 90.00 90.00 P 21 2 21 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 0.011653 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009657 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008920 0.00000