HEADER PROTEIN BINDING/IMMUNE SYSTEM 05-JUL-20 7CH5 TITLE CRYSTAL STRUCTURE OF THE SARS-COV-2 S RBD IN COMPLEX WITH BD-629 FAB COMPND MOL_ID: 1; COMPND 2 MOLECULE: BD-629 FAB H; COMPND 3 CHAIN: H; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: BD-629 FAB L; COMPND 7 CHAIN: L; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: SPIKE PROTEIN S1; COMPND 11 CHAIN: R; COMPND 12 SYNONYM: S GLYCOPROTEIN,E2,PEPLOMER PROTEIN,SPIKE GLYCOPROTEIN; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 6 EXPRESSION_SYSTEM_CELL_LINE: 293F; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_TAXID: 9606; SOURCE 10 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 12 EXPRESSION_SYSTEM_CELL_LINE: 293F; SOURCE 13 MOL_ID: 3; SOURCE 14 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 15 2; SOURCE 16 ORGANISM_COMMON: 2019-NCOV; SOURCE 17 ORGANISM_TAXID: 2697049; SOURCE 18 GENE: S, 2; SOURCE 19 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 20 EXPRESSION_SYSTEM_TAXID: 7111 KEYWDS COMPLEX, PROTEIN BINDING-IMMUNE SYSTEM COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.DU,J.Y.XIAO REVDAT 5 29-NOV-23 7CH5 1 REMARK REVDAT 4 10-MAR-21 7CH5 1 COMPND REVDAT 3 25-NOV-20 7CH5 1 JRNL REVDAT 2 07-OCT-20 7CH5 1 JRNL REVDAT 1 16-SEP-20 7CH5 0 JRNL AUTH S.DU,Y.CAO,Q.ZHU,P.YU,F.QI,G.WANG,X.DU,L.BAO,W.DENG,H.ZHU, JRNL AUTH 2 J.LIU,J.NIE,Y.ZHENG,H.LIANG,R.LIU,S.GONG,H.XU,A.YISIMAYI, JRNL AUTH 3 Q.LV,B.WANG,R.HE,Y.HAN,W.ZHAO,Y.BAI,Y.QU,X.GAO,C.JI,Q.WANG, JRNL AUTH 4 N.GAO,W.HUANG,Y.WANG,X.S.XIE,X.D.SU,J.XIAO,C.QIN JRNL TITL STRUCTURALLY RESOLVED SARS-COV-2 ANTIBODY SHOWS HIGH JRNL TITL 2 EFFICACY IN SEVERELY INFECTED HAMSTERS AND PROVIDES A POTENT JRNL TITL 3 COCKTAIL PAIRING STRATEGY. JRNL REF CELL V. 183 1013 2020 JRNL REFN ISSN 1097-4172 JRNL PMID 32970990 JRNL DOI 10.1016/J.CELL.2020.09.035 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.16 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 26713 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.229 REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1337 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 49.1600 - 5.8200 1.00 2718 143 0.2116 0.2368 REMARK 3 2 5.8100 - 4.6200 1.00 2591 137 0.1742 0.2029 REMARK 3 3 4.6200 - 4.0300 1.00 2546 134 0.1788 0.2067 REMARK 3 4 4.0300 - 3.6600 1.00 2544 134 0.2218 0.2253 REMARK 3 5 3.6600 - 3.4000 1.00 2543 134 0.2411 0.2645 REMARK 3 6 3.4000 - 3.2000 1.00 2511 132 0.2574 0.3284 REMARK 3 7 3.2000 - 3.0400 1.00 2521 133 0.2784 0.3102 REMARK 3 8 3.0400 - 2.9100 1.00 2485 131 0.2949 0.3840 REMARK 3 9 2.9100 - 2.8000 1.00 2489 131 0.2888 0.3174 REMARK 3 10 2.8000 - 2.7000 0.96 2428 128 0.2959 0.3732 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) : 0.340 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.500 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.80 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 : NULL 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 7CH5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-JUL-20. REMARK 100 THE DEPOSITION ID IS D_1300017632. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JUN-20 REMARK 200 TEMPERATURE (KELVIN) : 80 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 : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26831 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.20 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.7800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.75 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: 6M0J REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CITRATE TRIBASIC REMARK 280 DIHYDRATE PH 5.0 AND 18% W/V POLYETHYLENE GLYCOL 20000, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293.15K 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 28.02450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 82.41100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 51.17350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 82.41100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.02450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 51.17350 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: 5190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27040 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: H, L, R 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 SER H 132 REMARK 465 LYS H 133 REMARK 465 SER H 134 REMARK 465 THR H 135 REMARK 465 SER H 136 REMARK 465 GLY H 137 REMARK 465 LYS H 218 REMARK 465 SER H 219 REMARK 465 CYS H 220 REMARK 465 ASP H 221 REMARK 465 LYS H 222 REMARK 465 CYS L 214 REMARK 465 ARG R 319 REMARK 465 VAL R 320 REMARK 465 GLN R 321 REMARK 465 PRO R 322 REMARK 465 THR R 323 REMARK 465 GLU R 324 REMARK 465 SER R 325 REMARK 465 ILE R 326 REMARK 465 VAL R 327 REMARK 465 ARG R 328 REMARK 465 PHE R 329 REMARK 465 PRO R 330 REMARK 465 ASN R 331 REMARK 465 ILE R 332 REMARK 465 THR R 333 REMARK 465 LEU R 517 REMARK 465 LEU R 518 REMARK 465 HIS R 519 REMARK 465 ALA R 520 REMARK 465 PRO R 521 REMARK 465 ALA R 522 REMARK 465 THR R 523 REMARK 465 VAL R 524 REMARK 465 CYS R 525 REMARK 465 GLY R 526 REMARK 465 PRO R 527 REMARK 465 LYS R 528 REMARK 465 LYS R 529 REMARK 465 SER R 530 REMARK 465 THR R 531 REMARK 465 ASN R 532 REMARK 465 LEU R 533 REMARK 465 VAL R 534 REMARK 465 LYS R 535 REMARK 465 ASN R 536 REMARK 465 LYS R 537 REMARK 465 CYS R 538 REMARK 465 VAL R 539 REMARK 465 ASN R 540 REMARK 465 PHE R 541 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 ND2 ASN H 201 OD2 ASP H 212 2.10 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU H 88 CD GLU H 88 OE2 0.077 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 ARG R 466 NE - CZ - NH1 ANGL. DEV. = -5.1 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 LYS H 43 -168.86 -119.74 REMARK 500 GLU H 88 -69.08 27.93 REMARK 500 TYR H 102 -71.14 -112.12 REMARK 500 ASP H 148 63.51 61.31 REMARK 500 SER L 30 -129.07 58.30 REMARK 500 LEU L 47 -66.77 -102.73 REMARK 500 ALA L 51 -12.19 69.23 REMARK 500 SER L 52 3.13 -157.05 REMARK 500 ASP L 60 -2.44 -53.87 REMARK 500 ALA L 84 -160.76 -160.40 REMARK 500 SER L 94 -161.85 56.67 REMARK 500 ASN L 138 78.09 56.47 REMARK 500 ASN L 152 18.63 56.30 REMARK 500 ASN R 343 31.48 -91.64 REMARK 500 ASN R 370 78.71 -101.70 REMARK 500 ASN R 388 11.20 -68.77 REMARK 500 ASN R 422 -51.12 -133.77 REMARK 500 ASP R 428 38.51 -85.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ALA H 87 GLU H 88 115.27 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 GLU H 88 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 7CH5 H 1 222 PDB 7CH5 7CH5 1 222 DBREF 7CH5 L 1 214 PDB 7CH5 7CH5 1 214 DBREF 7CH5 R 319 541 UNP P0DTC2 SPIKE_SARS2 319 541 SEQRES 1 H 222 GLU VAL GLN LEU VAL GLU SER GLY GLY GLY LEU ILE GLN SEQRES 2 H 222 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLU SEQRES 3 H 222 PHE ILE VAL SER ARG ASN TYR MET SER TRP VAL ARG GLN SEQRES 4 H 222 ALA PRO GLY LYS GLY LEU GLU TRP VAL SER VAL ILE TYR SEQRES 5 H 222 SER GLY GLY SER THR TYR TYR ALA ASP SER VAL LYS GLY SEQRES 6 H 222 ARG PHE THR ILE SER ARG ASP ASN SER LYS ASN THR LEU SEQRES 7 H 222 ASN LEU GLN MET ASN SER LEU ARG ALA GLU ASP THR ALA SEQRES 8 H 222 VAL TYR TYR CYS ALA ARG ASP TYR GLY ASP TYR TYR PHE SEQRES 9 H 222 ASP TYR TRP GLY GLN GLY THR LEU VAL THR VAL SER SER SEQRES 10 H 222 ALA SER THR LYS GLY PRO SER VAL PHE PRO LEU ALA PRO SEQRES 11 H 222 SER SER LYS SER THR SER GLY GLY THR ALA ALA LEU GLY SEQRES 12 H 222 CYS LEU VAL LYS ASP TYR PHE PRO GLU PRO VAL THR VAL SEQRES 13 H 222 SER TRP ASN SER GLY ALA LEU THR SER GLY VAL HIS THR SEQRES 14 H 222 PHE PRO ALA VAL LEU GLN SER SER GLY LEU TYR SER LEU SEQRES 15 H 222 SER SER VAL VAL THR VAL PRO SER SER SER LEU GLY THR SEQRES 16 H 222 GLN THR TYR ILE CYS ASN VAL ASN HIS LYS PRO SER ASN SEQRES 17 H 222 THR LYS VAL ASP LYS LYS VAL GLU PRO LYS SER CYS ASP SEQRES 18 H 222 LYS SEQRES 1 L 214 GLU ILE VAL LEU THR GLN SER PRO GLY THR LEU SER LEU SEQRES 2 L 214 SER PRO GLY GLU ARG ALA THR LEU SER CYS ARG ALA SER SEQRES 3 L 214 GLN GLY VAL SER SER PHE LEU ALA TRP TYR GLN GLN LYS SEQRES 4 L 214 PRO GLY GLN ALA PRO ARG LEU LEU ILE HIS GLY ALA SER SEQRES 5 L 214 SER ARG ALA THR GLY ILE PRO ASP ARG PHE SER GLY SER SEQRES 6 L 214 GLY SER GLY THR ASP PHE THR LEU THR ILE THR ARG LEU SEQRES 7 L 214 GLU PRO GLU ASP PHE ALA VAL TYR TYR CYS GLN GLN TYR SEQRES 8 L 214 GLY SER SER PRO ARG THR PHE GLY GLN 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 SEQRES 1 R 223 ARG VAL GLN PRO THR GLU SER ILE VAL ARG PHE PRO ASN SEQRES 2 R 223 ILE THR ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN ALA SEQRES 3 R 223 THR ARG PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG SEQRES 4 R 223 ILE SER ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SEQRES 5 R 223 SER ALA SER PHE SER THR PHE LYS CYS TYR GLY VAL SER SEQRES 6 R 223 PRO THR LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR SEQRES 7 R 223 ALA ASP SER PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN SEQRES 8 R 223 ILE ALA PRO GLY GLN THR GLY LYS ILE ALA ASP TYR ASN SEQRES 9 R 223 TYR LYS LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA SEQRES 10 R 223 TRP ASN SER ASN ASN LEU ASP SER LYS VAL GLY GLY ASN SEQRES 11 R 223 TYR ASN TYR LEU TYR ARG LEU PHE ARG LYS SER ASN LEU SEQRES 12 R 223 LYS PRO PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN SEQRES 13 R 223 ALA GLY SER THR PRO CYS ASN GLY VAL GLU GLY PHE ASN SEQRES 14 R 223 CYS TYR PHE PRO LEU GLN SER TYR GLY PHE GLN PRO THR SEQRES 15 R 223 ASN GLY VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL LEU SEQRES 16 R 223 SER PHE GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY SEQRES 17 R 223 PRO LYS LYS SER THR ASN LEU VAL LYS ASN LYS CYS VAL SEQRES 18 R 223 ASN PHE HELIX 1 AA1 ILE H 28 ASN H 32 5 5 HELIX 2 AA2 ARG H 86 THR H 90 5 5 HELIX 3 AA3 SER H 160 ALA H 162 5 3 HELIX 4 AA4 SER H 191 LEU H 193 5 3 HELIX 5 AA5 LYS H 205 ASN H 208 5 4 HELIX 6 AA6 GLU L 79 PHE L 83 5 5 HELIX 7 AA7 SER L 121 LYS L 126 1 6 HELIX 8 AA8 LYS L 183 LYS L 188 1 6 HELIX 9 AA9 PHE R 338 ASN R 343 1 6 HELIX 10 AB1 SER R 349 TRP R 353 5 5 HELIX 11 AB2 TYR R 365 ASN R 370 1 6 HELIX 12 AB3 LYS R 386 LEU R 390 5 5 HELIX 13 AB4 ASP R 405 ILE R 410 5 6 HELIX 14 AB5 GLY R 416 ASN R 422 1 7 HELIX 15 AB6 SER R 438 SER R 443 1 6 HELIX 16 AB7 GLY R 502 TYR R 505 5 4 SHEET 1 AA1 4 LEU H 4 SER H 7 0 SHEET 2 AA1 4 LEU H 18 ALA H 24 -1 O SER H 21 N SER H 7 SHEET 3 AA1 4 THR H 77 MET H 82 -1 O MET H 82 N LEU H 18 SHEET 4 AA1 4 PHE H 67 ASP H 72 -1 N THR H 68 O GLN H 81 SHEET 1 AA2 6 GLY H 10 ILE H 12 0 SHEET 2 AA2 6 THR H 111 VAL H 115 1 O THR H 114 N ILE H 12 SHEET 3 AA2 6 ALA H 91 TYR H 99 -1 N TYR H 93 O THR H 111 SHEET 4 AA2 6 TYR H 33 GLN H 39 -1 N TYR H 33 O ASP H 98 SHEET 5 AA2 6 GLU H 46 ILE H 51 -1 O VAL H 48 N TRP H 36 SHEET 6 AA2 6 THR H 57 TYR H 59 -1 O TYR H 58 N VAL H 50 SHEET 1 AA3 4 GLY H 10 ILE H 12 0 SHEET 2 AA3 4 THR H 111 VAL H 115 1 O THR H 114 N ILE H 12 SHEET 3 AA3 4 ALA H 91 TYR H 99 -1 N TYR H 93 O THR H 111 SHEET 4 AA3 4 TYR H 103 TRP H 107 -1 O TYR H 106 N ARG H 97 SHEET 1 AA4 4 SER H 124 LEU H 128 0 SHEET 2 AA4 4 THR H 139 TYR H 149 -1 O GLY H 143 N LEU H 128 SHEET 3 AA4 4 TYR H 180 PRO H 189 -1 O VAL H 188 N ALA H 140 SHEET 4 AA4 4 VAL H 167 THR H 169 -1 N HIS H 168 O VAL H 185 SHEET 1 AA5 4 SER H 124 LEU H 128 0 SHEET 2 AA5 4 THR H 139 TYR H 149 -1 O GLY H 143 N LEU H 128 SHEET 3 AA5 4 TYR H 180 PRO H 189 -1 O VAL H 188 N ALA H 140 SHEET 4 AA5 4 VAL H 173 LEU H 174 -1 N VAL H 173 O SER H 181 SHEET 1 AA6 3 THR H 155 TRP H 158 0 SHEET 2 AA6 3 TYR H 198 HIS H 204 -1 O ASN H 201 N SER H 157 SHEET 3 AA6 3 THR H 209 VAL H 215 -1 O THR H 209 N HIS H 204 SHEET 1 AA7 4 LEU L 4 SER L 7 0 SHEET 2 AA7 4 ALA L 19 ALA L 25 -1 O ARG L 24 N THR L 5 SHEET 3 AA7 4 ASP L 70 ILE L 75 -1 O LEU L 73 N LEU L 21 SHEET 4 AA7 4 PHE L 62 SER L 67 -1 N SER L 63 O THR L 74 SHEET 1 AA8 6 THR L 10 LEU L 13 0 SHEET 2 AA8 6 THR L 102 ILE L 106 1 O LYS L 103 N LEU L 11 SHEET 3 AA8 6 VAL L 85 GLN L 90 -1 N TYR L 86 O THR L 102 SHEET 4 AA8 6 LEU L 33 GLN L 38 -1 N GLN L 38 O VAL L 85 SHEET 5 AA8 6 ARG L 45 HIS L 49 -1 O LEU L 47 N TRP L 35 SHEET 6 AA8 6 SER L 53 ARG L 54 -1 O SER L 53 N HIS L 49 SHEET 1 AA9 4 THR L 10 LEU L 13 0 SHEET 2 AA9 4 THR L 102 ILE L 106 1 O LYS L 103 N LEU L 11 SHEET 3 AA9 4 VAL L 85 GLN L 90 -1 N TYR L 86 O THR L 102 SHEET 4 AA9 4 THR L 97 PHE L 98 -1 O THR L 97 N GLN L 90 SHEET 1 AB1 4 SER L 114 PHE L 118 0 SHEET 2 AB1 4 THR L 129 PHE L 139 -1 O LEU L 135 N PHE L 116 SHEET 3 AB1 4 TYR L 173 SER L 182 -1 O LEU L 179 N VAL L 132 SHEET 4 AB1 4 SER L 159 VAL L 163 -1 N GLN L 160 O THR L 178 SHEET 1 AB2 4 ALA L 153 LEU L 154 0 SHEET 2 AB2 4 LYS L 145 VAL L 150 -1 N VAL L 150 O ALA L 153 SHEET 3 AB2 4 VAL L 191 THR L 197 -1 O GLU L 195 N GLN L 147 SHEET 4 AB2 4 VAL L 205 ASN L 210 -1 O LYS L 207 N CYS L 194 SHEET 1 AB3 5 ASN R 354 ILE R 358 0 SHEET 2 AB3 5 VAL R 395 ARG R 403 -1 O VAL R 395 N ILE R 358 SHEET 3 AB3 5 PRO R 507 PHE R 515 -1 O TYR R 508 N ILE R 402 SHEET 4 AB3 5 GLY R 431 ASN R 437 -1 N CYS R 432 O LEU R 513 SHEET 5 AB3 5 THR R 376 TYR R 380 -1 N TYR R 380 O GLY R 431 SHEET 1 AB4 2 LEU R 452 ARG R 454 0 SHEET 2 AB4 2 LEU R 492 SER R 494 -1 O GLN R 493 N TYR R 453 SHEET 1 AB5 2 TYR R 473 GLN R 474 0 SHEET 2 AB5 2 CYS R 488 TYR R 489 -1 O TYR R 489 N TYR R 473 SSBOND 1 CYS H 22 CYS H 95 1555 1555 2.04 SSBOND 2 CYS H 144 CYS H 200 1555 1555 2.03 SSBOND 3 CYS L 23 CYS L 88 1555 1555 2.05 SSBOND 4 CYS L 134 CYS L 194 1555 1555 2.03 SSBOND 5 CYS R 336 CYS R 361 1555 1555 2.04 SSBOND 6 CYS R 379 CYS R 432 1555 1555 2.04 SSBOND 7 CYS R 480 CYS R 488 1555 1555 2.04 CISPEP 1 PHE H 150 PRO H 151 0 -8.18 CISPEP 2 GLU H 152 PRO H 153 0 5.77 CISPEP 3 SER L 7 PRO L 8 0 -5.45 CISPEP 4 TYR L 140 PRO L 141 0 2.62 CRYST1 56.049 102.347 164.822 90.00 90.00 90.00 P 21 21 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 0.017842 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009771 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006067 0.00000