HEADER VIRAL PROTEIN 13-JUN-20 7CBT TITLE THE CRYSTAL STRUCTURE OF SARS-COV-2 MAIN PROTEASE IN COMPLEX WITH TITLE 2 GC376 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3C-LIKE PROTEINASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PP1AB,ORF1AB POLYPROTEIN,3CL-PRO,3CLP,MAIN PROTEASE,MPRO, COMPND 5 NON-STRUCTURAL PROTEIN 5,NSP5,SARS CORONAVIRUS MAIN PROTEINASE, COMPND 6 REPLICASE POLYPROTEIN 1AB; COMPND 7 EC: 3.4.22.69; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 3 2; SOURCE 4 ORGANISM_COMMON: 2019-NCOV; SOURCE 5 ORGANISM_TAXID: 2697049; SOURCE 6 GENE: REP, 1A-1B; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SARS-COV-2, MAIN PROTEASE, GC376, COMPLEX, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.SHI,G.PENG REVDAT 4 29-NOV-23 7CBT 1 REMARK REVDAT 3 09-JUN-21 7CBT 1 JRNL REVDAT 2 10-MAR-21 7CBT 1 COMPND REVDAT 1 02-SEP-20 7CBT 0 JRNL AUTH Y.SHI,L.SHUAI,Z.WEN,C.WANG,Y.YAN,Z.JIAO,F.GUO,Z.F.FU,H.CHEN, JRNL AUTH 2 Z.BU,G.PENG JRNL TITL THE PRECLINICAL INHIBITOR GS441524 IN COMBINATION WITH GC376 JRNL TITL 2 EFFICACIOUSLY INHIBITED THE PROLIFERATION OF SARS-COV-2 IN JRNL TITL 3 THE MOUSE RESPIRATORY TRACT. JRNL REF EMERG MICROBES INFECT V. 10 481 2021 JRNL REFN ESSN 2222-1751 JRNL PMID 33691601 JRNL DOI 10.1080/22221751.2021.1899770 REMARK 2 REMARK 2 RESOLUTION. 2.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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) : 2.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.15 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 25716 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.292 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.740 REMARK 3 FREE R VALUE TEST SET COUNT : 1991 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 28.1510 - 5.6405 0.99 1741 0 0.0000 0.0000 REMARK 3 2 5.6405 - 4.4829 1.00 1716 0 0.0000 0.0000 REMARK 3 3 4.4829 - 3.9179 0.97 1665 0 0.0000 0.0000 REMARK 3 4 3.9179 - 3.5605 1.00 1696 0 0.0000 0.0000 REMARK 3 5 3.5605 - 3.3057 0.96 1668 0 0.0000 0.0000 REMARK 3 6 3.3057 - 3.1111 1.00 1695 0 0.0000 0.0000 REMARK 3 7 3.1111 - 2.9554 1.00 1705 0 0.0000 0.0000 REMARK 3 8 2.9554 - 2.8269 1.00 1701 0 0.0000 0.0000 REMARK 3 9 2.8269 - 2.7182 1.00 1700 0 0.0000 0.0000 REMARK 3 10 2.7182 - 2.6245 1.00 1669 0 0.0000 0.0000 REMARK 3 11 2.6245 - 2.5424 1.00 1736 0 0.0000 0.0000 REMARK 3 12 2.5424 - 2.4698 1.00 1712 0 0.0000 0.0000 REMARK 3 13 2.4698 - 2.4048 1.00 1667 0 0.0000 0.0000 REMARK 3 14 2.4048 - 2.3462 0.96 1654 0 0.0000 0.0000 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) : 0.360 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.480 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.10 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 7CBT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-JUN-20. REMARK 100 THE DEPOSITION ID IS D_1300017259. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-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) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-X REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 R 200K-A REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25910 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.346 REMARK 200 RESOLUTION RANGE LOW (A) : 45.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 2.6250 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.43 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: PHENIX REMARK 200 STARTING MODEL: 6Y2E REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM MALONATE PH 6.0, 12% W/V REMARK 280 POLYETHYLENE GLYCOL 3,350, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 49.87300 REMARK 290 SMTRY3 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2050 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 MET A -26 REMARK 465 HIS A -25 REMARK 465 HIS A -24 REMARK 465 HIS A -23 REMARK 465 HIS A -22 REMARK 465 HIS A -21 REMARK 465 HIS A -20 REMARK 465 GLY A -19 REMARK 465 LEU A -18 REMARK 465 ASN A -17 REMARK 465 ASP A -16 REMARK 465 ILE A -15 REMARK 465 PHE A -14 REMARK 465 GLU A -13 REMARK 465 ALA A -12 REMARK 465 GLN A -11 REMARK 465 LYS A -10 REMARK 465 ILE A -9 REMARK 465 GLU A -8 REMARK 465 TRP A -7 REMARK 465 HIS A -6 REMARK 465 GLU A -5 REMARK 465 GLY A -4 REMARK 465 GLY A -3 REMARK 465 GLY A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 SER A 1 REMARK 465 GLY A 2 REMARK 465 PHE A 3 REMARK 465 GLY A 302 REMARK 465 VAL A 303 REMARK 465 THR A 304 REMARK 465 PHE A 305 REMARK 465 GLN A 306 REMARK 465 MET B -26 REMARK 465 HIS B -25 REMARK 465 HIS B -24 REMARK 465 HIS B -23 REMARK 465 HIS B -22 REMARK 465 HIS B -21 REMARK 465 HIS B -20 REMARK 465 GLY B -19 REMARK 465 LEU B -18 REMARK 465 ASN B -17 REMARK 465 ASP B -16 REMARK 465 ILE B -15 REMARK 465 PHE B -14 REMARK 465 GLU B -13 REMARK 465 ALA B -12 REMARK 465 GLN B -11 REMARK 465 LYS B -10 REMARK 465 ILE B -9 REMARK 465 GLU B -8 REMARK 465 TRP B -7 REMARK 465 HIS B -6 REMARK 465 GLU B -5 REMARK 465 GLY B -4 REMARK 465 GLY B -3 REMARK 465 GLY B -2 REMARK 465 GLY B -1 REMARK 465 SER B 0 REMARK 465 SER B 1 REMARK 465 GLY B 2 REMARK 465 PHE B 3 REMARK 465 GLY B 302 REMARK 465 VAL B 303 REMARK 465 THR B 304 REMARK 465 PHE B 305 REMARK 465 GLN B 306 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 OG1 THR B 292 H ASP B 295 1.41 REMARK 500 HE22 GLN B 107 O HOH B 503 1.51 REMARK 500 HG SER A 10 OE2 GLU A 14 1.56 REMARK 500 HH TYR A 54 O ASP A 187 1.59 REMARK 500 O ASN B 221 O HOH B 501 1.86 REMARK 500 O HOH B 524 O HOH B 571 1.95 REMARK 500 O ALA B 285 O HOH B 502 1.96 REMARK 500 O HOH B 545 O HOH B 560 1.98 REMARK 500 OD1 ASP A 229 O HOH A 501 2.07 REMARK 500 O HOH B 566 O HOH B 576 2.11 REMARK 500 O HOH A 583 O HOH A 596 2.12 REMARK 500 OG1 THR B 292 N ASP B 295 2.17 REMARK 500 NE2 GLN B 107 O HOH B 503 2.17 REMARK 500 OD1 ASN B 228 O HOH B 504 2.18 REMARK 500 OD1 ASN A 142 O HOH A 502 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OD1 ASP A 56 NH2 ARG A 222 1656 1.98 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 B 47 CB GLU B 47 CG 0.198 REMARK 500 CYS B 128 CB CYS B 128 SG -0.118 REMARK 500 LYS B 236 CE LYS B 236 NZ -0.274 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 A 105 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 ASP A 187 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 GLU B 47 CG - CD - OE1 ANGL. DEV. = -14.4 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 ASP A 33 -125.43 50.30 REMARK 500 ASN A 51 69.97 -159.37 REMARK 500 SER A 81 145.24 173.58 REMARK 500 ASN A 84 -119.30 51.56 REMARK 500 ASP A 153 78.11 -154.76 REMARK 500 TYR A 154 -95.85 73.64 REMARK 500 PRO A 184 45.36 -88.25 REMARK 500 PRO A 252 -70.60 -33.68 REMARK 500 ASN A 277 72.23 18.26 REMARK 500 ASP B 33 -123.89 43.73 REMARK 500 SER B 46 83.30 -43.30 REMARK 500 GLU B 47 -31.30 136.46 REMARK 500 ASN B 84 -112.82 50.86 REMARK 500 TYR B 154 -97.84 65.80 REMARK 500 ALA B 194 -74.69 -36.02 REMARK 500 ARG B 217 62.65 -103.12 REMARK 500 ARG B 222 69.32 -109.67 REMARK 500 THR B 226 -166.22 -123.02 REMARK 500 ASN B 238 64.95 82.27 REMARK 500 THR B 243 -127.43 -72.56 REMARK 500 GLN B 244 22.79 -145.19 REMARK 500 ASP B 245 -5.18 -146.28 REMARK 500 VAL B 261 -15.58 -40.31 REMARK 500 LYS B 269 -72.76 -36.71 REMARK 500 ASN B 274 44.07 -168.54 REMARK 500 LEU B 282 -5.35 77.92 REMARK 500 ALA B 285 4.84 -67.45 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 ASP B 245 HIS B 246 137.29 REMARK 500 ASP B 248 ILE B 249 146.34 REMARK 500 REMARK 500 REMARK: NULL REMARK 630 REMARK 630 MOLECULE TYPE: NULL REMARK 630 MOLECULE NAME: (1S,2S)-2-({N-[(BENZYLOXY)CARBONYL]-L-LEUCYL}AMINO)- REMARK 630 1-HYDROXY-3-[(3S)-2-OXOPYRROLIDIN-3-YL]PROPANE-1-SULFONIC ACID REMARK 630 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 630 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 630 REMARK 630 M RES C SSSEQI REMARK 630 K36 A 401 REMARK 630 K36 B 401 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: PHQ LEU 04F REMARK 630 DETAILS: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K36 A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide K36 B 401 and CYS B REMARK 800 145 DBREF 7CBT A 1 306 UNP P0DTD1 R1AB_SARS2 3264 3569 DBREF 7CBT B 1 306 UNP P0DTD1 R1AB_SARS2 3264 3569 SEQADV 7CBT MET A -26 UNP P0DTD1 INITIATING METHIONINE SEQADV 7CBT HIS A -25 UNP P0DTD1 EXPRESSION TAG SEQADV 7CBT HIS A -24 UNP P0DTD1 EXPRESSION TAG SEQADV 7CBT HIS A -23 UNP P0DTD1 EXPRESSION TAG SEQADV 7CBT HIS A -22 UNP P0DTD1 EXPRESSION TAG SEQADV 7CBT HIS A -21 UNP P0DTD1 EXPRESSION TAG SEQADV 7CBT HIS A -20 UNP P0DTD1 EXPRESSION TAG SEQADV 7CBT GLY A -19 UNP P0DTD1 EXPRESSION TAG SEQADV 7CBT LEU A -18 UNP P0DTD1 EXPRESSION TAG SEQADV 7CBT ASN A -17 UNP P0DTD1 EXPRESSION TAG SEQADV 7CBT ASP A -16 UNP P0DTD1 EXPRESSION TAG SEQADV 7CBT ILE A -15 UNP P0DTD1 EXPRESSION TAG SEQADV 7CBT PHE A -14 UNP P0DTD1 EXPRESSION TAG SEQADV 7CBT GLU A -13 UNP P0DTD1 EXPRESSION TAG SEQADV 7CBT ALA A -12 UNP P0DTD1 EXPRESSION TAG SEQADV 7CBT GLN A -11 UNP P0DTD1 EXPRESSION TAG SEQADV 7CBT LYS A -10 UNP P0DTD1 EXPRESSION TAG SEQADV 7CBT ILE A -9 UNP P0DTD1 EXPRESSION TAG SEQADV 7CBT GLU A -8 UNP P0DTD1 EXPRESSION TAG SEQADV 7CBT TRP A -7 UNP P0DTD1 EXPRESSION TAG SEQADV 7CBT HIS A -6 UNP P0DTD1 EXPRESSION TAG SEQADV 7CBT GLU A -5 UNP P0DTD1 EXPRESSION TAG SEQADV 7CBT GLY A -4 UNP P0DTD1 EXPRESSION TAG SEQADV 7CBT GLY A -3 UNP P0DTD1 EXPRESSION TAG SEQADV 7CBT GLY A -2 UNP P0DTD1 EXPRESSION TAG SEQADV 7CBT GLY A -1 UNP P0DTD1 EXPRESSION TAG SEQADV 7CBT SER A 0 UNP P0DTD1 EXPRESSION TAG SEQADV 7CBT MET B -26 UNP P0DTD1 INITIATING METHIONINE SEQADV 7CBT HIS B -25 UNP P0DTD1 EXPRESSION TAG SEQADV 7CBT HIS B -24 UNP P0DTD1 EXPRESSION TAG SEQADV 7CBT HIS B -23 UNP P0DTD1 EXPRESSION TAG SEQADV 7CBT HIS B -22 UNP P0DTD1 EXPRESSION TAG SEQADV 7CBT HIS B -21 UNP P0DTD1 EXPRESSION TAG SEQADV 7CBT HIS B -20 UNP P0DTD1 EXPRESSION TAG SEQADV 7CBT GLY B -19 UNP P0DTD1 EXPRESSION TAG SEQADV 7CBT LEU B -18 UNP P0DTD1 EXPRESSION TAG SEQADV 7CBT ASN B -17 UNP P0DTD1 EXPRESSION TAG SEQADV 7CBT ASP B -16 UNP P0DTD1 EXPRESSION TAG SEQADV 7CBT ILE B -15 UNP P0DTD1 EXPRESSION TAG SEQADV 7CBT PHE B -14 UNP P0DTD1 EXPRESSION TAG SEQADV 7CBT GLU B -13 UNP P0DTD1 EXPRESSION TAG SEQADV 7CBT ALA B -12 UNP P0DTD1 EXPRESSION TAG SEQADV 7CBT GLN B -11 UNP P0DTD1 EXPRESSION TAG SEQADV 7CBT LYS B -10 UNP P0DTD1 EXPRESSION TAG SEQADV 7CBT ILE B -9 UNP P0DTD1 EXPRESSION TAG SEQADV 7CBT GLU B -8 UNP P0DTD1 EXPRESSION TAG SEQADV 7CBT TRP B -7 UNP P0DTD1 EXPRESSION TAG SEQADV 7CBT HIS B -6 UNP P0DTD1 EXPRESSION TAG SEQADV 7CBT GLU B -5 UNP P0DTD1 EXPRESSION TAG SEQADV 7CBT GLY B -4 UNP P0DTD1 EXPRESSION TAG SEQADV 7CBT GLY B -3 UNP P0DTD1 EXPRESSION TAG SEQADV 7CBT GLY B -2 UNP P0DTD1 EXPRESSION TAG SEQADV 7CBT GLY B -1 UNP P0DTD1 EXPRESSION TAG SEQADV 7CBT SER B 0 UNP P0DTD1 EXPRESSION TAG SEQRES 1 A 333 MET HIS HIS HIS HIS HIS HIS GLY LEU ASN ASP ILE PHE SEQRES 2 A 333 GLU ALA GLN LYS ILE GLU TRP HIS GLU GLY GLY GLY GLY SEQRES 3 A 333 SER SER GLY PHE ARG LYS MET ALA PHE PRO SER GLY LYS SEQRES 4 A 333 VAL GLU GLY CYS MET VAL GLN VAL THR CYS GLY THR THR SEQRES 5 A 333 THR LEU ASN GLY LEU TRP LEU ASP ASP VAL VAL TYR CYS SEQRES 6 A 333 PRO ARG HIS VAL ILE CYS THR SER GLU ASP MET LEU ASN SEQRES 7 A 333 PRO ASN TYR GLU ASP LEU LEU ILE ARG LYS SER ASN HIS SEQRES 8 A 333 ASN PHE LEU VAL GLN ALA GLY ASN VAL GLN LEU ARG VAL SEQRES 9 A 333 ILE GLY HIS SER MET GLN ASN CYS VAL LEU LYS LEU LYS SEQRES 10 A 333 VAL ASP THR ALA ASN PRO LYS THR PRO LYS TYR LYS PHE SEQRES 11 A 333 VAL ARG ILE GLN PRO GLY GLN THR PHE SER VAL LEU ALA SEQRES 12 A 333 CYS TYR ASN GLY SER PRO SER GLY VAL TYR GLN CYS ALA SEQRES 13 A 333 MET ARG PRO ASN PHE THR ILE LYS GLY SER PHE LEU ASN SEQRES 14 A 333 GLY SER CYS GLY SER VAL GLY PHE ASN ILE ASP TYR ASP SEQRES 15 A 333 CYS VAL SER PHE CYS TYR MET HIS HIS MET GLU LEU PRO SEQRES 16 A 333 THR GLY VAL HIS ALA GLY THR ASP LEU GLU GLY ASN PHE SEQRES 17 A 333 TYR GLY PRO PHE VAL ASP ARG GLN THR ALA GLN ALA ALA SEQRES 18 A 333 GLY THR ASP THR THR ILE THR VAL ASN VAL LEU ALA TRP SEQRES 19 A 333 LEU TYR ALA ALA VAL ILE ASN GLY ASP ARG TRP PHE LEU SEQRES 20 A 333 ASN ARG PHE THR THR THR LEU ASN ASP PHE ASN LEU VAL SEQRES 21 A 333 ALA MET LYS TYR ASN TYR GLU PRO LEU THR GLN ASP HIS SEQRES 22 A 333 VAL ASP ILE LEU GLY PRO LEU SER ALA GLN THR GLY ILE SEQRES 23 A 333 ALA VAL LEU ASP MET CYS ALA SER LEU LYS GLU LEU LEU SEQRES 24 A 333 GLN ASN GLY MET ASN GLY ARG THR ILE LEU GLY SER ALA SEQRES 25 A 333 LEU LEU GLU ASP GLU PHE THR PRO PHE ASP VAL VAL ARG SEQRES 26 A 333 GLN CYS SER GLY VAL THR PHE GLN SEQRES 1 B 333 MET HIS HIS HIS HIS HIS HIS GLY LEU ASN ASP ILE PHE SEQRES 2 B 333 GLU ALA GLN LYS ILE GLU TRP HIS GLU GLY GLY GLY GLY SEQRES 3 B 333 SER SER GLY PHE ARG LYS MET ALA PHE PRO SER GLY LYS SEQRES 4 B 333 VAL GLU GLY CYS MET VAL GLN VAL THR CYS GLY THR THR SEQRES 5 B 333 THR LEU ASN GLY LEU TRP LEU ASP ASP VAL VAL TYR CYS SEQRES 6 B 333 PRO ARG HIS VAL ILE CYS THR SER GLU ASP MET LEU ASN SEQRES 7 B 333 PRO ASN TYR GLU ASP LEU LEU ILE ARG LYS SER ASN HIS SEQRES 8 B 333 ASN PHE LEU VAL GLN ALA GLY ASN VAL GLN LEU ARG VAL SEQRES 9 B 333 ILE GLY HIS SER MET GLN ASN CYS VAL LEU LYS LEU LYS SEQRES 10 B 333 VAL ASP THR ALA ASN PRO LYS THR PRO LYS TYR LYS PHE SEQRES 11 B 333 VAL ARG ILE GLN PRO GLY GLN THR PHE SER VAL LEU ALA SEQRES 12 B 333 CYS TYR ASN GLY SER PRO SER GLY VAL TYR GLN CYS ALA SEQRES 13 B 333 MET ARG PRO ASN PHE THR ILE LYS GLY SER PHE LEU ASN SEQRES 14 B 333 GLY SER CYS GLY SER VAL GLY PHE ASN ILE ASP TYR ASP SEQRES 15 B 333 CYS VAL SER PHE CYS TYR MET HIS HIS MET GLU LEU PRO SEQRES 16 B 333 THR GLY VAL HIS ALA GLY THR ASP LEU GLU GLY ASN PHE SEQRES 17 B 333 TYR GLY PRO PHE VAL ASP ARG GLN THR ALA GLN ALA ALA SEQRES 18 B 333 GLY THR ASP THR THR ILE THR VAL ASN VAL LEU ALA TRP SEQRES 19 B 333 LEU TYR ALA ALA VAL ILE ASN GLY ASP ARG TRP PHE LEU SEQRES 20 B 333 ASN ARG PHE THR THR THR LEU ASN ASP PHE ASN LEU VAL SEQRES 21 B 333 ALA MET LYS TYR ASN TYR GLU PRO LEU THR GLN ASP HIS SEQRES 22 B 333 VAL ASP ILE LEU GLY PRO LEU SER ALA GLN THR GLY ILE SEQRES 23 B 333 ALA VAL LEU ASP MET CYS ALA SER LEU LYS GLU LEU LEU SEQRES 24 B 333 GLN ASN GLY MET ASN GLY ARG THR ILE LEU GLY SER ALA SEQRES 25 B 333 LEU LEU GLU ASP GLU PHE THR PRO PHE ASP VAL VAL ARG SEQRES 26 B 333 GLN CYS SER GLY VAL THR PHE GLN HET K36 A 401 59 HET K36 B 401 59 HETNAM K36 (1S,2S)-2-({N-[(BENZYLOXY)CARBONYL]-L-LEUCYL}AMINO)-1- HETNAM 2 K36 HYDROXY-3-[(3S)-2-OXOPYRROLIDIN-3-YL]PROPANE-1- HETNAM 3 K36 SULFONIC ACID HETSYN K36 GC376 FORMUL 3 K36 2(C21 H31 N3 O8 S) FORMUL 5 HOH *177(H2 O) HELIX 1 AA1 SER A 10 GLY A 15 1 6 HELIX 2 AA2 HIS A 41 CYS A 44 5 4 HELIX 3 AA3 GLU A 47 ASN A 51 5 5 HELIX 4 AA4 ASN A 53 ARG A 60 1 8 HELIX 5 AA5 SER A 62 PHE A 66 5 5 HELIX 6 AA6 ILE A 200 ASN A 214 1 15 HELIX 7 AA7 THR A 226 TYR A 237 1 12 HELIX 8 AA8 THR A 243 GLY A 258 1 16 HELIX 9 AA9 ALA A 260 GLY A 275 1 16 HELIX 10 AB1 THR A 292 GLN A 299 1 8 HELIX 11 AB2 SER B 10 GLY B 15 1 6 HELIX 12 AB3 HIS B 41 CYS B 44 5 4 HELIX 13 AB4 ASN B 53 ARG B 60 1 8 HELIX 14 AB5 SER B 62 PHE B 66 5 5 HELIX 15 AB6 ILE B 200 ASN B 214 1 15 HELIX 16 AB7 THR B 226 LYS B 236 1 11 HELIX 17 AB8 LEU B 250 GLY B 258 1 9 HELIX 18 AB9 ALA B 260 LEU B 272 1 13 HELIX 19 AC1 THR B 292 CYS B 300 1 9 SHEET 1 AA1 7 VAL A 73 LEU A 75 0 SHEET 2 AA1 7 LEU A 67 ALA A 70 -1 N ALA A 70 O VAL A 73 SHEET 3 AA1 7 MET A 17 CYS A 22 -1 N THR A 21 O LEU A 67 SHEET 4 AA1 7 THR A 25 LEU A 32 -1 O LEU A 27 N VAL A 20 SHEET 5 AA1 7 VAL A 35 PRO A 39 -1 O VAL A 35 N LEU A 32 SHEET 6 AA1 7 VAL A 86 VAL A 91 -1 O LEU A 89 N VAL A 36 SHEET 7 AA1 7 VAL A 77 GLY A 79 -1 N ILE A 78 O LYS A 90 SHEET 1 AA2 7 VAL A 73 LEU A 75 0 SHEET 2 AA2 7 LEU A 67 ALA A 70 -1 N ALA A 70 O VAL A 73 SHEET 3 AA2 7 MET A 17 CYS A 22 -1 N THR A 21 O LEU A 67 SHEET 4 AA2 7 THR A 25 LEU A 32 -1 O LEU A 27 N VAL A 20 SHEET 5 AA2 7 VAL A 35 PRO A 39 -1 O VAL A 35 N LEU A 32 SHEET 6 AA2 7 VAL A 86 VAL A 91 -1 O LEU A 89 N VAL A 36 SHEET 7 AA2 7 MET A 82 GLN A 83 -1 N GLN A 83 O VAL A 86 SHEET 1 AA3 5 LYS A 100 PHE A 103 0 SHEET 2 AA3 5 CYS A 156 GLU A 166 1 O PHE A 159 N LYS A 102 SHEET 3 AA3 5 VAL A 148 ASP A 153 -1 N ASN A 151 O SER A 158 SHEET 4 AA3 5 THR A 111 TYR A 118 -1 N SER A 113 O PHE A 150 SHEET 5 AA3 5 SER A 121 ALA A 129 -1 O TYR A 126 N VAL A 114 SHEET 1 AA4 3 LYS A 100 PHE A 103 0 SHEET 2 AA4 3 CYS A 156 GLU A 166 1 O PHE A 159 N LYS A 102 SHEET 3 AA4 3 HIS A 172 THR A 175 -1 O ALA A 173 N MET A 165 SHEET 1 AA5 7 VAL B 73 LEU B 75 0 SHEET 2 AA5 7 LEU B 67 ALA B 70 -1 N VAL B 68 O LEU B 75 SHEET 3 AA5 7 MET B 17 CYS B 22 -1 N THR B 21 O LEU B 67 SHEET 4 AA5 7 THR B 25 LEU B 32 -1 O GLY B 29 N VAL B 18 SHEET 5 AA5 7 VAL B 35 PRO B 39 -1 O TYR B 37 N LEU B 30 SHEET 6 AA5 7 VAL B 86 VAL B 91 -1 O LEU B 87 N CYS B 38 SHEET 7 AA5 7 VAL B 77 GLN B 83 -1 N ILE B 78 O LYS B 90 SHEET 1 AA6 5 TYR B 101 PHE B 103 0 SHEET 2 AA6 5 CYS B 156 GLU B 166 1 O PHE B 159 N LYS B 102 SHEET 3 AA6 5 VAL B 148 ASP B 153 -1 N ASN B 151 O SER B 158 SHEET 4 AA6 5 THR B 111 TYR B 118 -1 N SER B 113 O PHE B 150 SHEET 5 AA6 5 SER B 121 ALA B 129 -1 O TYR B 126 N VAL B 114 SHEET 1 AA7 3 TYR B 101 PHE B 103 0 SHEET 2 AA7 3 CYS B 156 GLU B 166 1 O PHE B 159 N LYS B 102 SHEET 3 AA7 3 HIS B 172 THR B 175 -1 O ALA B 173 N MET B 165 LINK SG CYS A 145 C21 K36 A 401 1555 1555 1.77 LINK SG CYS B 145 C21 K36 B 401 1555 1555 1.83 SITE 1 AC1 13 HIS A 41 PHE A 140 ASN A 142 GLY A 143 SITE 2 AC1 13 SER A 144 CYS A 145 HIS A 163 HIS A 164 SITE 3 AC1 13 MET A 165 GLU A 166 HIS A 172 ARG A 188 SITE 4 AC1 13 GLN A 189 SITE 1 AC2 17 LEU B 27 ASN B 28 HIS B 41 PHE B 140 SITE 2 AC2 17 LEU B 141 ASN B 142 GLY B 143 SER B 144 SITE 3 AC2 17 GLY B 146 SER B 147 HIS B 163 HIS B 164 SITE 4 AC2 17 MET B 165 GLU B 166 HIS B 172 GLN B 189 SITE 5 AC2 17 HOH B 515 CRYST1 55.123 99.746 60.364 90.00 108.63 90.00 P 1 21 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 0.018141 0.000000 0.006114 0.00000 SCALE2 0.000000 0.010025 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017482 0.00000