HEADER VIRAL PROTEIN 21-FEB-23 8IGN TITLE CRYSTAL STRUCTURE OF SARS-COV-2 MAIN PROTEASE IN COMPLEX WITH RAY1216 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3C-LIKE PROTEINASE NSP5; COMPND 3 CHAIN: B, A; COMPND 4 SYNONYM: 3CL-PRO,3CLP,MAIN PROTEASE,MPRO,NON-STRUCTURAL PROTEIN 5, COMPND 5 NSP5,SARS CORONAVIRUS MAIN PROTEINASE; COMPND 6 EC: 3.4.22.69; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 3 2; SOURCE 4 ORGANISM_COMMON: 2019-NCOV, SARS-COV-2; SOURCE 5 ORGANISM_TAXID: 2697049; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS SARS-COV-2, NSP5, MAIN PROTEASE, CORONAVIRUS, PROTEASE INHIBITOR, KEYWDS 2 ALPHA-KETOAMIDE INHIBITOR, PEPTIDOMIMETIC INHIBITOR, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR X.HUANG,B.ZHOU,J.XU,Z.YANG,N.ZHONG,X.XIONG REVDAT 4 17-APR-24 8IGN 1 JRNL REVDAT 3 10-APR-24 8IGN 1 JRNL REVDAT 2 07-FEB-24 8IGN 1 REMARK REVDAT 1 05-APR-23 8IGN 0 JRNL AUTH X.CHEN,X.HUANG,Q.MA,P.KUZMIC,B.ZHOU,S.ZHANG,J.CHEN,J.XU, JRNL AUTH 2 B.LIU,H.JIANG,W.ZHANG,C.YANG,S.WU,J.HUANG,H.LI,C.LONG, JRNL AUTH 3 X.ZHAO,H.XU,Y.SHENG,Y.GUO,C.NIU,L.XUE,Y.XU,J.LIU,T.ZHANG, JRNL AUTH 4 J.SPENCER,Z.ZHU,W.DENG,X.CHEN,S.H.CHEN,N.ZHONG,X.XIONG, JRNL AUTH 5 Z.YANG JRNL TITL PRECLINICAL EVALUATION OF THE SARS-COV-2 M PRO INHIBITOR JRNL TITL 2 RAY1216 SHOWS IMPROVED PHARMACOKINETICS COMPARED WITH JRNL TITL 3 NIRMATRELVIR. JRNL REF NAT MICROBIOL V. 9 1075 2024 JRNL REFN ESSN 2058-5276 JRNL PMID 38553607 JRNL DOI 10.1038/S41564-024-01618-9 REMARK 2 REMARK 2 RESOLUTION. 2.02 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0267 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.02 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 57.47 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 45281 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 2275 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.02 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.07 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3336 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.37 REMARK 3 BIN R VALUE (WORKING SET) : 0.2930 REMARK 3 BIN FREE R VALUE SET COUNT : 190 REMARK 3 BIN FREE R VALUE : 0.2930 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4642 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 90 REMARK 3 SOLVENT ATOMS : 255 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.08 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.45000 REMARK 3 B22 (A**2) : -1.55000 REMARK 3 B33 (A**2) : 0.30000 REMARK 3 B12 (A**2) : 2.11000 REMARK 3 B13 (A**2) : 1.04000 REMARK 3 B23 (A**2) : 2.61000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 1.200 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.159 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.162 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 14.329 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.940 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4860 ; 0.007 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 4494 ; 0.002 ; 0.015 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6624 ; 1.479 ; 1.645 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10348 ; 1.267 ; 1.576 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 604 ; 7.476 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 246 ;32.474 ;22.439 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 760 ;14.395 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;17.796 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 642 ; 0.091 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5572 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1136 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2416 ; 2.456 ; 2.524 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2415 ; 2.442 ; 2.522 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3020 ; 3.204 ; 3.787 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3021 ; 3.213 ; 3.788 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2444 ; 2.704 ; 2.845 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2440 ; 2.687 ; 2.842 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3605 ; 3.528 ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 20561 ; 4.882 ;48.550 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 20562 ; 4.882 ;48.548 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 9302 ; 7.633 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 B A 9662 0.05 0.05 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 79 REMARK 3 ORIGIN FOR THE GROUP (A): 15.6055 -0.0690 -17.8323 REMARK 3 T TENSOR REMARK 3 T11: 0.0150 T22: 0.2227 REMARK 3 T33: 0.1322 T12: -0.0150 REMARK 3 T13: 0.0039 T23: -0.0467 REMARK 3 L TENSOR REMARK 3 L11: 0.9383 L22: 0.2839 REMARK 3 L33: 1.0455 L12: -0.2374 REMARK 3 L13: -0.7597 L23: 0.0421 REMARK 3 S TENSOR REMARK 3 S11: 0.0071 S12: 0.0663 S13: -0.0158 REMARK 3 S21: -0.0561 S22: -0.0222 S23: -0.0056 REMARK 3 S31: 0.0334 S32: 0.0525 S33: 0.0151 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 80 A 198 REMARK 3 ORIGIN FOR THE GROUP (A): 15.4277 -0.1033 -6.1852 REMARK 3 T TENSOR REMARK 3 T11: 0.0028 T22: 0.2131 REMARK 3 T33: 0.1331 T12: -0.0120 REMARK 3 T13: 0.0056 T23: -0.0483 REMARK 3 L TENSOR REMARK 3 L11: 0.6442 L22: 0.1315 REMARK 3 L33: 0.5505 L12: -0.1387 REMARK 3 L13: -0.3133 L23: -0.0749 REMARK 3 S TENSOR REMARK 3 S11: -0.0138 S12: -0.0279 S13: 0.0156 REMARK 3 S21: -0.0097 S22: 0.0070 S23: -0.0050 REMARK 3 S31: 0.0247 S32: 0.0927 S33: 0.0068 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 199 A 301 REMARK 3 ORIGIN FOR THE GROUP (A): 8.8411 -0.7050 21.7507 REMARK 3 T TENSOR REMARK 3 T11: 0.0052 T22: 0.2458 REMARK 3 T33: 0.1297 T12: -0.0084 REMARK 3 T13: 0.0058 T23: -0.0450 REMARK 3 L TENSOR REMARK 3 L11: 0.6585 L22: 0.2562 REMARK 3 L33: 1.1869 L12: -0.1461 REMARK 3 L13: -0.3993 L23: 0.1405 REMARK 3 S TENSOR REMARK 3 S11: -0.0457 S12: -0.1336 S13: -0.0048 REMARK 3 S21: 0.0188 S22: 0.0458 S23: 0.0137 REMARK 3 S31: 0.0129 S32: 0.1691 S33: -0.0001 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 78 REMARK 3 ORIGIN FOR THE GROUP (A): -16.5764 17.1128 -0.1771 REMARK 3 T TENSOR REMARK 3 T11: 0.0332 T22: 0.2012 REMARK 3 T33: 0.1530 T12: -0.0122 REMARK 3 T13: 0.0013 T23: -0.0520 REMARK 3 L TENSOR REMARK 3 L11: 1.0986 L22: 0.9197 REMARK 3 L33: 0.5032 L12: -0.8352 REMARK 3 L13: -0.3966 L23: 0.0346 REMARK 3 S TENSOR REMARK 3 S11: 0.0067 S12: 0.0176 S13: 0.1141 REMARK 3 S21: 0.0818 S22: 0.0149 S23: -0.0341 REMARK 3 S31: -0.1040 S32: -0.0216 S33: -0.0216 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 79 B 197 REMARK 3 ORIGIN FOR THE GROUP (A): -15.6967 5.8098 0.6932 REMARK 3 T TENSOR REMARK 3 T11: 0.0023 T22: 0.1973 REMARK 3 T33: 0.1450 T12: -0.0142 REMARK 3 T13: -0.0022 T23: -0.0498 REMARK 3 L TENSOR REMARK 3 L11: 0.8820 L22: 0.4816 REMARK 3 L33: 0.4878 L12: -0.1282 REMARK 3 L13: -0.1817 L23: -0.2712 REMARK 3 S TENSOR REMARK 3 S11: 0.0195 S12: 0.0514 S13: -0.0160 REMARK 3 S21: 0.0072 S22: -0.0212 S23: 0.0236 REMARK 3 S31: -0.0177 S32: -0.0159 S33: 0.0017 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 198 B 301 REMARK 3 ORIGIN FOR THE GROUP (A): -7.3435 -21.6568 3.5466 REMARK 3 T TENSOR REMARK 3 T11: 0.0077 T22: 0.2061 REMARK 3 T33: 0.1658 T12: 0.0001 REMARK 3 T13: 0.0184 T23: -0.0407 REMARK 3 L TENSOR REMARK 3 L11: 0.7829 L22: 1.5252 REMARK 3 L33: 0.1656 L12: -0.3766 REMARK 3 L13: -0.3382 L23: 0.0198 REMARK 3 S TENSOR REMARK 3 S11: -0.0492 S12: -0.0043 S13: -0.1095 REMARK 3 S21: -0.0154 S22: -0.0088 S23: 0.1243 REMARK 3 S31: 0.0290 S32: 0.0121 S33: 0.0580 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 8IGN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 01-MAR-23. REMARK 100 THE DEPOSITION ID IS D_1300035580. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-SEP-22 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 : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97853 REMARK 200 MONOCHROMATOR : DOUBLE MIRROR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS BUILT 20220220 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.7 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48627 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 59.420 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.50400 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 2.8.3 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.82 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES MONOHYDRATE PH 6.5, 12% W/V REMARK 280 POLYETHYLENE GLYCOL 20,000. PROTEIN CONCENTRATION 10MG/ML., REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: 25340 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY B 302 REMARK 465 VAL B 303 REMARK 465 THR B 304 REMARK 465 PHE B 305 REMARK 465 GLN B 306 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 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 GLN B 74 CG CD OE1 NE2 REMARK 470 GLN B 110 CG CD OE1 NE2 REMARK 470 GLN A 74 CG CD OE1 NE2 REMARK 470 GLN A 110 CG CD OE1 NE2 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 SG CYS A 145 C7 7ON A 401 1.76 REMARK 500 SG CYS B 145 C7 7ON B 401 1.77 REMARK 500 O VAL A 114 O HOH A 501 1.86 REMARK 500 OG SER A 1 O HOH A 502 1.93 REMARK 500 O GLY A 124 O HOH A 501 2.05 REMARK 500 O HOH B 535 O HOH B 620 2.06 REMARK 500 O HOH B 614 O HOH B 626 2.07 REMARK 500 OG SER B 1 O HOH B 501 2.12 REMARK 500 O LEU B 57 O HOH B 502 2.18 REMARK 500 OD1 ASN A 142 O HOH A 503 2.19 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 B 33 -129.32 54.14 REMARK 500 ASN B 51 64.92 -163.05 REMARK 500 ASN B 84 -122.70 54.74 REMARK 500 TYR B 154 -116.40 64.13 REMARK 500 PRO B 184 48.35 -87.91 REMARK 500 ASP A 33 -129.86 53.83 REMARK 500 ASN A 51 68.56 -171.32 REMARK 500 ASN A 84 -121.12 53.67 REMARK 500 TYR A 154 -113.85 59.66 REMARK 500 THR A 224 -168.24 -126.84 REMARK 500 REMARK 500 REMARK: NULL DBREF 8IGN B 1 306 UNP P0DTC1 R1A_SARS2 3264 3569 DBREF 8IGN A 1 306 UNP P0DTC1 R1A_SARS2 3264 3569 SEQRES 1 B 306 SER GLY PHE ARG LYS MET ALA PHE PRO SER GLY LYS VAL SEQRES 2 B 306 GLU GLY CYS MET VAL GLN VAL THR CYS GLY THR THR THR SEQRES 3 B 306 LEU ASN GLY LEU TRP LEU ASP ASP VAL VAL TYR CYS PRO SEQRES 4 B 306 ARG HIS VAL ILE CYS THR SER GLU ASP MET LEU ASN PRO SEQRES 5 B 306 ASN TYR GLU ASP LEU LEU ILE ARG LYS SER ASN HIS ASN SEQRES 6 B 306 PHE LEU VAL GLN ALA GLY ASN VAL GLN LEU ARG VAL ILE SEQRES 7 B 306 GLY HIS SER MET GLN ASN CYS VAL LEU LYS LEU LYS VAL SEQRES 8 B 306 ASP THR ALA ASN PRO LYS THR PRO LYS TYR LYS PHE VAL SEQRES 9 B 306 ARG ILE GLN PRO GLY GLN THR PHE SER VAL LEU ALA CYS SEQRES 10 B 306 TYR ASN GLY SER PRO SER GLY VAL TYR GLN CYS ALA MET SEQRES 11 B 306 ARG PRO ASN PHE THR ILE LYS GLY SER PHE LEU ASN GLY SEQRES 12 B 306 SER CYS GLY SER VAL GLY PHE ASN ILE ASP TYR ASP CYS SEQRES 13 B 306 VAL SER PHE CYS TYR MET HIS HIS MET GLU LEU PRO THR SEQRES 14 B 306 GLY VAL HIS ALA GLY THR ASP LEU GLU GLY ASN PHE TYR SEQRES 15 B 306 GLY PRO PHE VAL ASP ARG GLN THR ALA GLN ALA ALA GLY SEQRES 16 B 306 THR ASP THR THR ILE THR VAL ASN VAL LEU ALA TRP LEU SEQRES 17 B 306 TYR ALA ALA VAL ILE ASN GLY ASP ARG TRP PHE LEU ASN SEQRES 18 B 306 ARG PHE THR THR THR LEU ASN ASP PHE ASN LEU VAL ALA SEQRES 19 B 306 MET LYS TYR ASN TYR GLU PRO LEU THR GLN ASP HIS VAL SEQRES 20 B 306 ASP ILE LEU GLY PRO LEU SER ALA GLN THR GLY ILE ALA SEQRES 21 B 306 VAL LEU ASP MET CYS ALA SER LEU LYS GLU LEU LEU GLN SEQRES 22 B 306 ASN GLY MET ASN GLY ARG THR ILE LEU GLY SER ALA LEU SEQRES 23 B 306 LEU GLU ASP GLU PHE THR PRO PHE ASP VAL VAL ARG GLN SEQRES 24 B 306 CYS SER GLY VAL THR PHE GLN SEQRES 1 A 306 SER GLY PHE ARG LYS MET ALA PHE PRO SER GLY LYS VAL SEQRES 2 A 306 GLU GLY CYS MET VAL GLN VAL THR CYS GLY THR THR THR SEQRES 3 A 306 LEU ASN GLY LEU TRP LEU ASP ASP VAL VAL TYR CYS PRO SEQRES 4 A 306 ARG HIS VAL ILE CYS THR SER GLU ASP MET LEU ASN PRO SEQRES 5 A 306 ASN TYR GLU ASP LEU LEU ILE ARG LYS SER ASN HIS ASN SEQRES 6 A 306 PHE LEU VAL GLN ALA GLY ASN VAL GLN LEU ARG VAL ILE SEQRES 7 A 306 GLY HIS SER MET GLN ASN CYS VAL LEU LYS LEU LYS VAL SEQRES 8 A 306 ASP THR ALA ASN PRO LYS THR PRO LYS TYR LYS PHE VAL SEQRES 9 A 306 ARG ILE GLN PRO GLY GLN THR PHE SER VAL LEU ALA CYS SEQRES 10 A 306 TYR ASN GLY SER PRO SER GLY VAL TYR GLN CYS ALA MET SEQRES 11 A 306 ARG PRO ASN PHE THR ILE LYS GLY SER PHE LEU ASN GLY SEQRES 12 A 306 SER CYS GLY SER VAL GLY PHE ASN ILE ASP TYR ASP CYS SEQRES 13 A 306 VAL SER PHE CYS TYR MET HIS HIS MET GLU LEU PRO THR SEQRES 14 A 306 GLY VAL HIS ALA GLY THR ASP LEU GLU GLY ASN PHE TYR SEQRES 15 A 306 GLY PRO PHE VAL ASP ARG GLN THR ALA GLN ALA ALA GLY SEQRES 16 A 306 THR ASP THR THR ILE THR VAL ASN VAL LEU ALA TRP LEU SEQRES 17 A 306 TYR ALA ALA VAL ILE ASN GLY ASP ARG TRP PHE LEU ASN SEQRES 18 A 306 ARG PHE THR THR THR LEU ASN ASP PHE ASN LEU VAL ALA SEQRES 19 A 306 MET LYS TYR ASN TYR GLU PRO LEU THR GLN ASP HIS VAL SEQRES 20 A 306 ASP ILE LEU GLY PRO LEU SER ALA GLN THR GLY ILE ALA SEQRES 21 A 306 VAL LEU ASP MET CYS ALA SER LEU LYS GLU LEU LEU GLN SEQRES 22 A 306 ASN GLY MET ASN GLY ARG THR ILE LEU GLY SER ALA LEU SEQRES 23 A 306 LEU GLU ASP GLU PHE THR PRO PHE ASP VAL VAL ARG GLN SEQRES 24 A 306 CYS SER GLY VAL THR PHE GLN HET 7ON B 401 45 HET 7ON A 401 45 HETNAM 7ON (3~{S},3~{A}~{S},6~{A}~{R})-2-[(2~{S})-2-CYCLOHEXYL-2- HETNAM 2 7ON [2,2,2-TRIS(FLUORANYL)ETHANOYLAMINO]ETHANOYL]-~{N}- HETNAM 3 7ON [(2~{S})-4-(CYCLOPENTYLAMINO)-3,4-BIS(OXIDANYLIDENE)- HETNAM 4 7ON 1-[(3~{S})-2-OXIDANYLIDENEPYRROLIDIN-3-YL]BUTAN-2-YL]- HETNAM 5 7ON 3,3~{A},4,5,6,6~{A}-HEXAHYDRO-1~{H}- HETNAM 6 7ON CYCLOPENTA[C]PYRROLE-3-CARBOXAMIDE FORMUL 3 7ON 2(C31 H44 F3 N5 O6) FORMUL 5 HOH *255(H2 O) HELIX 1 AA1 SER B 10 GLY B 15 1 6 HELIX 2 AA2 HIS B 41 CYS B 44 5 4 HELIX 3 AA3 GLU B 47 ASN B 51 5 5 HELIX 4 AA4 ASN B 53 ARG B 60 1 8 HELIX 5 AA5 SER B 62 HIS B 64 5 3 HELIX 6 AA6 ILE B 200 ASN B 214 1 15 HELIX 7 AA7 THR B 226 TYR B 237 1 12 HELIX 8 AA8 THR B 243 LEU B 250 1 8 HELIX 9 AA9 LEU B 250 GLY B 258 1 9 HELIX 10 AB1 ALA B 260 GLY B 275 1 16 HELIX 11 AB2 THR B 292 SER B 301 1 10 HELIX 12 AB3 SER A 10 GLY A 15 1 6 HELIX 13 AB4 HIS A 41 CYS A 44 5 4 HELIX 14 AB5 GLU A 47 ASN A 51 5 5 HELIX 15 AB6 ASN A 53 ARG A 60 1 8 HELIX 16 AB7 SER A 62 HIS A 64 5 3 HELIX 17 AB8 ILE A 200 ASN A 214 1 15 HELIX 18 AB9 THR A 226 TYR A 237 1 12 HELIX 19 AC1 THR A 243 LEU A 250 1 8 HELIX 20 AC2 LEU A 250 GLY A 258 1 9 HELIX 21 AC3 ALA A 260 GLY A 275 1 16 HELIX 22 AC4 THR A 292 SER A 301 1 10 SHEET 1 AA1 7 VAL B 73 LEU B 75 0 SHEET 2 AA1 7 PHE B 66 ALA B 70 -1 N VAL B 68 O LEU B 75 SHEET 3 AA1 7 MET B 17 CYS B 22 -1 N THR B 21 O LEU B 67 SHEET 4 AA1 7 THR B 25 LEU B 32 -1 O LEU B 27 N VAL B 20 SHEET 5 AA1 7 VAL B 35 PRO B 39 -1 O TYR B 37 N LEU B 30 SHEET 6 AA1 7 VAL B 86 VAL B 91 -1 O LEU B 89 N VAL B 36 SHEET 7 AA1 7 VAL B 77 GLN B 83 -1 N SER B 81 O LYS B 88 SHEET 1 AA2 5 TYR B 101 PHE B 103 0 SHEET 2 AA2 5 CYS B 156 GLU B 166 1 O PHE B 159 N LYS B 102 SHEET 3 AA2 5 VAL B 148 ASP B 153 -1 N ASN B 151 O SER B 158 SHEET 4 AA2 5 THR B 111 TYR B 118 -1 N SER B 113 O PHE B 150 SHEET 5 AA2 5 SER B 121 ALA B 129 -1 O TYR B 126 N VAL B 114 SHEET 1 AA3 3 TYR B 101 PHE B 103 0 SHEET 2 AA3 3 CYS B 156 GLU B 166 1 O PHE B 159 N LYS B 102 SHEET 3 AA3 3 HIS B 172 THR B 175 -1 O ALA B 173 N MET B 165 SHEET 1 AA4 7 VAL A 73 LEU A 75 0 SHEET 2 AA4 7 PHE A 66 ALA A 70 -1 N VAL A 68 O LEU A 75 SHEET 3 AA4 7 MET A 17 CYS A 22 -1 N THR A 21 O LEU A 67 SHEET 4 AA4 7 THR A 25 LEU A 32 -1 O LEU A 27 N VAL A 20 SHEET 5 AA4 7 VAL A 35 PRO A 39 -1 O TYR A 37 N LEU A 30 SHEET 6 AA4 7 VAL A 86 VAL A 91 -1 O LEU A 89 N VAL A 36 SHEET 7 AA4 7 VAL A 77 GLN A 83 -1 N SER A 81 O LYS A 88 SHEET 1 AA5 5 TYR A 101 PHE A 103 0 SHEET 2 AA5 5 CYS A 156 GLU A 166 1 O PHE A 159 N LYS A 102 SHEET 3 AA5 5 VAL A 148 ASP A 153 -1 N ASN A 151 O SER A 158 SHEET 4 AA5 5 THR A 111 TYR A 118 -1 N SER A 113 O PHE A 150 SHEET 5 AA5 5 SER A 121 ALA A 129 -1 O TYR A 126 N VAL A 114 SHEET 1 AA6 3 TYR A 101 PHE A 103 0 SHEET 2 AA6 3 CYS A 156 GLU A 166 1 O PHE A 159 N LYS A 102 SHEET 3 AA6 3 HIS A 172 THR A 175 -1 O ALA A 173 N MET A 165 CRYST1 55.829 60.935 64.037 80.03 68.34 70.67 P 1 2 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 0.017912 -0.006282 -0.006758 0.00000 SCALE2 0.000000 0.017391 -0.001014 0.00000 SCALE3 0.000000 0.000000 0.016831 0.00000