HEADER VIRAL PROTEIN,HYDROLASE/INHIBITOR 15-SEP-21 7S74 TITLE STRUCTURE OF THE SARS-COV-2 MAIN PROTEASE IN COMPLEX WITH INHIBITOR TITLE 2 MPI38 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3C-LIKE PROTEINASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: MAIN PROTEASE, 3CL PROTEASE; 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, SARS-COV-2, COVID-19 VIRUS; SOURCE 5 ORGANISM_TAXID: 2697049; SOURCE 6 GENE: REP, 1A-1B; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MAIN PROTEASE, VIRAL PROTEIN, HYDROLASE-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.S.YANG,B.SANKARAN,W.R.LIU REVDAT 3 23-OCT-24 7S74 1 REMARK REVDAT 2 18-OCT-23 7S74 1 REMARK REVDAT 1 27-JUL-22 7S74 0 JRNL AUTH Y.R.ALUGUBELLI,Z.Z.GENG,K.S.YANG,N.SHAABANI,K.KHATUA,X.R.MA, JRNL AUTH 2 E.C.VATANSEVER,C.C.CHO,Y.MA,J.XIAO,L.R.BLANKENSHIP,G.YU, JRNL AUTH 3 B.SANKARAN,P.LI,R.ALLEN,H.JI,S.XU,W.R.LIU JRNL TITL A SYSTEMATIC EXPLORATION OF BOCEPREVIR-BASED MAIN PROTEASE JRNL TITL 2 INHIBITORS AS SARS-COV-2 ANTIVIRALS. JRNL REF EUR.J.MED.CHEM. V. 240 14596 2022 JRNL REFN ISSN 0223-5234 JRNL PMID 35839690 JRNL DOI 10.1016/J.EJMECH.2022.114596 REMARK 2 REMARK 2 RESOLUTION. 1.70 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.21 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.960 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 3 NUMBER OF REFLECTIONS : 76581 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.252 REMARK 3 R VALUE (WORKING SET) : 0.251 REMARK 3 FREE R VALUE : 0.272 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 3815 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 48.2100 - 5.1000 0.84 2362 134 0.2535 0.2319 REMARK 3 2 5.1000 - 4.0500 0.93 2621 132 0.2182 0.2384 REMARK 3 3 4.0500 - 3.5400 0.97 2711 169 0.2228 0.2431 REMARK 3 4 3.5400 - 3.2100 0.98 2781 127 0.2275 0.2371 REMARK 3 5 3.2100 - 2.9800 0.99 2774 149 0.2350 0.2413 REMARK 3 6 2.9800 - 2.8100 0.98 2779 163 0.2451 0.2614 REMARK 3 7 2.8100 - 2.6700 0.98 2771 137 0.2399 0.2775 REMARK 3 8 2.6700 - 2.5500 0.98 2740 147 0.2464 0.2812 REMARK 3 9 2.5500 - 2.4500 0.97 2804 127 0.2492 0.3207 REMARK 3 10 2.4500 - 2.3700 0.98 2741 142 0.2504 0.2943 REMARK 3 11 2.3700 - 2.2900 0.97 2769 118 0.2499 0.3671 REMARK 3 12 2.2900 - 2.2300 0.97 2712 174 0.2554 0.2381 REMARK 3 13 2.2300 - 2.1700 0.97 2714 130 0.2462 0.2964 REMARK 3 14 2.1700 - 2.1200 0.97 2770 137 0.2414 0.3127 REMARK 3 15 2.1200 - 2.0700 0.96 2759 153 0.2493 0.3161 REMARK 3 16 2.0700 - 2.0200 0.96 2653 141 0.2590 0.2626 REMARK 3 17 2.0200 - 1.9800 0.96 2759 114 0.2729 0.2581 REMARK 3 18 1.9800 - 1.9500 0.96 2720 143 0.2763 0.2883 REMARK 3 19 1.9500 - 1.9100 0.95 2610 144 0.2901 0.2750 REMARK 3 20 1.9100 - 1.8800 0.95 2721 145 0.3025 0.3378 REMARK 3 21 1.8800 - 1.8500 0.95 2664 149 0.3101 0.3019 REMARK 3 22 1.8500 - 1.8200 0.95 2667 145 0.3028 0.3193 REMARK 3 23 1.8200 - 1.7900 0.95 2653 138 0.3260 0.4123 REMARK 3 24 1.7900 - 1.7700 0.94 2675 131 0.3354 0.3715 REMARK 3 25 1.7700 - 1.7400 0.94 2617 165 0.3768 0.3568 REMARK 3 26 1.7400 - 1.7200 0.92 2645 113 0.3686 0.4147 REMARK 3 27 1.7200 - 1.7000 0.92 2574 148 0.3893 0.4350 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) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.740 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.22 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 : 0.010 4808 REMARK 3 ANGLE : 1.492 6542 REMARK 3 CHIRALITY : 0.081 740 REMARK 3 PLANARITY : 0.008 844 REMARK 3 DIHEDRAL : 13.173 682 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 25.0298 -9.4044 12.3567 REMARK 3 T TENSOR REMARK 3 T11: 0.1665 T22: 0.1157 REMARK 3 T33: 0.1126 T12: -0.0067 REMARK 3 T13: -0.0047 T23: -0.0027 REMARK 3 L TENSOR REMARK 3 L11: 2.7247 L22: 0.4871 REMARK 3 L33: 0.4978 L12: -0.3157 REMARK 3 L13: -0.2159 L23: 0.1697 REMARK 3 S TENSOR REMARK 3 S11: 0.0378 S12: 0.0544 S13: 0.0719 REMARK 3 S21: -0.0357 S22: -0.0092 S23: 0.0008 REMARK 3 S31: -0.0225 S32: 0.0287 S33: -0.0180 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 7S74 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-SEP-21. REMARK 100 THE DEPOSITION ID IS D_1000259745. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-MAY-21 REMARK 200 TEMPERATURE (KELVIN) : 120 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0332 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 77234 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 58.860 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 3.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 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: 7JPY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM PHOSPHATE DIBASIC, 17% REMARK 280 W/V PEG3350, PH8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 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: 3280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 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 THR A 45 REMARK 465 SER A 46 REMARK 465 GLU A 47 REMARK 465 ASP A 48 REMARK 465 MET A 49 REMARK 465 LEU A 50 REMARK 465 THR B 45 REMARK 465 SER B 46 REMARK 465 GLU B 47 REMARK 465 ASP B 48 REMARK 465 MET B 49 REMARK 465 LEU B 50 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 O HOH A 540 O HOH A 630 1.77 REMARK 500 O ILE A 106 O HOH A 501 1.82 REMARK 500 O HOH B 599 O HOH B 656 1.87 REMARK 500 O HOH B 660 O HOH B 675 1.89 REMARK 500 O HOH B 572 O HOH B 654 1.91 REMARK 500 O LEU A 232 O HOH A 502 1.93 REMARK 500 O PHE A 112 O HOH A 503 1.94 REMARK 500 OD2 ASP A 33 O HOH A 504 1.94 REMARK 500 O ALA B 193 O HOH B 501 1.94 REMARK 500 OE1 GLU A 14 O HOH A 505 1.97 REMARK 500 O HOH B 674 O HOH B 677 1.98 REMARK 500 O HOH A 515 O HOH A 618 1.99 REMARK 500 O HOH B 605 O HOH B 628 1.99 REMARK 500 OD1 ASP A 248 O HOH A 506 2.00 REMARK 500 O HOH B 577 O HOH B 644 2.00 REMARK 500 NE2 GLN A 244 O HOH A 506 2.02 REMARK 500 O HOH A 515 O HOH A 530 2.02 REMARK 500 O HOH A 578 O HOH A 666 2.03 REMARK 500 O HOH A 518 O HOH A 662 2.04 REMARK 500 O VAL A 261 O HOH A 507 2.05 REMARK 500 OH TYR A 237 O HOH A 508 2.07 REMARK 500 NH1 ARG B 188 O HOH B 502 2.07 REMARK 500 OE2 GLU A 270 O HOH A 509 2.07 REMARK 500 OD1 ASN B 274 O HOH B 503 2.07 REMARK 500 O LEU A 75 O HOH A 510 2.08 REMARK 500 ND2 ASN B 238 O HOH B 504 2.08 REMARK 500 OD1 ASP A 56 O HOH A 511 2.08 REMARK 500 O HOH A 670 O HOH A 678 2.09 REMARK 500 O HOH A 514 O HOH A 652 2.09 REMARK 500 O HOH B 542 O HOH B 669 2.10 REMARK 500 O HOH A 666 O HOH A 672 2.12 REMARK 500 N ASN A 51 O HOH A 512 2.13 REMARK 500 NZ LYS B 61 O HOH B 505 2.14 REMARK 500 O HOH B 659 O HOH B 664 2.15 REMARK 500 OG SER B 267 O HOH B 506 2.15 REMARK 500 SG CYS B 85 O HOH B 656 2.16 REMARK 500 O HOH B 570 O HOH B 640 2.16 REMARK 500 O HOH B 613 O HOH B 621 2.17 REMARK 500 O LYS A 12 O HOH A 513 2.18 REMARK 500 O HOH B 626 O HOH B 656 2.18 REMARK 500 O THR A 111 O HOH A 515 2.19 REMARK 500 OG SER A 62 O HOH A 514 2.19 REMARK 500 OE2 GLU A 270 O HOH A 516 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 O HOH A 540 O HOH B 546 1455 2.13 REMARK 500 O HOH A 543 O HOH A 652 1645 2.18 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 LYS A 102 CE LYS A 102 NZ 0.170 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 GLN A 69 CA - CB - CG ANGL. DEV. = 18.2 DEGREES REMARK 500 ARG A 76 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 LYS A 102 CD - CE - NZ ANGL. DEV. = -19.1 DEGREES REMARK 500 ASN A 238 OD1 - CG - ND2 ANGL. DEV. = -20.0 DEGREES REMARK 500 ASN A 238 CB - CG - OD1 ANGL. DEV. = 39.5 DEGREES REMARK 500 ASN A 238 CB - CG - ND2 ANGL. DEV. = -41.7 DEGREES REMARK 500 ASN A 238 N - CA - C ANGL. DEV. = -17.2 DEGREES REMARK 500 LEU B 27 CB - CG - CD2 ANGL. DEV. = -11.3 DEGREES REMARK 500 LEU B 232 CB - CG - CD2 ANGL. DEV. = 12.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASP A 33 -131.57 53.75 REMARK 500 ALA A 70 74.90 -107.87 REMARK 500 ASN A 84 -123.16 59.25 REMARK 500 TYR A 154 -98.54 45.31 REMARK 500 ASP A 187 57.58 -97.34 REMARK 500 ASN A 238 16.29 115.59 REMARK 500 ASP B 33 -134.73 56.12 REMARK 500 ALA B 70 78.44 -110.99 REMARK 500 ASN B 84 -119.88 57.19 REMARK 500 TYR B 154 -89.14 50.37 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 TYR A 237 ASN A 238 144.25 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 ARG A 76 0.08 SIDE CHAIN REMARK 500 ASN A 238 0.10 SIDE CHAIN 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 A 684 DISTANCE = 6.12 ANGSTROMS REMARK 525 HOH A 685 DISTANCE = 6.17 ANGSTROMS DBREF 7S74 A 1 306 UNP P0DTD1 R1AB_SARS2 3264 3569 DBREF 7S74 B 1 306 UNP P0DTD1 R1AB_SARS2 3264 3569 SEQADV 7S74 ALA A 178 UNP P0DTD1 GLU 3441 CONFLICT SEQADV 7S74 ALA B 178 UNP P0DTD1 GLU 3441 CONFLICT 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 ALA 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 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 ALA 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 HET I68 A 401 35 HET I68 B 401 35 HETNAM I68 N-(TERT-BUTYLCARBAMOYL)-3-METHYL-L-VALYL-N-{(2S)-1- HETNAM 2 I68 HYDROXY-3-[(3S)-2-OXOPYRROLIDIN-3-YL]PROPAN-2-YL}-4- HETNAM 3 I68 METHYL-L-LEUCINAMIDE FORMUL 3 I68 2(C25 H47 N5 O5) FORMUL 5 HOH *366(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 ASN A 53 ARG A 60 1 8 HELIX 4 AA4 SER A 62 HIS A 64 5 3 HELIX 5 AA5 ILE A 200 ASN A 214 1 15 HELIX 6 AA6 THR A 226 ASN A 238 1 13 HELIX 7 AA7 THR A 243 LEU A 250 1 8 HELIX 8 AA8 LEU A 250 GLY A 258 1 9 HELIX 9 AA9 ALA A 260 GLY A 275 1 16 HELIX 10 AB1 THR A 292 GLY A 302 1 11 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 TYR B 237 1 12 HELIX 17 AB8 THR B 243 LEU B 250 1 8 HELIX 18 AB9 LEU B 250 GLY B 258 1 9 HELIX 19 AC1 ALA B 260 GLY B 275 1 16 HELIX 20 AC2 THR B 292 GLY B 302 1 11 SHEET 1 AA1 7 GLN A 74 LEU A 75 0 SHEET 2 AA1 7 PHE A 66 GLN A 69 -1 N VAL A 68 O LEU A 75 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 TYR A 37 N LEU A 30 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 TYR A 101 PHE A 103 0 SHEET 2 AA2 5 CYS A 156 GLU A 166 1 O PHE A 159 N LYS A 102 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 SER A 123 N ALA A 116 SHEET 1 AA3 3 TYR A 101 PHE A 103 0 SHEET 2 AA3 3 CYS A 156 GLU A 166 1 O PHE A 159 N LYS A 102 SHEET 3 AA3 3 HIS A 172 THR A 175 -1 O THR A 175 N MET A 162 SHEET 1 AA4 7 VAL B 73 LEU B 75 0 SHEET 2 AA4 7 LEU B 67 ALA B 70 -1 N ALA B 70 O VAL B 73 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 SER B 81 O LYS B 88 SHEET 1 AA5 5 TYR B 101 PHE B 103 0 SHEET 2 AA5 5 CYS B 156 GLU B 166 1 O PHE B 159 N LYS B 102 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 SER B 123 N ALA B 116 SHEET 1 AA6 3 TYR B 101 PHE B 103 0 SHEET 2 AA6 3 CYS B 156 GLU B 166 1 O PHE B 159 N LYS B 102 SHEET 3 AA6 3 HIS B 172 THR B 175 -1 O ALA B 173 N MET B 165 LINK SG CYS A 145 C8 I68 A 401 1555 1555 1.82 LINK SG CYS B 145 C8 I68 B 401 1555 1555 1.77 CRYST1 54.220 62.973 62.973 79.89 69.46 69.46 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 0.018443 -0.006909 -0.006507 0.00000 SCALE2 0.000000 0.016958 -0.001018 0.00000 SCALE3 0.000000 0.000000 0.016988 0.00000