HEADER VIRAL PROTEIN/INHIBITOR 20-MAR-20 6W81 TITLE STRUCTURE OF PEDV MAIN PROTEASE BOUND TO POTENT BROAD-SPECTRUM NON- TITLE 2 COVALENT INHIBITOR X77 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDASE C30; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: MAIN PROTEASE; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PORCINE EPIDEMIC DIARRHEA VIRUS; SOURCE 3 ORGANISM_TAXID: 28295; SOURCE 4 GENE: ORF1AB; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS COVID-19, PORCINE EPIDEMIC DIARRHEA VIRUS, PEDV, MAIN PROTEASE, 3C- KEYWDS 2 LIKE PROTEASE, 3CL PROTEASE, 3CLPRO, MPRO, BROAD-SPECTRUM, KEYWDS 3 INHIBITOR, PROTEINASE, NON-COVALENT, REVERSIBLE, STRUCTURAL KEYWDS 4 GENOMICS, CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES, KEYWDS 5 CSGID, ANTIVIRAL PROTEIN, VIRAL PROTEIN, VIRAL PROTEIN-INHIBITOR KEYWDS 6 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.D.MESECAR,CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES AUTHOR 2 (CSGID) REVDAT 2 18-OCT-23 6W81 1 REMARK REVDAT 1 24-MAR-21 6W81 0 JRNL AUTH A.D.MESECAR JRNL TITL A TAXONOMICALLY-DRIVEN APPROACH TO DEVELOPMENT OF POTENT, JRNL TITL 2 BROAD-SPECTRUM INHIBITORS OF CORONAVIRUS MAIN PROTEASE JRNL TITL 3 INCLUDING SARS-COV-2 (COVID-19) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.87 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 76888 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.600 REMARK 3 FREE R VALUE TEST SET COUNT : 1998 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 27.8700 - 3.7300 0.99 5563 155 0.1285 0.1539 REMARK 3 2 3.7300 - 2.9600 1.00 5514 150 0.1540 0.1889 REMARK 3 3 2.9600 - 2.5900 1.00 5509 148 0.1821 0.1967 REMARK 3 4 2.5900 - 2.3500 1.00 5480 145 0.1826 0.2198 REMARK 3 5 2.3500 - 2.1800 1.00 5486 145 0.1891 0.2585 REMARK 3 6 2.1800 - 2.0500 1.00 5511 147 0.1958 0.2617 REMARK 3 7 2.0500 - 1.9500 1.00 5449 143 0.2052 0.2565 REMARK 3 8 1.9500 - 1.8700 1.00 5495 142 0.2026 0.2738 REMARK 3 9 1.8700 - 1.7900 1.00 5473 149 0.2061 0.2762 REMARK 3 10 1.7900 - 1.7300 1.00 5446 146 0.2220 0.2294 REMARK 3 11 1.7300 - 1.6800 1.00 5474 148 0.2487 0.2888 REMARK 3 12 1.6800 - 1.6300 0.98 5399 137 0.2754 0.3300 REMARK 3 13 1.6300 - 1.5900 0.91 4992 134 0.2849 0.3400 REMARK 3 14 1.5900 - 1.5500 0.75 4099 109 0.2933 0.3358 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.366 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.34 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.69 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 : 0.006 4820 REMARK 3 ANGLE : 0.841 6566 REMARK 3 CHIRALITY : 0.052 739 REMARK 3 PLANARITY : 0.005 845 REMARK 3 DIHEDRAL : 14.767 2775 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 11 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 43 ) REMARK 3 ORIGIN FOR THE GROUP (A): -28.5335 73.2451 7.6247 REMARK 3 T TENSOR REMARK 3 T11: 0.1473 T22: 0.1151 REMARK 3 T33: 0.1269 T12: 0.0138 REMARK 3 T13: 0.0126 T23: -0.0307 REMARK 3 L TENSOR REMARK 3 L11: 2.1374 L22: 1.1276 REMARK 3 L33: 3.0878 L12: 0.9913 REMARK 3 L13: -1.0468 L23: -0.8228 REMARK 3 S TENSOR REMARK 3 S11: 0.0930 S12: -0.0594 S13: 0.0233 REMARK 3 S21: 0.0050 S22: -0.0078 S23: 0.0168 REMARK 3 S31: -0.0757 S32: 0.1523 S33: -0.0775 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 44 THROUGH 109 ) REMARK 3 ORIGIN FOR THE GROUP (A): -23.5895 74.6163 -1.0020 REMARK 3 T TENSOR REMARK 3 T11: 0.1620 T22: 0.1728 REMARK 3 T33: 0.1702 T12: 0.0232 REMARK 3 T13: 0.0337 T23: -0.0358 REMARK 3 L TENSOR REMARK 3 L11: 1.8926 L22: 1.9451 REMARK 3 L33: 3.4751 L12: 0.8644 REMARK 3 L13: -0.2702 L23: -0.7430 REMARK 3 S TENSOR REMARK 3 S11: 0.0171 S12: 0.0093 S13: 0.1618 REMARK 3 S21: -0.0732 S22: 0.0269 S23: -0.1107 REMARK 3 S31: -0.2903 S32: 0.2646 S33: -0.0076 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 110 THROUGH 212 ) REMARK 3 ORIGIN FOR THE GROUP (A): -40.4163 68.0591 4.3332 REMARK 3 T TENSOR REMARK 3 T11: 0.1453 T22: 0.1536 REMARK 3 T33: 0.1307 T12: -0.0032 REMARK 3 T13: -0.0083 T23: 0.0104 REMARK 3 L TENSOR REMARK 3 L11: 2.4382 L22: 1.1669 REMARK 3 L33: 1.8661 L12: 0.9278 REMARK 3 L13: -0.2294 L23: -0.6677 REMARK 3 S TENSOR REMARK 3 S11: 0.0651 S12: 0.0946 S13: 0.0344 REMARK 3 S21: -0.0555 S22: 0.0172 S23: 0.1126 REMARK 3 S31: 0.0577 S32: -0.2545 S33: -0.0931 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 213 THROUGH 268 ) REMARK 3 ORIGIN FOR THE GROUP (A): -59.0377 49.7151 7.2985 REMARK 3 T TENSOR REMARK 3 T11: 0.4206 T22: 0.5182 REMARK 3 T33: 0.4572 T12: -0.2535 REMARK 3 T13: -0.1742 T23: 0.1263 REMARK 3 L TENSOR REMARK 3 L11: 0.6612 L22: 2.0183 REMARK 3 L33: 2.2148 L12: 0.0738 REMARK 3 L13: -0.5473 L23: -1.7791 REMARK 3 S TENSOR REMARK 3 S11: 0.5333 S12: -0.3227 S13: -0.8075 REMARK 3 S21: -0.2609 S22: -0.1047 S23: 0.1177 REMARK 3 S31: 0.8552 S32: -0.7252 S33: -0.1791 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 269 THROUGH 300 ) REMARK 3 ORIGIN FOR THE GROUP (A): -52.7561 58.3227 14.7164 REMARK 3 T TENSOR REMARK 3 T11: 0.1874 T22: 0.2511 REMARK 3 T33: 0.1767 T12: -0.1411 REMARK 3 T13: -0.0419 T23: 0.0173 REMARK 3 L TENSOR REMARK 3 L11: 6.1519 L22: 5.8529 REMARK 3 L33: 4.6568 L12: -3.3283 REMARK 3 L13: 0.9830 L23: -0.7571 REMARK 3 S TENSOR REMARK 3 S11: 0.1606 S12: -0.4531 S13: -0.0038 REMARK 3 S21: 0.0738 S22: -0.0512 S23: -0.0541 REMARK 3 S31: 0.1890 S32: -0.3574 S33: -0.1009 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 52 ) REMARK 3 ORIGIN FOR THE GROUP (A): -34.3178 60.5081 34.5023 REMARK 3 T TENSOR REMARK 3 T11: 0.1956 T22: 0.1489 REMARK 3 T33: 0.1315 T12: -0.0388 REMARK 3 T13: 0.0165 T23: -0.0003 REMARK 3 L TENSOR REMARK 3 L11: 1.3616 L22: 1.2188 REMARK 3 L33: 4.1810 L12: -0.7543 REMARK 3 L13: 0.7240 L23: -1.3022 REMARK 3 S TENSOR REMARK 3 S11: 0.0058 S12: -0.1577 S13: -0.1034 REMARK 3 S21: 0.0287 S22: -0.0110 S23: 0.0396 REMARK 3 S31: 0.3591 S32: -0.0890 S33: 0.0292 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 53 THROUGH 119 ) REMARK 3 ORIGIN FOR THE GROUP (A): -30.1532 62.6452 39.3415 REMARK 3 T TENSOR REMARK 3 T11: 0.1629 T22: 0.2184 REMARK 3 T33: 0.1889 T12: -0.0346 REMARK 3 T13: -0.0139 T23: 0.0301 REMARK 3 L TENSOR REMARK 3 L11: 0.4672 L22: 1.4735 REMARK 3 L33: 3.0488 L12: -0.3194 REMARK 3 L13: -0.1862 L23: -0.5254 REMARK 3 S TENSOR REMARK 3 S11: -0.0110 S12: -0.0744 S13: -0.0362 REMARK 3 S21: 0.1017 S22: -0.0938 S23: -0.1733 REMARK 3 S31: 0.0826 S32: 0.2391 S33: 0.1081 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 120 THROUGH 138 ) REMARK 3 ORIGIN FOR THE GROUP (A): -46.1709 66.4604 28.2716 REMARK 3 T TENSOR REMARK 3 T11: 0.1752 T22: 0.3137 REMARK 3 T33: 0.1557 T12: -0.0299 REMARK 3 T13: -0.0268 T23: 0.0284 REMARK 3 L TENSOR REMARK 3 L11: 4.2481 L22: 6.5391 REMARK 3 L33: 6.7121 L12: -4.7144 REMARK 3 L13: -4.8012 L23: 3.9586 REMARK 3 S TENSOR REMARK 3 S11: -0.0255 S12: -0.0409 S13: 0.0676 REMARK 3 S21: -0.0204 S22: 0.0467 S23: 0.2006 REMARK 3 S31: 0.0682 S32: -0.5330 S33: 0.0244 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 139 THROUGH 212 ) REMARK 3 ORIGIN FOR THE GROUP (A): -46.2670 68.1540 32.2690 REMARK 3 T TENSOR REMARK 3 T11: 0.1749 T22: 0.2911 REMARK 3 T33: 0.1508 T12: -0.0349 REMARK 3 T13: 0.0200 T23: 0.0058 REMARK 3 L TENSOR REMARK 3 L11: 1.7254 L22: 0.9785 REMARK 3 L33: 1.7650 L12: -0.9205 REMARK 3 L13: 1.7046 L23: -0.5258 REMARK 3 S TENSOR REMARK 3 S11: 0.0572 S12: -0.3146 S13: -0.1032 REMARK 3 S21: 0.0624 S22: 0.0043 S23: 0.1401 REMARK 3 S31: 0.0969 S32: -0.4483 S33: -0.0478 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 213 THROUGH 243 ) REMARK 3 ORIGIN FOR THE GROUP (A): -64.3949 83.0321 23.4667 REMARK 3 T TENSOR REMARK 3 T11: 0.2216 T22: 0.6225 REMARK 3 T33: 0.4307 T12: 0.0123 REMARK 3 T13: 0.0297 T23: -0.2796 REMARK 3 L TENSOR REMARK 3 L11: 2.7773 L22: 1.6625 REMARK 3 L33: 7.4595 L12: -0.2582 REMARK 3 L13: -2.6904 L23: 0.3473 REMARK 3 S TENSOR REMARK 3 S11: 0.0661 S12: -0.7094 S13: 0.7262 REMARK 3 S21: 0.1106 S22: -0.4720 S23: 0.6091 REMARK 3 S31: -0.5433 S32: -0.2082 S33: 0.1246 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 244 THROUGH 300 ) REMARK 3 ORIGIN FOR THE GROUP (A): -55.1959 81.7924 18.6276 REMARK 3 T TENSOR REMARK 3 T11: 0.1904 T22: 0.2722 REMARK 3 T33: 0.1727 T12: 0.0619 REMARK 3 T13: -0.0217 T23: -0.0582 REMARK 3 L TENSOR REMARK 3 L11: 4.5592 L22: 4.9533 REMARK 3 L33: 2.2522 L12: 1.1048 REMARK 3 L13: -0.3654 L23: 0.6747 REMARK 3 S TENSOR REMARK 3 S11: 0.0813 S12: -0.4234 S13: 0.3080 REMARK 3 S21: -0.2112 S22: -0.2678 S23: 0.1085 REMARK 3 S31: -0.3357 S32: -0.2611 S33: 0.1452 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 6W81 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1000247777. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-MAR-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-G REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.988 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 76919 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 79.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.73900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.350 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: 5HYO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEDV-3CLPRO:77 INHIBITOR COMPLEX WAS REMARK 280 CO-CRYSTALLIZED BY SETTING UP 2 UL DROPS THAT WERE COMPOSED OF 1 REMARK 280 UL OF PURIFIED PEDV-3CLPRO (2.4 MG/ML) THAT HAD BEEN INCUBATED REMARK 280 FOR THREE HOURS WITH A 3 MOLAR EXCESS OF COMPOUND 77, AND 1 UL REMARK 280 OF RESERVOIR SOLUTION: 0.20 M MALONIC ACID (MIB) PH 4.0 AND 25% REMARK 280 PEG-3350, VAPOR DIFFUSION, HANGING 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 42.62850 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: 3290 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24520 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 LEU B 301 REMARK 465 GLN B 302 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 521 O HOH A 557 1.84 REMARK 500 O HOH B 755 O HOH B 768 1.86 REMARK 500 O HOH A 527 O HOH A 671 2.03 REMARK 500 O HOH B 587 O HOH B 765 2.07 REMARK 500 O HOH B 661 O HOH B 734 2.10 REMARK 500 O HOH A 560 O HOH A 742 2.10 REMARK 500 O HOH B 655 O HOH B 706 2.12 REMARK 500 OG SER A 220 O HOH A 501 2.15 REMARK 500 O HOH B 657 O HOH B 780 2.17 REMARK 500 O HOH B 663 O HOH B 760 2.17 REMARK 500 O HOH A 642 O HOH A 743 2.18 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 701 O HOH B 537 1554 2.11 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 SER A 46 165.99 75.48 REMARK 500 THR A 47 62.93 -110.63 REMARK 500 THR A 48 145.30 142.41 REMARK 500 SER A 49 -135.86 -92.56 REMARK 500 SER A 222 -108.41 -64.54 REMARK 500 ARG A 223 146.19 122.00 REMARK 500 LYS A 270 -77.65 -66.73 REMARK 500 SER B 46 -165.44 63.24 REMARK 500 LEU B 283 51.52 -101.51 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 752 DISTANCE = 6.69 ANGSTROMS REMARK 525 HOH A 753 DISTANCE = 11.32 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue X77 A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue X77 B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MLA B 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5HYO RELATED DB: PDB REMARK 900 UNBOUND PEDV MAIN PROTEASE REMARK 900 RELATED ID: 6W79 RELATED DB: PDB REMARK 900 SARS MAIN PROTEASE BOUND TO INHIBITOR X77 REMARK 900 RELATED ID: 6W63 RELATED DB: PDB REMARK 900 COVID-19 MAIN PROTEASE BOUND TO INHIBITOR X77 DBREF 6W81 A 1 302 UNP S0AP56 S0AP56_9ALPC 2998 3299 DBREF 6W81 B 1 302 UNP S0AP56 S0AP56_9ALPC 2998 3299 SEQRES 1 A 302 ALA GLY LEU ARG LYS MET ALA GLN PRO SER GLY VAL VAL SEQRES 2 A 302 GLU LYS CYS ILE VAL ARG VAL CYS TYR GLY ASN MET ALA SEQRES 3 A 302 LEU ASN GLY LEU TRP LEU GLY ASP THR VAL ILE CYS PRO SEQRES 4 A 302 ARG HIS VAL ILE ALA SER SER THR THR SER THR ILE ASP SEQRES 5 A 302 TYR ASP TYR ALA LEU SER VAL LEU ARG LEU HIS ASN PHE SEQRES 6 A 302 SER ILE SER SER GLY ASN VAL PHE LEU GLY VAL VAL GLY SEQRES 7 A 302 VAL THR MET ARG GLY ALA LEU LEU GLN ILE LYS VAL ASN SEQRES 8 A 302 GLN ASN ASN VAL HIS THR PRO LYS TYR THR TYR ARG THR SEQRES 9 A 302 VAL ARG PRO GLY GLU SER PHE ASN ILE LEU ALA CYS TYR SEQRES 10 A 302 ASP GLY SER ALA ALA GLY VAL TYR GLY VAL ASN MET ARG SEQRES 11 A 302 SER ASN TYR THR ILE ARG GLY SER PHE ILE ASN GLY ALA SEQRES 12 A 302 CYS GLY SER PRO GLY TYR ASN ILE ASN ASN GLY THR VAL SEQRES 13 A 302 GLU PHE CYS TYR LEU HIS GLN LEU GLU LEU GLY SER GLY SEQRES 14 A 302 CYS HIS VAL GLY SER ASP LEU ASP GLY VAL MET TYR GLY SEQRES 15 A 302 GLY TYR GLU ASP GLN PRO THR LEU GLN VAL GLU GLY ALA SEQRES 16 A 302 SER SER LEU PHE THR GLU ASN VAL LEU ALA PHE LEU TYR SEQRES 17 A 302 ALA ALA LEU ILE ASN GLY SER THR TRP TRP LEU SER SER SEQRES 18 A 302 SER ARG ILE ALA VAL ASP ARG PHE ASN GLU TRP ALA VAL SEQRES 19 A 302 HIS ASN GLY MET THR THR VAL VAL ASN THR ASP CYS PHE SEQRES 20 A 302 SER ILE LEU ALA ALA LYS THR GLY VAL ASP VAL GLN ARG SEQRES 21 A 302 LEU LEU ALA SER ILE GLN SER LEU HIS LYS ASN PHE GLY SEQRES 22 A 302 GLY LYS GLN ILE LEU GLY TYR THR SER LEU THR ASP GLU SEQRES 23 A 302 PHE THR THR GLY GLU VAL ILE ARG GLN MET TYR GLY VAL SEQRES 24 A 302 ASN LEU GLN SEQRES 1 B 302 ALA GLY LEU ARG LYS MET ALA GLN PRO SER GLY VAL VAL SEQRES 2 B 302 GLU LYS CYS ILE VAL ARG VAL CYS TYR GLY ASN MET ALA SEQRES 3 B 302 LEU ASN GLY LEU TRP LEU GLY ASP THR VAL ILE CYS PRO SEQRES 4 B 302 ARG HIS VAL ILE ALA SER SER THR THR SER THR ILE ASP SEQRES 5 B 302 TYR ASP TYR ALA LEU SER VAL LEU ARG LEU HIS ASN PHE SEQRES 6 B 302 SER ILE SER SER GLY ASN VAL PHE LEU GLY VAL VAL GLY SEQRES 7 B 302 VAL THR MET ARG GLY ALA LEU LEU GLN ILE LYS VAL ASN SEQRES 8 B 302 GLN ASN ASN VAL HIS THR PRO LYS TYR THR TYR ARG THR SEQRES 9 B 302 VAL ARG PRO GLY GLU SER PHE ASN ILE LEU ALA CYS TYR SEQRES 10 B 302 ASP GLY SER ALA ALA GLY VAL TYR GLY VAL ASN MET ARG SEQRES 11 B 302 SER ASN TYR THR ILE ARG GLY SER PHE ILE ASN GLY ALA SEQRES 12 B 302 CYS GLY SER PRO GLY TYR ASN ILE ASN ASN GLY THR VAL SEQRES 13 B 302 GLU PHE CYS TYR LEU HIS GLN LEU GLU LEU GLY SER GLY SEQRES 14 B 302 CYS HIS VAL GLY SER ASP LEU ASP GLY VAL MET TYR GLY SEQRES 15 B 302 GLY TYR GLU ASP GLN PRO THR LEU GLN VAL GLU GLY ALA SEQRES 16 B 302 SER SER LEU PHE THR GLU ASN VAL LEU ALA PHE LEU TYR SEQRES 17 B 302 ALA ALA LEU ILE ASN GLY SER THR TRP TRP LEU SER SER SEQRES 18 B 302 SER ARG ILE ALA VAL ASP ARG PHE ASN GLU TRP ALA VAL SEQRES 19 B 302 HIS ASN GLY MET THR THR VAL VAL ASN THR ASP CYS PHE SEQRES 20 B 302 SER ILE LEU ALA ALA LYS THR GLY VAL ASP VAL GLN ARG SEQRES 21 B 302 LEU LEU ALA SER ILE GLN SER LEU HIS LYS ASN PHE GLY SEQRES 22 B 302 GLY LYS GLN ILE LEU GLY TYR THR SER LEU THR ASP GLU SEQRES 23 B 302 PHE THR THR GLY GLU VAL ILE ARG GLN MET TYR GLY VAL SEQRES 24 B 302 ASN LEU GLN HET X77 A 401 66 HET X77 B 401 66 HET MLA B 402 9 HETNAM X77 N-(4-TERT-BUTYLPHENYL)-N-[(1R)-2-(CYCLOHEXYLAMINO)-2- HETNAM 2 X77 OXO-1-(PYRIDIN-3-YL)ETHYL]-1H-IMIDAZOLE-4-CARBOXAMIDE HETNAM MLA MALONIC ACID HETSYN MLA DICARBOXYLIC ACID C3; PROPANEDIOLIC ACID; HETSYN 2 MLA METHANEDICARBOXYLIC ACID FORMUL 3 X77 2(C27 H33 N5 O2) FORMUL 5 MLA C3 H4 O4 FORMUL 6 HOH *534(H2 O) HELIX 1 AA1 SER A 10 LYS A 15 1 6 HELIX 2 AA2 HIS A 41 ALA A 44 5 4 HELIX 3 AA3 ASP A 52 VAL A 59 1 8 HELIX 4 AA4 ARG A 61 HIS A 63 5 3 HELIX 5 AA5 MET A 180 TYR A 184 5 5 HELIX 6 AA6 PHE A 199 ASN A 213 1 15 HELIX 7 AA7 ALA A 225 VAL A 234 1 10 HELIX 8 AA8 THR A 244 CYS A 246 5 3 HELIX 9 AA9 PHE A 247 GLY A 255 1 9 HELIX 10 AB1 ASP A 257 ASN A 271 1 15 HELIX 11 AB2 THR A 288 GLY A 298 1 11 HELIX 12 AB3 SER B 10 LYS B 15 1 6 HELIX 13 AB4 HIS B 41 ALA B 44 5 4 HELIX 14 AB5 ASP B 52 VAL B 59 1 8 HELIX 15 AB6 LEU B 60 HIS B 63 5 4 HELIX 16 AB7 MET B 180 TYR B 184 5 5 HELIX 17 AB8 PHE B 199 ASN B 213 1 15 HELIX 18 AB9 ALA B 225 VAL B 234 1 10 HELIX 19 AC1 THR B 244 CYS B 246 5 3 HELIX 20 AC2 PHE B 247 GLY B 255 1 9 HELIX 21 AC3 ASP B 257 ASN B 271 1 15 HELIX 22 AC4 THR B 288 GLY B 298 1 11 SHEET 1 AA1 7 VAL A 72 LEU A 74 0 SHEET 2 AA1 7 PHE A 65 SER A 69 -1 N SER A 69 O VAL A 72 SHEET 3 AA1 7 ILE A 17 TYR A 22 -1 N ARG A 19 O SER A 68 SHEET 4 AA1 7 MET A 25 LEU A 32 -1 O LEU A 27 N VAL A 20 SHEET 5 AA1 7 THR A 35 PRO A 39 -1 O THR A 35 N LEU A 32 SHEET 6 AA1 7 LEU A 85 VAL A 90 -1 O ILE A 88 N VAL A 36 SHEET 7 AA1 7 VAL A 76 ARG A 82 -1 N VAL A 77 O LYS A 89 SHEET 1 AA2 5 TYR A 100 TYR A 102 0 SHEET 2 AA2 5 THR A 155 GLU A 165 1 O PHE A 158 N THR A 101 SHEET 3 AA2 5 PRO A 147 ASN A 152 -1 N ASN A 150 O GLU A 157 SHEET 4 AA2 5 SER A 110 TYR A 117 -1 N ASN A 112 O TYR A 149 SHEET 5 AA2 5 SER A 120 ASN A 128 -1 O ALA A 122 N ALA A 115 SHEET 1 AA3 3 TYR A 100 TYR A 102 0 SHEET 2 AA3 3 THR A 155 GLU A 165 1 O PHE A 158 N THR A 101 SHEET 3 AA3 3 HIS A 171 SER A 174 -1 O VAL A 172 N LEU A 164 SHEET 1 AA4 7 VAL B 72 LEU B 74 0 SHEET 2 AA4 7 PHE B 65 SER B 69 -1 N ILE B 67 O LEU B 74 SHEET 3 AA4 7 ILE B 17 TYR B 22 -1 N ARG B 19 O SER B 68 SHEET 4 AA4 7 MET B 25 LEU B 32 -1 O MET B 25 N TYR B 22 SHEET 5 AA4 7 THR B 35 PRO B 39 -1 O THR B 35 N LEU B 32 SHEET 6 AA4 7 LEU B 85 VAL B 90 -1 O ILE B 88 N VAL B 36 SHEET 7 AA4 7 VAL B 76 ARG B 82 -1 N ARG B 82 O LEU B 85 SHEET 1 AA5 5 TYR B 100 TYR B 102 0 SHEET 2 AA5 5 THR B 155 GLU B 165 1 O PHE B 158 N THR B 101 SHEET 3 AA5 5 PRO B 147 ASN B 152 -1 N ASN B 150 O GLU B 157 SHEET 4 AA5 5 SER B 110 TYR B 117 -1 N ASN B 112 O TYR B 149 SHEET 5 AA5 5 SER B 120 ASN B 128 -1 O ALA B 122 N ALA B 115 SHEET 1 AA6 3 TYR B 100 TYR B 102 0 SHEET 2 AA6 3 THR B 155 GLU B 165 1 O PHE B 158 N THR B 101 SHEET 3 AA6 3 HIS B 171 SER B 174 -1 O VAL B 172 N LEU B 164 CISPEP 1 THR A 48 SER A 49 0 -2.78 SITE 1 AC1 15 MET A 25 ALA A 26 HIS A 41 PHE A 139 SITE 2 AC1 15 ASN A 141 GLY A 142 CYS A 144 HIS A 162 SITE 3 AC1 15 GLN A 163 LEU A 164 GLU A 165 ASP A 186 SITE 4 AC1 15 PRO A 188 HOH A 521 HOH A 554 SITE 1 AC2 16 ALA B 26 HIS B 41 THR B 47 PHE B 139 SITE 2 AC2 16 ILE B 140 ASN B 141 GLY B 142 CYS B 144 SITE 3 AC2 16 HIS B 162 GLN B 163 LEU B 164 GLU B 165 SITE 4 AC2 16 PRO B 188 HOH B 551 HOH B 575 HOH B 671 SITE 1 AC3 11 ARG A 4 ARG A 136 HOH A 507 ARG B 4 SITE 2 AC3 11 LYS B 5 ARG B 136 TYR B 280 GLU B 286 SITE 3 AC3 11 HOH B 528 HOH B 557 HOH B 621 CRYST1 56.679 85.257 58.186 90.00 100.46 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 0.017643 0.000000 0.003257 0.00000 SCALE2 0.000000 0.011729 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017477 0.00000