HEADER VIRAL PROTEIN 10-JUN-20 7CB7 TITLE 1.7A RESOLUTION STRUCTURE OF SARS-COV-2 MAIN PROTEASE (MPRO) IN TITLE 2 COMPLEX WITH BROAD-SPECTRUM CORONAVIRUS PROTEASE INHIBITOR GC376 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3C-LIKE PROTEINASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: 3CL-PRO,3CLP; COMPND 5 EC: 3.4.22.69; COMPND 6 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS MAIN PROTEASE, 3C-LIKE PROTEINASE, PROTEIN-INHIBITOR COMPLEX, GC376, KEYWDS 2 VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.C.WANG,C.S.YANG,M.H.HOU,C.L.TSAI,Y.Z.CHOU,Y.CHEN,M.C.HUNG REVDAT 2 29-NOV-23 7CB7 1 REMARK REVDAT 1 05-MAY-21 7CB7 0 JRNL AUTH Y.C.WANG,W.H.YANG,C.S.YANG,M.H.HOU,C.L.TSAI,Y.Z.CHOU, JRNL AUTH 2 M.C.HUNG,Y.CHEN JRNL TITL STRUCTURAL BASIS OF SARS-COV-2 MAIN PROTEASE INHIBITION BY A JRNL TITL 2 BROAD-SPECTRUM ANTI-CORONAVIRAL DRUG. JRNL REF AM J CANCER RES V. 10 2535 2020 JRNL REFN ISSN 2156-6976 JRNL PMID 32905393 REMARK 2 REMARK 2 RESOLUTION. 1.69 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.69 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.78 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 80.8 REMARK 3 NUMBER OF REFLECTIONS : 106790 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.158 REMARK 3 R VALUE (WORKING SET) : 0.157 REMARK 3 FREE R VALUE : 0.192 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.090 REMARK 3 FREE R VALUE TEST SET COUNT : 3300 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 27.7800 - 4.8800 0.94 5000 158 0.1615 0.2119 REMARK 3 2 4.8800 - 3.8800 0.95 5089 155 0.1365 0.1526 REMARK 3 3 3.8700 - 3.3900 0.95 5084 158 0.1442 0.1877 REMARK 3 4 3.3900 - 3.0800 0.95 5043 166 0.1561 0.1988 REMARK 3 5 3.0800 - 2.8600 0.95 5100 170 0.1610 0.2109 REMARK 3 6 2.8600 - 2.6900 0.96 5092 168 0.1666 0.2054 REMARK 3 7 2.6900 - 2.5500 0.96 5189 161 0.1685 0.1970 REMARK 3 8 2.5500 - 2.4400 0.96 5154 168 0.1632 0.1917 REMARK 3 9 2.4400 - 2.3500 0.97 5157 162 0.1598 0.2060 REMARK 3 10 2.3500 - 2.2700 0.96 5123 173 0.1552 0.1971 REMARK 3 11 2.2700 - 2.2000 0.95 5106 138 0.1615 0.2014 REMARK 3 12 2.2000 - 2.1300 0.93 4921 176 0.1540 0.2058 REMARK 3 13 2.1300 - 2.0800 0.90 4844 172 0.1519 0.1843 REMARK 3 14 2.0800 - 2.0300 0.86 4533 145 0.1513 0.2104 REMARK 3 15 2.0300 - 1.9800 0.81 4385 104 0.1606 0.1719 REMARK 3 16 1.9800 - 1.9400 0.76 4104 138 0.1557 0.1672 REMARK 3 17 1.9400 - 1.9000 0.70 3703 119 0.1563 0.1550 REMARK 3 18 1.9000 - 1.8600 0.65 3462 118 0.1559 0.1804 REMARK 3 19 1.8600 - 1.8300 0.61 3276 101 0.1528 0.2037 REMARK 3 20 1.8300 - 1.8000 0.58 3060 92 0.1544 0.1519 REMARK 3 21 1.8000 - 1.7700 0.55 2992 103 0.1670 0.1769 REMARK 3 22 1.7700 - 1.7400 0.53 2833 84 0.1849 0.2025 REMARK 3 23 1.7400 - 1.7200 0.51 2669 82 0.1966 0.2227 REMARK 3 24 1.7200 - 1.6900 0.48 2571 89 0.2097 0.2346 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) : 0.149 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.194 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.50 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 : 0.009 4966 REMARK 3 ANGLE : 1.042 6745 REMARK 3 CHIRALITY : 0.066 752 REMARK 3 PLANARITY : 0.008 876 REMARK 3 DIHEDRAL : 18.310 688 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID -4 THROUGH 110 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.2554 -4.9056 29.5354 REMARK 3 T TENSOR REMARK 3 T11: 0.0894 T22: 0.1872 REMARK 3 T33: 0.0709 T12: -0.0135 REMARK 3 T13: 0.0048 T23: 0.0401 REMARK 3 L TENSOR REMARK 3 L11: 3.0707 L22: 1.1275 REMARK 3 L33: 0.8222 L12: 0.8608 REMARK 3 L13: 0.3996 L23: 0.0038 REMARK 3 S TENSOR REMARK 3 S11: 0.1198 S12: -0.5661 S13: -0.1574 REMARK 3 S21: 0.1424 S22: -0.1355 S23: -0.0803 REMARK 3 S31: 0.0267 S32: -0.0185 S33: 0.0099 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 111 THROUGH 155 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.4841 -1.7786 19.1200 REMARK 3 T TENSOR REMARK 3 T11: 0.0687 T22: 0.0672 REMARK 3 T33: 0.0536 T12: -0.0191 REMARK 3 T13: -0.0089 T23: 0.0002 REMARK 3 L TENSOR REMARK 3 L11: 3.5811 L22: 1.8624 REMARK 3 L33: 1.6183 L12: 1.1797 REMARK 3 L13: 0.0590 L23: -0.6778 REMARK 3 S TENSOR REMARK 3 S11: -0.0581 S12: -0.0362 S13: 0.1125 REMARK 3 S21: -0.1017 S22: 0.0356 S23: 0.0703 REMARK 3 S31: 0.0269 S32: -0.0628 S33: 0.0055 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 156 THROUGH 213 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.7840 3.8441 13.7511 REMARK 3 T TENSOR REMARK 3 T11: 0.0633 T22: 0.0706 REMARK 3 T33: 0.0851 T12: -0.0214 REMARK 3 T13: 0.0052 T23: 0.0293 REMARK 3 L TENSOR REMARK 3 L11: 1.3779 L22: 0.2605 REMARK 3 L33: 1.5635 L12: 0.3209 REMARK 3 L13: 0.2845 L23: 0.1112 REMARK 3 S TENSOR REMARK 3 S11: -0.1164 S12: 0.0508 S13: 0.1873 REMARK 3 S21: -0.0828 S22: 0.0620 S23: -0.0439 REMARK 3 S31: -0.0945 S32: 0.0192 S33: 0.0711 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 214 THROUGH 302 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.4212 2.4190 -6.2037 REMARK 3 T TENSOR REMARK 3 T11: 0.1416 T22: 0.1541 REMARK 3 T33: 0.0582 T12: -0.0348 REMARK 3 T13: 0.0092 T23: 0.0275 REMARK 3 L TENSOR REMARK 3 L11: 2.3698 L22: 2.0072 REMARK 3 L33: 2.3640 L12: 0.7067 REMARK 3 L13: -0.5238 L23: 0.1292 REMARK 3 S TENSOR REMARK 3 S11: 0.0748 S12: 0.0287 S13: -0.0370 REMARK 3 S21: -0.1171 S22: -0.0576 S23: -0.0912 REMARK 3 S31: 0.1212 S32: -0.4069 S33: -0.0111 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 180 ) REMARK 3 ORIGIN FOR THE GROUP (A): -17.4002 -18.4255 15.8872 REMARK 3 T TENSOR REMARK 3 T11: 0.0574 T22: 0.0464 REMARK 3 T33: 0.0321 T12: -0.0140 REMARK 3 T13: 0.0235 T23: -0.0156 REMARK 3 L TENSOR REMARK 3 L11: 1.3477 L22: 3.3165 REMARK 3 L33: 0.9436 L12: -0.3369 REMARK 3 L13: 0.1706 L23: -0.7940 REMARK 3 S TENSOR REMARK 3 S11: -0.0260 S12: 0.0699 S13: -0.0370 REMARK 3 S21: -0.1945 S22: 0.0546 S23: 0.0464 REMARK 3 S31: 0.0076 S32: -0.0006 S33: -0.0260 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 181 THROUGH 305 ) REMARK 3 ORIGIN FOR THE GROUP (A): -19.9796 10.8645 16.1567 REMARK 3 T TENSOR REMARK 3 T11: 0.0861 T22: 0.0813 REMARK 3 T33: 0.0804 T12: -0.0126 REMARK 3 T13: 0.0058 T23: 0.0053 REMARK 3 L TENSOR REMARK 3 L11: 1.5308 L22: 2.6259 REMARK 3 L33: 1.4119 L12: 0.8418 REMARK 3 L13: 0.6400 L23: 0.6329 REMARK 3 S TENSOR REMARK 3 S11: -0.0484 S12: 0.0327 S13: 0.1365 REMARK 3 S21: -0.2517 S22: 0.0887 S23: 0.0272 REMARK 3 S31: -0.1436 S32: 0.1628 S33: -0.0314 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 1 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: (CHAIN 'A' AND (RESID 23 OR RESID 26 REMARK 3 THROUGH 79 OR RESID 81 THROUGH 93 OR REMARK 3 RESID 95 THROUGH 116 OR RESID 118 THROUGH REMARK 3 147 OR RESID 149 THROUGH 207 OR RESID 209 REMARK 3 THROUGH 236 OR RESID 238 THROUGH 241 OR REMARK 3 RESID 244 THROUGH 289 OR RESID 291 REMARK 3 THROUGH 298 OR RESID 300 THROUGH 313 OR REMARK 3 RESID 315 THROUGH 317 OR RESID 319 REMARK 3 THROUGH 320)) REMARK 3 SELECTION : (CHAIN 'B' AND (RESID 23 OR RESID 26 REMARK 3 THROUGH 79 OR RESID 81 THROUGH 93 OR REMARK 3 RESID 95 THROUGH 116 OR RESID 118 THROUGH REMARK 3 147 OR RESID 149 THROUGH 207 OR RESID 209 REMARK 3 THROUGH 236 OR RESID 238 THROUGH 241 OR REMARK 3 RESID 244 THROUGH 289 OR RESID 291 REMARK 3 THROUGH 298 OR RESID 300 THROUGH 313 OR REMARK 3 RESID 315 THROUGH 317 OR RESID 319 REMARK 3 THROUGH 320)) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7CB7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-JUN-20. REMARK 100 THE DEPOSITION ID IS D_1300017287. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-MAY-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : BL15A1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : M REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 106790 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.690 REMARK 200 RESOLUTION RANGE LOW (A) : 27.780 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.02300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.69 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.75 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.12800 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: 7CAM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PROPANE, 0.02 M REMARK 280 SODIUM/POTASSIUM PHOSPHATE, 20% (W/V) PEG3350, PH 6.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, 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 49.39600 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: 2660 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.0 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 VAL A 303 REMARK 465 THR A 304 REMARK 465 PHE A 305 REMARK 465 GLN A 306 REMARK 465 GLY B -4 REMARK 465 SER B -3 REMARK 465 GLY B -2 REMARK 465 GLY B -1 REMARK 465 GLY B 0 REMARK 465 GLN B 306 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 ARG B 4 CG CD NE CZ NH1 NH2 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 OD1 ASP A 153 O HOH A 501 1.79 REMARK 500 NZ LYS B 97 O HOH B 501 1.85 REMARK 500 NZ LYS B 5 O HOH B 502 2.13 REMARK 500 OE1 GLU A 47 O HOH A 502 2.15 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 ARG A 222 CG ARG A 222 CD -0.161 REMARK 500 CYS B 22 CB CYS B 22 SG -0.098 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 -127.04 52.68 REMARK 500 ASN A 51 74.40 -163.98 REMARK 500 ASN A 84 -123.31 52.55 REMARK 500 TYR A 154 -112.41 62.45 REMARK 500 PRO A 184 35.79 -85.55 REMARK 500 ASP B 33 -129.85 52.35 REMARK 500 ASN B 51 73.41 -162.42 REMARK 500 ASN B 84 -124.15 50.67 REMARK 500 TYR B 154 -106.60 58.37 REMARK 500 PRO B 184 31.61 -90.24 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 ARG A 222 PHE A 223 146.24 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 B 784 DISTANCE = 5.86 ANGSTROMS REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 K36 AND B1S HAVE ALTERNATE CONFORMATIONS. REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 401 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A -2 O REMARK 620 2 SER A 1 OG 124.4 REMARK 620 3 HOH A 745 O 126.0 89.9 REMARK 620 N 1 2 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 402 REMARK 630 K36 B 402 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: PHQ LEU 04F REMARK 630 DETAILS: NULL REMARK 630 MOLECULE TYPE: NULL REMARK 630 MOLECULE NAME: (1R,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 B1S A 403 REMARK 630 B1S B 401 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: PHQ LEU B1Y 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 NA A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K36 A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue B1S A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide B1S B 401 and CYS B REMARK 800 165 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide K36 B 402 and CYS B REMARK 800 165 DBREF 7CB7 A 1 306 UNP P0DTD1 R1AB_SARS2 3264 3569 DBREF 7CB7 B 1 306 UNP P0DTD1 R1AB_SARS2 3264 3569 SEQADV 7CB7 GLY A -4 UNP P0DTD1 EXPRESSION TAG SEQADV 7CB7 SER A -3 UNP P0DTD1 EXPRESSION TAG SEQADV 7CB7 GLY A -2 UNP P0DTD1 EXPRESSION TAG SEQADV 7CB7 GLY A -1 UNP P0DTD1 EXPRESSION TAG SEQADV 7CB7 GLY A 0 UNP P0DTD1 EXPRESSION TAG SEQADV 7CB7 GLY B -4 UNP P0DTD1 EXPRESSION TAG SEQADV 7CB7 SER B -3 UNP P0DTD1 EXPRESSION TAG SEQADV 7CB7 GLY B -2 UNP P0DTD1 EXPRESSION TAG SEQADV 7CB7 GLY B -1 UNP P0DTD1 EXPRESSION TAG SEQADV 7CB7 GLY B 0 UNP P0DTD1 EXPRESSION TAG SEQRES 1 A 311 GLY SER GLY GLY GLY SER GLY PHE ARG LYS MET ALA PHE SEQRES 2 A 311 PRO SER GLY LYS VAL GLU GLY CYS MET VAL GLN VAL THR SEQRES 3 A 311 CYS GLY THR THR THR LEU ASN GLY LEU TRP LEU ASP ASP SEQRES 4 A 311 VAL VAL TYR CYS PRO ARG HIS VAL ILE CYS THR SER GLU SEQRES 5 A 311 ASP MET LEU ASN PRO ASN TYR GLU ASP LEU LEU ILE ARG SEQRES 6 A 311 LYS SER ASN HIS ASN PHE LEU VAL GLN ALA GLY ASN VAL SEQRES 7 A 311 GLN LEU ARG VAL ILE GLY HIS SER MET GLN ASN CYS VAL SEQRES 8 A 311 LEU LYS LEU LYS VAL ASP THR ALA ASN PRO LYS THR PRO SEQRES 9 A 311 LYS TYR LYS PHE VAL ARG ILE GLN PRO GLY GLN THR PHE SEQRES 10 A 311 SER VAL LEU ALA CYS TYR ASN GLY SER PRO SER GLY VAL SEQRES 11 A 311 TYR GLN CYS ALA MET ARG PRO ASN PHE THR ILE LYS GLY SEQRES 12 A 311 SER PHE LEU ASN GLY SER CYS GLY SER VAL GLY PHE ASN SEQRES 13 A 311 ILE ASP TYR ASP CYS VAL SER PHE CYS TYR MET HIS HIS SEQRES 14 A 311 MET GLU LEU PRO THR GLY VAL HIS ALA GLY THR ASP LEU SEQRES 15 A 311 GLU GLY ASN PHE TYR GLY PRO PHE VAL ASP ARG GLN THR SEQRES 16 A 311 ALA GLN ALA ALA GLY THR ASP THR THR ILE THR VAL ASN SEQRES 17 A 311 VAL LEU ALA TRP LEU TYR ALA ALA VAL ILE ASN GLY ASP SEQRES 18 A 311 ARG TRP PHE LEU ASN ARG PHE THR THR THR LEU ASN ASP SEQRES 19 A 311 PHE ASN LEU VAL ALA MET LYS TYR ASN TYR GLU PRO LEU SEQRES 20 A 311 THR GLN ASP HIS VAL ASP ILE LEU GLY PRO LEU SER ALA SEQRES 21 A 311 GLN THR GLY ILE ALA VAL LEU ASP MET CYS ALA SER LEU SEQRES 22 A 311 LYS GLU LEU LEU GLN ASN GLY MET ASN GLY ARG THR ILE SEQRES 23 A 311 LEU GLY SER ALA LEU LEU GLU ASP GLU PHE THR PRO PHE SEQRES 24 A 311 ASP VAL VAL ARG GLN CYS SER GLY VAL THR PHE GLN SEQRES 1 B 311 GLY SER GLY GLY GLY SER GLY PHE ARG LYS MET ALA PHE SEQRES 2 B 311 PRO SER GLY LYS VAL GLU GLY CYS MET VAL GLN VAL THR SEQRES 3 B 311 CYS GLY THR THR THR LEU ASN GLY LEU TRP LEU ASP ASP SEQRES 4 B 311 VAL VAL TYR CYS PRO ARG HIS VAL ILE CYS THR SER GLU SEQRES 5 B 311 ASP MET LEU ASN PRO ASN TYR GLU ASP LEU LEU ILE ARG SEQRES 6 B 311 LYS SER ASN HIS ASN PHE LEU VAL GLN ALA GLY ASN VAL SEQRES 7 B 311 GLN LEU ARG VAL ILE GLY HIS SER MET GLN ASN CYS VAL SEQRES 8 B 311 LEU LYS LEU LYS VAL ASP THR ALA ASN PRO LYS THR PRO SEQRES 9 B 311 LYS TYR LYS PHE VAL ARG ILE GLN PRO GLY GLN THR PHE SEQRES 10 B 311 SER VAL LEU ALA CYS TYR ASN GLY SER PRO SER GLY VAL SEQRES 11 B 311 TYR GLN CYS ALA MET ARG PRO ASN PHE THR ILE LYS GLY SEQRES 12 B 311 SER PHE LEU ASN GLY SER CYS GLY SER VAL GLY PHE ASN SEQRES 13 B 311 ILE ASP TYR ASP CYS VAL SER PHE CYS TYR MET HIS HIS SEQRES 14 B 311 MET GLU LEU PRO THR GLY VAL HIS ALA GLY THR ASP LEU SEQRES 15 B 311 GLU GLY ASN PHE TYR GLY PRO PHE VAL ASP ARG GLN THR SEQRES 16 B 311 ALA GLN ALA ALA GLY THR ASP THR THR ILE THR VAL ASN SEQRES 17 B 311 VAL LEU ALA TRP LEU TYR ALA ALA VAL ILE ASN GLY ASP SEQRES 18 B 311 ARG TRP PHE LEU ASN ARG PHE THR THR THR LEU ASN ASP SEQRES 19 B 311 PHE ASN LEU VAL ALA MET LYS TYR ASN TYR GLU PRO LEU SEQRES 20 B 311 THR GLN ASP HIS VAL ASP ILE LEU GLY PRO LEU SER ALA SEQRES 21 B 311 GLN THR GLY ILE ALA VAL LEU ASP MET CYS ALA SER LEU SEQRES 22 B 311 LYS GLU LEU LEU GLN ASN GLY MET ASN GLY ARG THR ILE SEQRES 23 B 311 LEU GLY SER ALA LEU LEU GLU ASP GLU PHE THR PRO PHE SEQRES 24 B 311 ASP VAL VAL ARG GLN CYS SER GLY VAL THR PHE GLN HET NA A 401 1 HET K36 A 402 59 HET B1S A 403 59 HET B1S B 401 58 HET K36 B 402 58 HETNAM NA SODIUM ION 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 HETNAM B1S (1R,2S)-2-({N-[(BENZYLOXY)CARBONYL]-L-LEUCYL}AMINO)-1- HETNAM 2 B1S HYDROXY-3-[(3S)-2-OXOPYRROLIDIN-3-YL]PROPANE-1- HETNAM 3 B1S SULFONIC ACID HETSYN K36 GC376 FORMUL 3 NA NA 1+ FORMUL 4 K36 2(C21 H31 N3 O8 S) FORMUL 5 B1S 2(C21 H31 N3 O8 S) FORMUL 8 HOH *565(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 LEU A 250 1 8 HELIX 9 AA9 LEU A 250 GLY A 258 1 9 HELIX 10 AB1 ALA A 260 GLY A 275 1 16 HELIX 11 AB2 THR A 292 SER A 301 1 10 HELIX 12 AB3 SER B 10 GLY B 15 1 6 HELIX 13 AB4 HIS B 41 CYS B 44 5 4 HELIX 14 AB5 GLU B 47 ASN B 51 5 5 HELIX 15 AB6 ASN B 53 ARG B 60 1 8 HELIX 16 AB7 SER B 62 PHE B 66 5 5 HELIX 17 AB8 ILE B 200 ASN B 214 1 15 HELIX 18 AB9 THR B 226 TYR B 237 1 12 HELIX 19 AC1 THR B 243 LEU B 250 1 8 HELIX 20 AC2 LEU B 250 GLY B 258 1 9 HELIX 21 AC3 ALA B 260 GLY B 275 1 16 HELIX 22 AC4 THR B 292 GLY B 302 1 11 SHEET 1 AA1 7 VAL A 73 LEU A 75 0 SHEET 2 AA1 7 LEU A 67 ALA A 70 -1 N VAL A 68 O LEU A 75 SHEET 3 AA1 7 MET A 17 CYS A 22 -1 N GLN A 19 O GLN A 69 SHEET 4 AA1 7 THR A 25 LEU A 32 -1 O THR A 25 N CYS A 22 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 87 N CYS A 38 SHEET 7 AA1 7 VAL A 77 GLN A 83 -1 N SER A 81 O LYS A 88 SHEET 1 AA2 5 LYS A 100 PHE A 103 0 SHEET 2 AA2 5 CYS A 156 GLU A 166 1 O VAL A 157 N LYS A 100 SHEET 3 AA2 5 VAL A 148 ASP A 153 -1 N ASN A 151 O SER A 158 SHEET 4 AA2 5 THR A 111 TYR A 118 -1 N SER A 113 O PHE A 150 SHEET 5 AA2 5 SER A 121 ALA A 129 -1 O TYR A 126 N VAL A 114 SHEET 1 AA3 3 LYS A 100 PHE A 103 0 SHEET 2 AA3 3 CYS A 156 GLU A 166 1 O VAL A 157 N LYS A 100 SHEET 3 AA3 3 HIS A 172 THR A 175 -1 O ALA A 173 N MET A 165 SHEET 1 AA4 7 VAL B 73 LEU B 75 0 SHEET 2 AA4 7 LEU B 67 ALA B 70 -1 N VAL B 68 O LEU B 75 SHEET 3 AA4 7 MET B 17 CYS B 22 -1 N GLN B 19 O GLN B 69 SHEET 4 AA4 7 THR B 25 LEU B 32 -1 O LEU B 27 N VAL B 20 SHEET 5 AA4 7 VAL B 35 PRO B 39 -1 O VAL B 35 N LEU B 32 SHEET 6 AA4 7 VAL B 86 VAL B 91 -1 O LEU B 87 N CYS B 38 SHEET 7 AA4 7 VAL B 77 GLN B 83 -1 N ILE B 78 O LYS B 90 SHEET 1 AA5 5 LYS B 100 PHE B 103 0 SHEET 2 AA5 5 CYS B 156 GLU B 166 1 O VAL B 157 N LYS B 100 SHEET 3 AA5 5 VAL B 148 ASP B 153 -1 N ASN B 151 O SER B 158 SHEET 4 AA5 5 THR B 111 TYR B 118 -1 N SER B 113 O PHE B 150 SHEET 5 AA5 5 SER B 121 ALA B 129 -1 O TYR B 126 N VAL B 114 SHEET 1 AA6 3 LYS B 100 PHE B 103 0 SHEET 2 AA6 3 CYS B 156 GLU B 166 1 O VAL B 157 N LYS B 100 SHEET 3 AA6 3 HIS B 172 THR B 175 -1 O ALA B 173 N MET B 165 LINK SG CYS A 145 C21AK36 A 402 1555 1555 1.77 LINK SG CYS A 145 C21BB1S A 403 1555 1555 1.77 LINK SG CYS B 145 C21AB1S B 401 1555 1555 1.73 LINK SG CYS B 145 C21BK36 B 402 1555 1555 1.73 LINK O GLY A -2 NA NA A 401 1555 1555 2.71 LINK OG SER A 1 NA NA A 401 1555 1555 2.60 LINK NA NA A 401 O HOH A 745 1555 1555 2.99 SITE 1 AC1 5 GLY A -2 GLY A -1 GLY A 0 SER A 1 SITE 2 AC1 5 HOH A 745 SITE 1 AC2 14 PHE A 140 ASN A 142 GLY A 143 SER A 144 SITE 2 AC2 14 CYS A 145 HIS A 163 HIS A 164 MET A 165 SITE 3 AC2 14 GLU A 166 HIS A 172 GLN A 189 B1S A 403 SITE 4 AC2 14 HOH A 517 HOH A 588 SITE 1 AC3 13 HIS A 41 PHE A 140 ASN A 142 CYS A 145 SITE 2 AC3 13 HIS A 163 HIS A 164 MET A 165 GLU A 166 SITE 3 AC3 13 HIS A 172 GLN A 189 K36 A 402 HOH A 517 SITE 4 AC3 13 HOH A 588 SITE 1 AC4 18 LEU B 27 ASN B 28 HIS B 41 PHE B 140 SITE 2 AC4 18 ASN B 142 GLY B 143 SER B 144 GLY B 146 SITE 3 AC4 18 SER B 147 HIS B 163 HIS B 164 MET B 165 SITE 4 AC4 18 GLU B 166 HIS B 172 GLN B 189 K36 B 402 SITE 5 AC4 18 HOH B 554 HOH B 666 SITE 1 AC5 17 LEU B 27 ASN B 28 HIS B 41 PHE B 140 SITE 2 AC5 17 ASN B 142 GLY B 143 SER B 144 GLY B 146 SITE 3 AC5 17 SER B 147 HIS B 163 HIS B 164 MET B 165 SITE 4 AC5 17 GLU B 166 HIS B 172 GLN B 189 B1S B 401 SITE 5 AC5 17 HOH B 554 CRYST1 55.029 98.792 59.492 90.00 108.41 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 0.018172 0.000000 0.006049 0.00000 SCALE2 0.000000 0.010122 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017716 0.00000