HEADER VIRAL PROTEIN 19-JUN-20 7CDJ TITLE CRYSTAL STRUCTURE OF SARS-COV-2 ANTIBODY P2C-1A3 WITH RBD COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE PROTEIN S1; COMPND 3 CHAIN: E; COMPND 4 FRAGMENT: RECEPTOR BINDING DOMAIN; COMPND 5 SYNONYM: S GLYCOPROTEIN,E2,PEPLOMER PROTEIN; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: ANTIBODY P2C-1A3 HEAVY CHAIN; COMPND 9 CHAIN: H; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: ANTIBODY P2C-1A3 LIGHT CHAIN; COMPND 13 CHAIN: L; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 3 2; SOURCE 4 ORGANISM_COMMON: 2019-NCOV; SOURCE 5 ORGANISM_TAXID: 2697049; SOURCE 6 GENE: S, 2; SOURCE 7 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 14 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 16 EXPRESSION_SYSTEM_CELL_LINE: HEK 293F; SOURCE 17 MOL_ID: 3; SOURCE 18 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 19 ORGANISM_COMMON: HUMAN; SOURCE 20 ORGANISM_TAXID: 9606; SOURCE 21 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 22 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 23 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 24 EXPRESSION_SYSTEM_CELL_LINE: HEK 293F KEYWDS SPIKE, RECEPTOR BINDING DOMAIN, ANTIBODY, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR X.WANG,L.ZHANG,J.GE,R.WANG REVDAT 4 06-NOV-24 7CDJ 1 REMARK REVDAT 3 29-NOV-23 7CDJ 1 REMARK REVDAT 2 01-DEC-21 7CDJ 1 JRNL REVDAT 1 18-NOV-20 7CDJ 0 JRNL AUTH J.GE,R.WANG,B.JU,Q.ZHANG,J.SUN,P.CHEN,S.ZHANG,Y.TIAN,S.SHAN, JRNL AUTH 2 L.CHENG,B.ZHOU,S.SONG,J.ZHAO,H.WANG,X.SHI,Q.DING,L.LIU, JRNL AUTH 3 J.ZHAO,Z.ZHANG,X.WANG,L.ZHANG JRNL TITL ANTIBODY NEUTRALIZATION OF SARS-COV-2 THROUGH ACE2 RECEPTOR JRNL TITL 2 MIMICRY. JRNL REF NAT COMMUN V. 12 250 2021 JRNL REFN ESSN 2041-1723 JRNL PMID 33431856 JRNL DOI 10.1038/S41467-020-20501-9 REMARK 2 REMARK 2 RESOLUTION. 3.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15_3459 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) : 3.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.31 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 15025 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.233 REMARK 3 R VALUE (WORKING SET) : 0.231 REMARK 3 FREE R VALUE : 0.271 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.710 REMARK 3 FREE R VALUE TEST SET COUNT : 707 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 20.3119 - 5.7719 1.00 3102 161 0.1997 0.2403 REMARK 3 2 5.7719 - 4.5988 1.00 2915 139 0.2175 0.2665 REMARK 3 3 4.5988 - 4.0226 0.99 2845 143 0.2192 0.2745 REMARK 3 4 4.0226 - 3.6572 0.99 2808 139 0.2879 0.3184 REMARK 3 5 3.6572 - 3.3963 0.94 2648 125 0.3529 0.3742 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) : 0.430 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 35.190 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 125.6 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN E REMARK 3 ORIGIN FOR THE GROUP (A): -35.8218 28.5826 -18.5421 REMARK 3 T TENSOR REMARK 3 T11: 0.7371 T22: 1.0161 REMARK 3 T33: 0.8000 T12: 0.0364 REMARK 3 T13: -0.0173 T23: -0.0594 REMARK 3 L TENSOR REMARK 3 L11: 4.8917 L22: 3.8289 REMARK 3 L33: 8.5416 L12: 0.9994 REMARK 3 L13: -0.5661 L23: -1.1230 REMARK 3 S TENSOR REMARK 3 S11: 0.3075 S12: -0.3360 S13: -0.3837 REMARK 3 S21: -0.2020 S22: -0.1105 S23: -0.1804 REMARK 3 S31: 0.1521 S32: 0.1388 S33: -0.2147 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN H AND RESID 1:119 REMARK 3 ORIGIN FOR THE GROUP (A): -61.5514 19.2629 4.1683 REMARK 3 T TENSOR REMARK 3 T11: 0.5705 T22: 1.1683 REMARK 3 T33: 0.9756 T12: -0.0891 REMARK 3 T13: -0.0529 T23: 0.0886 REMARK 3 L TENSOR REMARK 3 L11: 3.7358 L22: 5.1567 REMARK 3 L33: 3.8540 L12: -0.1730 REMARK 3 L13: -1.5713 L23: -0.3732 REMARK 3 S TENSOR REMARK 3 S11: 0.0148 S12: 0.7178 S13: 0.2915 REMARK 3 S21: -0.1603 S22: -0.2775 S23: -0.2019 REMARK 3 S31: 0.3251 S32: 0.4609 S33: 0.2887 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN H AND RESID 120:216 REMARK 3 ORIGIN FOR THE GROUP (A): -89.9734 22.3081 18.0529 REMARK 3 T TENSOR REMARK 3 T11: 0.9201 T22: 1.4819 REMARK 3 T33: 1.1386 T12: -0.1405 REMARK 3 T13: -0.0843 T23: 0.1041 REMARK 3 L TENSOR REMARK 3 L11: 3.3648 L22: 3.2472 REMARK 3 L33: 3.0507 L12: 1.2215 REMARK 3 L13: 1.5671 L23: 1.6619 REMARK 3 S TENSOR REMARK 3 S11: -0.0963 S12: -0.0063 S13: -0.6003 REMARK 3 S21: -0.2318 S22: 0.1668 S23: 0.4361 REMARK 3 S31: -0.1769 S32: -0.7652 S33: -0.0842 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN L AND RESID -1:106 REMARK 3 ORIGIN FOR THE GROUP (A): -56.6857 22.8163 25.4844 REMARK 3 T TENSOR REMARK 3 T11: 0.6726 T22: 1.0362 REMARK 3 T33: 0.9268 T12: -0.0813 REMARK 3 T13: -0.1462 T23: 0.1937 REMARK 3 L TENSOR REMARK 3 L11: 2.3409 L22: 2.0067 REMARK 3 L33: 5.2458 L12: 0.5445 REMARK 3 L13: -1.2468 L23: 0.7052 REMARK 3 S TENSOR REMARK 3 S11: -0.1070 S12: -0.5190 S13: 0.0346 REMARK 3 S21: -0.1902 S22: 0.0150 S23: 0.0823 REMARK 3 S31: 0.3192 S32: -0.5682 S33: 0.1377 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN L AND RESID 107:211 REMARK 3 ORIGIN FOR THE GROUP (A): -92.2174 13.3825 31.9729 REMARK 3 T TENSOR REMARK 3 T11: 0.9746 T22: 1.5469 REMARK 3 T33: 1.3030 T12: -0.3625 REMARK 3 T13: -0.1390 T23: 0.3374 REMARK 3 L TENSOR REMARK 3 L11: 3.2905 L22: 1.4293 REMARK 3 L33: 6.6717 L12: -0.5757 REMARK 3 L13: 3.0896 L23: 1.8447 REMARK 3 S TENSOR REMARK 3 S11: 0.5198 S12: 0.0093 S13: -0.2659 REMARK 3 S21: 0.1414 S22: -0.1901 S23: 0.5867 REMARK 3 S31: 0.7106 S32: -0.7137 S33: -0.2594 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 7CDJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-JUN-20. REMARK 100 THE DEPOSITION ID IS D_1300017396. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-MAY-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 : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9796 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 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15108 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.396 REMARK 200 RESOLUTION RANGE LOW (A) : 20.312 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 8.700 REMARK 200 R MERGE (I) : 0.11800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.48 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.93300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: 6M0J REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M LITHIUM SULFATE MONOHYDRATE, 0.1M REMARK 280 CITRIC ACID, PH 3.5, 18% PEG 6000, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 145.97433 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 291.94867 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 218.96150 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 364.93583 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 72.98717 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 145.97433 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 291.94867 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 364.93583 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 218.96150 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 72.98717 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: 5300 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27710 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -30.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, 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 E 319 REMARK 465 VAL E 320 REMARK 465 GLN E 321 REMARK 465 PRO E 322 REMARK 465 THR E 323 REMARK 465 GLU E 324 REMARK 465 SER E 325 REMARK 465 ILE E 326 REMARK 465 VAL E 327 REMARK 465 ARG E 328 REMARK 465 PHE E 329 REMARK 465 PRO E 330 REMARK 465 ASN E 331 REMARK 465 ILE E 332 REMARK 465 PRO E 527 REMARK 465 LYS E 528 REMARK 465 LYS E 529 REMARK 465 HIS E 530 REMARK 465 HIS E 531 REMARK 465 HIS E 532 REMARK 465 HIS E 533 REMARK 465 HIS E 534 REMARK 465 HIS E 535 REMARK 465 SER H 134 REMARK 465 LYS H 135 REMARK 465 SER H 136 REMARK 465 THR H 137 REMARK 465 SER H 138 REMARK 465 GLY H 139 REMARK 465 CYS L 212 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLY H 140 N CA 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 OE1 GLU H 6 N CYS H 96 2.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 CYS H 22 CA - CB - SG ANGL. DEV. = 7.5 DEGREES REMARK 500 PRO L 117 C - N - CD ANGL. DEV. = -12.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 PRO E 337 41.81 -78.69 REMARK 500 ASN E 370 9.14 -67.05 REMARK 500 ARG E 408 -9.04 -57.58 REMARK 500 TYR E 423 111.61 -163.48 REMARK 500 TYR E 449 30.78 -97.80 REMARK 500 PRO E 479 -175.71 -67.73 REMARK 500 ASN E 487 14.35 59.03 REMARK 500 SER H 52 173.04 -59.62 REMARK 500 ASN H 77 7.43 -67.67 REMARK 500 PHE H 100 149.18 -173.80 REMARK 500 PRO H 107 171.13 -57.63 REMARK 500 SER H 108 149.62 -174.14 REMARK 500 PHE H 152 144.86 -174.22 REMARK 500 PRO H 153 -159.01 -84.10 REMARK 500 SER H 194 22.16 -76.37 REMARK 500 SER L 28 56.79 34.65 REMARK 500 SER L 29 8.08 81.39 REMARK 500 ALA L 49 -21.14 71.74 REMARK 500 SER L 50 -12.62 -141.11 REMARK 500 LEU L 76 155.05 -48.27 REMARK 500 PRO L 118 28.05 -79.93 REMARK 500 SER L 119 -135.19 50.11 REMARK 500 ASP L 120 31.90 -149.81 REMARK 500 GLU L 121 -35.17 -132.22 REMARK 500 ASN L 136 62.75 61.98 REMARK 500 ARG L 209 108.36 -55.10 REMARK 500 REMARK 500 REMARK: NULL DBREF 7CDJ E 319 529 UNP P0DTC2 SPIKE_SARS2 319 529 DBREF 7CDJ H 1 218 PDB 7CDJ 7CDJ 1 218 DBREF 7CDJ L -1 212 PDB 7CDJ 7CDJ -1 212 SEQADV 7CDJ HIS E 530 UNP P0DTC2 EXPRESSION TAG SEQADV 7CDJ HIS E 531 UNP P0DTC2 EXPRESSION TAG SEQADV 7CDJ HIS E 532 UNP P0DTC2 EXPRESSION TAG SEQADV 7CDJ HIS E 533 UNP P0DTC2 EXPRESSION TAG SEQADV 7CDJ HIS E 534 UNP P0DTC2 EXPRESSION TAG SEQADV 7CDJ HIS E 535 UNP P0DTC2 EXPRESSION TAG SEQRES 1 E 217 ARG VAL GLN PRO THR GLU SER ILE VAL ARG PHE PRO ASN SEQRES 2 E 217 ILE THR ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN ALA SEQRES 3 E 217 THR ARG PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG SEQRES 4 E 217 ILE SER ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SEQRES 5 E 217 SER ALA SER PHE SER THR PHE LYS CYS TYR GLY VAL SER SEQRES 6 E 217 PRO THR LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR SEQRES 7 E 217 ALA ASP SER PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN SEQRES 8 E 217 ILE ALA PRO GLY GLN THR GLY LYS ILE ALA ASP TYR ASN SEQRES 9 E 217 TYR LYS LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA SEQRES 10 E 217 TRP ASN SER ASN ASN LEU ASP SER LYS VAL GLY GLY ASN SEQRES 11 E 217 TYR ASN TYR LEU TYR ARG LEU PHE ARG LYS SER ASN LEU SEQRES 12 E 217 LYS PRO PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN SEQRES 13 E 217 ALA GLY SER THR PRO CYS ASN GLY VAL GLU GLY PHE ASN SEQRES 14 E 217 CYS TYR PHE PRO LEU GLN SER TYR GLY PHE GLN PRO THR SEQRES 15 E 217 ASN GLY VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL LEU SEQRES 16 E 217 SER PHE GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY SEQRES 17 E 217 PRO LYS LYS HIS HIS HIS HIS HIS HIS SEQRES 1 H 218 GLN VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL LYS SEQRES 2 H 218 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 H 218 PHE THR PHE SER ASP TYR TYR MET SER TRP ILE ARG GLN SEQRES 4 H 218 ALA PRO GLY LYS GLY LEU GLU TRP VAL SER TYR ILE SER SEQRES 5 H 218 SER SER GLY SER THR ILE TYR TYR ALA ASP SER VAL LYS SEQRES 6 H 218 GLY ARG PHE THR ILE SER ARG ASP ASN ALA LYS ASN SER SEQRES 7 H 218 LEU TYR LEU GLN MET ASN SER LEU ARG ALA GLU ASP THR SEQRES 8 H 218 ALA VAL TYR TYR CYS ALA ARG ASP PHE SER HIS GLN GLN SEQRES 9 H 218 LEU VAL PRO SER TRP GLY GLN GLY THR LEU VAL THR VAL SEQRES 10 H 218 SER SER ALA SER THR LYS GLY PRO SER VAL PHE PRO LEU SEQRES 11 H 218 ALA PRO SER SER LYS SER THR SER GLY GLY THR ALA ALA SEQRES 12 H 218 LEU GLY CYS LEU VAL LYS ASP TYR PHE PRO GLU PRO VAL SEQRES 13 H 218 THR VAL SER TRP ASN SER GLY ALA LEU THR SER GLY VAL SEQRES 14 H 218 HIS THR PHE PRO ALA VAL LEU GLN SER SER GLY LEU TYR SEQRES 15 H 218 SER LEU SER SER VAL VAL THR VAL PRO SER SER SER LEU SEQRES 16 H 218 GLY THR GLN THR TYR ILE CYS ASN VAL ASN HIS LYS PRO SEQRES 17 H 218 SER ASN THR LYS VAL ASP LYS LYS VAL GLU SEQRES 1 L 214 ASP ILE GLN LEU THR GLN SER PRO SER PHE LEU SER ALA SEQRES 2 L 214 SER VAL GLY ASP ARG VAL THR ILE THR CYS ARG ALA SER SEQRES 3 L 214 GLN GLY ILE SER SER TYR LEU ALA TRP TYR GLN GLN LYS SEQRES 4 L 214 PRO GLY LYS ALA PRO LYS LEU LEU ILE TYR ALA ALA SER SEQRES 5 L 214 THR LEU GLN SER GLY VAL PRO SER ARG PHE SER GLY SER SEQRES 6 L 214 GLY SER GLY THR GLU PHE THR LEU THR ILE SER SER LEU SEQRES 7 L 214 GLN PRO GLU ASP PHE ALA THR TYR TYR CYS GLN GLN LEU SEQRES 8 L 214 ASN SER TYR PRO LEU THR PHE GLY GLY GLY THR LYS VAL SEQRES 9 L 214 GLU ILE LYS ARG THR VAL ALA ALA PRO SER VAL PHE ILE SEQRES 10 L 214 PHE PRO PRO SER ASP GLU GLN LEU LYS SER GLY THR ALA SEQRES 11 L 214 SER VAL VAL CYS LEU LEU ASN ASN PHE TYR PRO ARG GLU SEQRES 12 L 214 ALA LYS VAL GLN TRP LYS VAL ASP ASN ALA LEU GLN SER SEQRES 13 L 214 GLY ASN SER GLN GLU SER VAL THR GLU GLN ASP SER LYS SEQRES 14 L 214 ASP SER THR TYR SER LEU SER SER THR LEU THR LEU SER SEQRES 15 L 214 LYS ALA ASP TYR GLU LYS HIS LYS VAL TYR ALA CYS GLU SEQRES 16 L 214 VAL THR HIS GLN GLY LEU SER SER PRO VAL THR LYS SER SEQRES 17 L 214 PHE ASN ARG GLY GLU CYS HET NAG E 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 4 NAG C8 H15 N O6 HELIX 1 AA1 PRO E 337 ASN E 343 1 7 HELIX 2 AA2 TYR E 351 TRP E 353 5 3 HELIX 3 AA3 ASP E 364 ASN E 370 1 7 HELIX 4 AA4 ASP E 405 ILE E 410 5 6 HELIX 5 AA5 GLY E 416 ASN E 422 1 7 HELIX 6 AA6 SER E 438 SER E 443 1 6 HELIX 7 AA7 GLY E 502 TYR E 505 5 4 HELIX 8 AA8 THR H 28 TYR H 32 5 5 HELIX 9 AA9 PRO H 191 LEU H 195 5 5 HELIX 10 AB1 LYS L 181 LYS L 186 1 6 SHEET 1 AA1 3 ALA E 348 SER E 349 0 SHEET 2 AA1 3 ASN E 394 ARG E 403 1 O VAL E 401 N ALA E 348 SHEET 3 AA1 3 ASN E 354 ILE E 358 -1 N ILE E 358 O VAL E 395 SHEET 1 AA2 5 ALA E 348 SER E 349 0 SHEET 2 AA2 5 ASN E 394 ARG E 403 1 O VAL E 401 N ALA E 348 SHEET 3 AA2 5 PRO E 507 GLU E 516 -1 O SER E 514 N TYR E 396 SHEET 4 AA2 5 GLY E 431 ASN E 437 -1 N ILE E 434 O VAL E 511 SHEET 5 AA2 5 THR E 376 CYS E 379 -1 N LYS E 378 O VAL E 433 SHEET 1 AA3 2 CYS E 361 VAL E 362 0 SHEET 2 AA3 2 VAL E 524 CYS E 525 1 O CYS E 525 N CYS E 361 SHEET 1 AA4 2 LEU E 452 ARG E 454 0 SHEET 2 AA4 2 LEU E 492 SER E 494 -1 O GLN E 493 N TYR E 453 SHEET 1 AA5 4 GLN H 3 GLY H 8 0 SHEET 2 AA5 4 LEU H 18 SER H 25 -1 O SER H 21 N SER H 7 SHEET 3 AA5 4 LEU H 79 MET H 83 -1 O MET H 83 N LEU H 18 SHEET 4 AA5 4 PHE H 68 ARG H 72 -1 N SER H 71 O TYR H 80 SHEET 1 AA6 5 ILE H 58 TYR H 60 0 SHEET 2 AA6 5 GLU H 46 ILE H 51 -1 N TYR H 50 O TYR H 59 SHEET 3 AA6 5 MET H 34 GLN H 39 -1 N ARG H 38 O GLU H 46 SHEET 4 AA6 5 ALA H 92 ARG H 98 -1 O TYR H 95 N ILE H 37 SHEET 5 AA6 5 SER H 108 TRP H 109 -1 O SER H 108 N ARG H 98 SHEET 1 AA7 5 ILE H 58 TYR H 60 0 SHEET 2 AA7 5 GLU H 46 ILE H 51 -1 N TYR H 50 O TYR H 59 SHEET 3 AA7 5 MET H 34 GLN H 39 -1 N ARG H 38 O GLU H 46 SHEET 4 AA7 5 ALA H 92 ARG H 98 -1 O TYR H 95 N ILE H 37 SHEET 5 AA7 5 THR H 113 VAL H 115 -1 O VAL H 115 N ALA H 92 SHEET 1 AA8 4 SER H 126 LEU H 130 0 SHEET 2 AA8 4 ALA H 142 TYR H 151 -1 O GLY H 145 N LEU H 130 SHEET 3 AA8 4 TYR H 182 VAL H 190 -1 O LEU H 184 N VAL H 148 SHEET 4 AA8 4 VAL H 169 THR H 171 -1 N HIS H 170 O VAL H 187 SHEET 1 AA9 4 SER H 126 LEU H 130 0 SHEET 2 AA9 4 ALA H 142 TYR H 151 -1 O GLY H 145 N LEU H 130 SHEET 3 AA9 4 TYR H 182 VAL H 190 -1 O LEU H 184 N VAL H 148 SHEET 4 AA9 4 VAL H 175 LEU H 176 -1 N VAL H 175 O SER H 183 SHEET 1 AB1 3 VAL H 158 TRP H 160 0 SHEET 2 AB1 3 TYR H 200 HIS H 206 -1 O ASN H 203 N SER H 159 SHEET 3 AB1 3 THR H 211 VAL H 217 -1 O VAL H 217 N TYR H 200 SHEET 1 AB2 4 LEU L 2 SER L 5 0 SHEET 2 AB2 4 VAL L 17 ALA L 23 -1 O ARG L 22 N THR L 3 SHEET 3 AB2 4 GLU L 68 ILE L 73 -1 O LEU L 71 N ILE L 19 SHEET 4 AB2 4 PHE L 60 GLY L 64 -1 N SER L 61 O THR L 72 SHEET 1 AB3 6 PHE L 8 SER L 12 0 SHEET 2 AB3 6 THR L 100 LYS L 105 1 O LYS L 105 N ALA L 11 SHEET 3 AB3 6 THR L 83 GLN L 88 -1 N TYR L 84 O THR L 100 SHEET 4 AB3 6 LEU L 31 GLN L 36 -1 N TYR L 34 O TYR L 85 SHEET 5 AB3 6 LYS L 43 TYR L 47 -1 O ILE L 46 N TRP L 33 SHEET 6 AB3 6 THR L 51 LEU L 52 -1 O THR L 51 N TYR L 47 SHEET 1 AB4 4 PHE L 8 SER L 12 0 SHEET 2 AB4 4 THR L 100 LYS L 105 1 O LYS L 105 N ALA L 11 SHEET 3 AB4 4 THR L 83 GLN L 88 -1 N TYR L 84 O THR L 100 SHEET 4 AB4 4 THR L 95 PHE L 96 -1 O THR L 95 N GLN L 88 SHEET 1 AB5 4 SER L 112 PHE L 116 0 SHEET 2 AB5 4 THR L 127 PHE L 137 -1 O VAL L 131 N PHE L 116 SHEET 3 AB5 4 TYR L 171 SER L 180 -1 O LEU L 173 N LEU L 134 SHEET 4 AB5 4 SER L 157 VAL L 161 -1 N GLN L 158 O THR L 176 SHEET 1 AB6 3 LYS L 143 VAL L 148 0 SHEET 2 AB6 3 VAL L 189 THR L 195 -1 O GLU L 193 N GLN L 145 SHEET 3 AB6 3 VAL L 203 ASN L 208 -1 O VAL L 203 N VAL L 194 SSBOND 1 CYS E 336 CYS E 361 1555 1555 2.05 SSBOND 2 CYS E 379 CYS E 432 1555 1555 2.06 SSBOND 3 CYS E 391 CYS E 525 1555 1555 2.05 SSBOND 4 CYS E 480 CYS E 488 1555 1555 2.05 SSBOND 5 CYS H 22 CYS H 96 1555 1555 2.08 SSBOND 6 CYS H 146 CYS H 202 1555 1555 2.06 SSBOND 7 CYS L 21 CYS L 86 1555 1555 2.06 SSBOND 8 CYS L 132 CYS L 192 1555 1555 2.02 LINK ND2 ASN E 343 C1 NAG E 601 1555 1555 1.46 CISPEP 1 PHE H 152 PRO H 153 0 -11.16 CISPEP 2 GLU H 154 PRO H 155 0 2.24 CISPEP 3 SER L 5 PRO L 6 0 -4.16 CISPEP 4 TYR L 92 PRO L 93 0 -3.01 CISPEP 5 TYR L 138 PRO L 139 0 5.55 CRYST1 89.411 89.411 437.923 90.00 90.00 120.00 P 61 2 2 12 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 0.011184 0.006457 0.000000 0.00000 SCALE2 0.000000 0.012915 0.000000 0.00000 SCALE3 0.000000 0.000000 0.002284 0.00000