HEADER VIRAL PROTEIN 03-NOV-23 8R26 TITLE SARS-COV-2 MPRO (OMICRON,P132H) IN COMPLEX WITH ALPHA-KETOAMIDE 13B-K TITLE 2 AT PH 8.5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3C-LIKE PROTEINASE NSP5; COMPND 3 CHAIN: A, B, D, C; 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_TAXID: 2697049; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SARS-COV-2; MAIN PROTEASE; OMICRON; MOLECULAR DYNAMICS; PRO>HIS KEYWDS 2 MUTANT; DOUBLE MUTANT, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.IBRAHIM,X.SUN,R.HILGENFELD REVDAT 1 13-NOV-24 8R26 0 JRNL AUTH M.IBRAHIM,R.HILGENFELD,X.SUN JRNL TITL SARS-COV-2 MPRO (OMICRON,P132H) IN COMPLEX WITH JRNL TITL 2 ALPHA-KETOAMIDE 13B-K AT PH 8.5 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.90 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.960 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.8 REMARK 3 NUMBER OF REFLECTIONS : 41635 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.850 REMARK 3 FREE R VALUE TEST SET COUNT : 2020 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 40.9000 - 5.5400 0.88 2797 130 0.1758 0.2132 REMARK 3 2 5.5400 - 4.4000 0.93 2940 154 0.1507 0.2025 REMARK 3 3 4.4000 - 3.8400 0.86 2685 147 0.1525 0.1988 REMARK 3 4 3.8400 - 3.4900 0.89 2813 135 0.1727 0.2150 REMARK 3 5 3.4900 - 3.2400 0.92 2900 138 0.1879 0.2290 REMARK 3 6 3.2400 - 3.0500 0.93 2928 150 0.1976 0.2609 REMARK 3 7 3.0500 - 2.9000 0.94 2969 169 0.2058 0.2374 REMARK 3 8 2.9000 - 2.7700 0.86 2694 131 0.2265 0.2915 REMARK 3 9 2.7700 - 2.6600 0.85 2660 131 0.2336 0.3047 REMARK 3 10 2.6600 - 2.5700 0.87 2738 163 0.2296 0.2725 REMARK 3 11 2.5700 - 2.4900 0.91 2883 134 0.2347 0.3124 REMARK 3 12 2.4900 - 2.4200 0.91 2839 152 0.2451 0.3241 REMARK 3 13 2.4200 - 2.3600 0.92 2925 134 0.2508 0.3186 REMARK 3 14 2.3600 - 2.3000 0.91 2844 152 0.2556 0.3416 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.560 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 NULL REMARK 3 ANGLE : 1.103 NULL REMARK 3 CHIRALITY : 0.059 1502 REMARK 3 PLANARITY : 0.008 1735 REMARK 3 DIHEDRAL : 14.079 3478 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8R26 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-NOV-23. REMARK 100 THE DEPOSITION ID IS D_1292134432. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAR-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PETRA III, DESY REMARK 200 BEAMLINE : P11 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 PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41704 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 40.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.8 REMARK 200 DATA REDUNDANCY : 2.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.9600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.2 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 : 1.940 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 BISTRIS 25% PEG3350, PH 8.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 296K 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, 2 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: 3260 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 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 350 REMARK 350 BIOMOLECULE: 2 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: 3370 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -29.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, C 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 GLN A 306 REMARK 465 GLN B 306 REMARK 465 GLN D 306 REMARK 465 GLN C 306 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 TYR A 154 CG CD1 CD2 CE1 CE2 CZ OH REMARK 480 TYR B 154 CG CD1 CD2 CE1 CE2 CZ OH REMARK 480 TYR D 154 CG CD1 CD2 CE1 CE2 CZ OH REMARK 480 TYR C 154 CG CD1 CD2 CE1 CE2 CZ OH 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 D 155 O HOH D 501 1.81 REMARK 500 O PHE D 66 O HOH D 502 1.84 REMARK 500 O HOH D 587 O HOH D 589 1.86 REMARK 500 OD1 ASP B 92 O HOH B 501 1.89 REMARK 500 SG CYS A 128 O HOH A 508 1.90 REMARK 500 OG1 THR B 93 O HOH B 501 1.91 REMARK 500 OG1 THR C 243 O HOH C 501 1.91 REMARK 500 C CYS A 128 O HOH A 508 1.93 REMARK 500 O HOH B 508 O HOH B 585 1.93 REMARK 500 O ALA B 194 O HOH B 502 1.97 REMARK 500 OG1 THR A 45 O HOH A 501 1.98 REMARK 500 O HOH B 502 O HOH B 583 1.99 REMARK 500 NH2 ARG C 298 O HOH C 502 1.99 REMARK 500 OH TYR C 154 O HOH C 503 2.00 REMARK 500 OD1 ASP A 197 O HOH A 502 2.00 REMARK 500 NH2 ARG D 217 O HOH D 503 2.01 REMARK 500 NZ LYS C 88 O HOH C 504 2.02 REMARK 500 OD1 ASN C 277 O HOH C 505 2.02 REMARK 500 O HOH D 561 O HOH D 577 2.03 REMARK 500 O HOH A 521 O HOH D 569 2.05 REMARK 500 O HOH B 553 O HOH B 588 2.05 REMARK 500 O LYS B 5 O HOH B 503 2.06 REMARK 500 O CYS B 156 O HOH B 504 2.08 REMARK 500 OE1 GLU A 288 O HOH A 503 2.10 REMARK 500 OE1 GLN C 69 O HOH C 506 2.10 REMARK 500 OD1 ASP B 248 O HOH B 505 2.11 REMARK 500 CA CYS A 128 O HOH A 508 2.12 REMARK 500 CB CYS A 128 O HOH A 508 2.13 REMARK 500 O GLY A 23 O HOH A 504 2.13 REMARK 500 O GLN C 19 O HOH C 507 2.13 REMARK 500 O VAL A 212 O HOH A 505 2.14 REMARK 500 NE ARG D 217 O HOH D 503 2.14 REMARK 500 O HOH C 567 O HOH C 578 2.14 REMARK 500 O HOH A 503 O HOH A 590 2.14 REMARK 500 O LYS C 97 O HOH C 508 2.15 REMARK 500 O HOH B 589 O HOH B 593 2.16 REMARK 500 OE2 GLU A 178 O HOH A 506 2.16 REMARK 500 O HOH C 536 O HOH C 562 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 CL CL A 402 O HOH D 583 1655 1.84 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASP A 33 -125.95 55.14 REMARK 500 ASP A 48 33.66 -76.18 REMARK 500 ASN A 84 -119.22 49.53 REMARK 500 TYR A 154 -93.62 59.00 REMARK 500 ASP B 33 -127.33 56.30 REMARK 500 ASP B 48 31.48 -76.86 REMARK 500 ASN B 84 -116.24 48.89 REMARK 500 TYR B 154 -99.79 61.92 REMARK 500 HIS B 164 -40.60 -130.21 REMARK 500 ASP D 33 -127.19 55.77 REMARK 500 ASP D 48 30.65 -77.99 REMARK 500 ASN D 51 81.30 -150.20 REMARK 500 ASN D 84 -117.70 51.26 REMARK 500 TYR D 154 -96.29 60.55 REMARK 500 ASP C 33 -126.21 54.21 REMARK 500 ASP C 48 31.92 -78.41 REMARK 500 ASN C 84 -115.91 50.13 REMARK 500 TYR C 154 -95.40 60.41 REMARK 500 HIS C 164 -42.22 -131.20 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 GLU B 240 10.63 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 593 DISTANCE = 5.95 ANGSTROMS REMARK 525 HOH D 589 DISTANCE = 5.92 ANGSTROMS DBREF 8R26 A 1 306 UNP P0DTC1 R1A_SARS2 3264 3569 DBREF 8R26 B 1 306 UNP P0DTC1 R1A_SARS2 3264 3569 DBREF 8R26 D 1 306 UNP P0DTC1 R1A_SARS2 3264 3569 DBREF 8R26 C 1 306 UNP P0DTC1 R1A_SARS2 3264 3569 SEQADV 8R26 HIS A 132 UNP P0DTC1 PRO 3395 VARIANT SEQADV 8R26 HIS B 132 UNP P0DTC1 PRO 3395 VARIANT SEQADV 8R26 HIS D 132 UNP P0DTC1 PRO 3395 VARIANT SEQADV 8R26 HIS C 132 UNP P0DTC1 PRO 3395 VARIANT 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 HIS 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 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 HIS 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 D 306 SER GLY PHE ARG LYS MET ALA PHE PRO SER GLY LYS VAL SEQRES 2 D 306 GLU GLY CYS MET VAL GLN VAL THR CYS GLY THR THR THR SEQRES 3 D 306 LEU ASN GLY LEU TRP LEU ASP ASP VAL VAL TYR CYS PRO SEQRES 4 D 306 ARG HIS VAL ILE CYS THR SER GLU ASP MET LEU ASN PRO SEQRES 5 D 306 ASN TYR GLU ASP LEU LEU ILE ARG LYS SER ASN HIS ASN SEQRES 6 D 306 PHE LEU VAL GLN ALA GLY ASN VAL GLN LEU ARG VAL ILE SEQRES 7 D 306 GLY HIS SER MET GLN ASN CYS VAL LEU LYS LEU LYS VAL SEQRES 8 D 306 ASP THR ALA ASN PRO LYS THR PRO LYS TYR LYS PHE VAL SEQRES 9 D 306 ARG ILE GLN PRO GLY GLN THR PHE SER VAL LEU ALA CYS SEQRES 10 D 306 TYR ASN GLY SER PRO SER GLY VAL TYR GLN CYS ALA MET SEQRES 11 D 306 ARG HIS ASN PHE THR ILE LYS GLY SER PHE LEU ASN GLY SEQRES 12 D 306 SER CYS GLY SER VAL GLY PHE ASN ILE ASP TYR ASP CYS SEQRES 13 D 306 VAL SER PHE CYS TYR MET HIS HIS MET GLU LEU PRO THR SEQRES 14 D 306 GLY VAL HIS ALA GLY THR ASP LEU GLU GLY ASN PHE TYR SEQRES 15 D 306 GLY PRO PHE VAL ASP ARG GLN THR ALA GLN ALA ALA GLY SEQRES 16 D 306 THR ASP THR THR ILE THR VAL ASN VAL LEU ALA TRP LEU SEQRES 17 D 306 TYR ALA ALA VAL ILE ASN GLY ASP ARG TRP PHE LEU ASN SEQRES 18 D 306 ARG PHE THR THR THR LEU ASN ASP PHE ASN LEU VAL ALA SEQRES 19 D 306 MET LYS TYR ASN TYR GLU PRO LEU THR GLN ASP HIS VAL SEQRES 20 D 306 ASP ILE LEU GLY PRO LEU SER ALA GLN THR GLY ILE ALA SEQRES 21 D 306 VAL LEU ASP MET CYS ALA SER LEU LYS GLU LEU LEU GLN SEQRES 22 D 306 ASN GLY MET ASN GLY ARG THR ILE LEU GLY SER ALA LEU SEQRES 23 D 306 LEU GLU ASP GLU PHE THR PRO PHE ASP VAL VAL ARG GLN SEQRES 24 D 306 CYS SER GLY VAL THR PHE GLN SEQRES 1 C 306 SER GLY PHE ARG LYS MET ALA PHE PRO SER GLY LYS VAL SEQRES 2 C 306 GLU GLY CYS MET VAL GLN VAL THR CYS GLY THR THR THR SEQRES 3 C 306 LEU ASN GLY LEU TRP LEU ASP ASP VAL VAL TYR CYS PRO SEQRES 4 C 306 ARG HIS VAL ILE CYS THR SER GLU ASP MET LEU ASN PRO SEQRES 5 C 306 ASN TYR GLU ASP LEU LEU ILE ARG LYS SER ASN HIS ASN SEQRES 6 C 306 PHE LEU VAL GLN ALA GLY ASN VAL GLN LEU ARG VAL ILE SEQRES 7 C 306 GLY HIS SER MET GLN ASN CYS VAL LEU LYS LEU LYS VAL SEQRES 8 C 306 ASP THR ALA ASN PRO LYS THR PRO LYS TYR LYS PHE VAL SEQRES 9 C 306 ARG ILE GLN PRO GLY GLN THR PHE SER VAL LEU ALA CYS SEQRES 10 C 306 TYR ASN GLY SER PRO SER GLY VAL TYR GLN CYS ALA MET SEQRES 11 C 306 ARG HIS ASN PHE THR ILE LYS GLY SER PHE LEU ASN GLY SEQRES 12 C 306 SER CYS GLY SER VAL GLY PHE ASN ILE ASP TYR ASP CYS SEQRES 13 C 306 VAL SER PHE CYS TYR MET HIS HIS MET GLU LEU PRO THR SEQRES 14 C 306 GLY VAL HIS ALA GLY THR ASP LEU GLU GLY ASN PHE TYR SEQRES 15 C 306 GLY PRO PHE VAL ASP ARG GLN THR ALA GLN ALA ALA GLY SEQRES 16 C 306 THR ASP THR THR ILE THR VAL ASN VAL LEU ALA TRP LEU SEQRES 17 C 306 TYR ALA ALA VAL ILE ASN GLY ASP ARG TRP PHE LEU ASN SEQRES 18 C 306 ARG PHE THR THR THR LEU ASN ASP PHE ASN LEU VAL ALA SEQRES 19 C 306 MET LYS TYR ASN TYR GLU PRO LEU THR GLN ASP HIS VAL SEQRES 20 C 306 ASP ILE LEU GLY PRO LEU SER ALA GLN THR GLY ILE ALA SEQRES 21 C 306 VAL LEU ASP MET CYS ALA SER LEU LYS GLU LEU LEU GLN SEQRES 22 C 306 ASN GLY MET ASN GLY ARG THR ILE LEU GLY SER ALA LEU SEQRES 23 C 306 LEU GLU ASP GLU PHE THR PRO PHE ASP VAL VAL ARG GLN SEQRES 24 C 306 CYS SER GLY VAL THR PHE GLN HET O6K A 401 43 HET CL A 402 1 HET O6K B 401 43 HET O6K D 401 43 HET CL D 402 1 HET O6K C 401 43 HET CL C 402 1 HETNAM O6K ~{TERT}-BUTYL ~{N}-[1-[(2~{S})-3-CYCLOPROPYL-1- HETNAM 2 O6K OXIDANYLIDENE-1-[[(2~{S},3~{R})-3-OXIDANYL-4- HETNAM 3 O6K OXIDANYLIDENE-1-[(3~{S})-2-OXIDANYLIDENEPYRROLIDIN-3- HETNAM 4 O6K YL]-4-[(PHENYLMETHYL)AMINO]BUTAN-2-YL]AMINO]PROPAN-2- HETNAM 5 O6K YL]-2-OXIDANYLIDENE-PYRIDIN-3-YL]CARBAMATE HETNAM CL CHLORIDE ION HETSYN O6K (S,S,S)-13B; 13B-K; KETOAMIDE INHIBITOR 13B (BOUND) FORMUL 5 O6K 4(C31 H41 N5 O7) FORMUL 6 CL 3(CL 1-) FORMUL 12 HOH *365(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 SER A 46 LEU A 50 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 GLY A 302 1 11 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 SER B 46 LEU B 50 5 5 HELIX 15 AB6 ASN B 53 ARG B 60 1 8 HELIX 16 AB7 LYS B 61 HIS B 64 5 4 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 HELIX 23 AC5 SER D 10 GLY D 15 1 6 HELIX 24 AC6 HIS D 41 CYS D 44 5 4 HELIX 25 AC7 SER D 46 LEU D 50 5 5 HELIX 26 AC8 ASN D 53 ARG D 60 1 8 HELIX 27 AC9 SER D 62 PHE D 66 5 5 HELIX 28 AD1 ILE D 200 ASN D 214 1 15 HELIX 29 AD2 THR D 226 TYR D 237 1 12 HELIX 30 AD3 THR D 243 LEU D 250 1 8 HELIX 31 AD4 LEU D 250 GLY D 258 1 9 HELIX 32 AD5 ALA D 260 GLY D 275 1 16 HELIX 33 AD6 THR D 292 GLY D 302 1 11 HELIX 34 AD7 SER C 10 GLY C 15 1 6 HELIX 35 AD8 HIS C 41 CYS C 44 5 4 HELIX 36 AD9 SER C 46 LEU C 50 5 5 HELIX 37 AE1 ASN C 53 ARG C 60 1 8 HELIX 38 AE2 LYS C 61 PHE C 66 5 6 HELIX 39 AE3 ILE C 200 ASN C 214 1 15 HELIX 40 AE4 THR C 226 TYR C 237 1 12 HELIX 41 AE5 THR C 243 LEU C 250 1 8 HELIX 42 AE6 LEU C 250 GLY C 258 1 9 HELIX 43 AE7 ALA C 260 GLY C 275 1 16 HELIX 44 AE8 THR C 292 GLY C 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 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 ILE A 78 O LYS A 90 SHEET 1 AA2 5 TYR A 101 PHE A 103 0 SHEET 2 AA2 5 CYS A 156 LEU A 167 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 TYR A 126 N VAL A 114 SHEET 1 AA3 3 TYR A 101 PHE A 103 0 SHEET 2 AA3 3 CYS A 156 LEU A 167 1 O PHE A 159 N LYS A 102 SHEET 3 AA3 3 VAL A 171 THR A 175 -1 O VAL A 171 N LEU A 167 SHEET 1 AA4 7 VAL B 73 LEU B 75 0 SHEET 2 AA4 7 PHE B 66 ALA B 70 -1 N VAL B 68 O LEU B 75 SHEET 3 AA4 7 MET B 17 CYS B 22 -1 N THR B 21 O LEU B 67 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 LEU B 167 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 LEU B 167 1 O PHE B 159 N LYS B 102 SHEET 3 AA6 3 VAL B 171 THR B 175 -1 O VAL B 171 N LEU B 167 SHEET 1 AA7 7 VAL D 73 LEU D 75 0 SHEET 2 AA7 7 LEU D 67 ALA D 70 -1 N VAL D 68 O LEU D 75 SHEET 3 AA7 7 MET D 17 CYS D 22 -1 N THR D 21 O LEU D 67 SHEET 4 AA7 7 THR D 25 LEU D 32 -1 O LEU D 27 N VAL D 20 SHEET 5 AA7 7 VAL D 35 PRO D 39 -1 O TYR D 37 N LEU D 30 SHEET 6 AA7 7 VAL D 86 VAL D 91 -1 O LEU D 87 N CYS D 38 SHEET 7 AA7 7 VAL D 77 GLN D 83 -1 N SER D 81 O LYS D 88 SHEET 1 AA8 5 TYR D 101 PHE D 103 0 SHEET 2 AA8 5 CYS D 156 GLU D 166 1 O PHE D 159 N LYS D 102 SHEET 3 AA8 5 VAL D 148 ASP D 153 -1 N ASN D 151 O SER D 158 SHEET 4 AA8 5 THR D 111 TYR D 118 -1 N SER D 113 O PHE D 150 SHEET 5 AA8 5 SER D 121 ALA D 129 -1 O TYR D 126 N VAL D 114 SHEET 1 AA9 3 TYR D 101 PHE D 103 0 SHEET 2 AA9 3 CYS D 156 GLU D 166 1 O PHE D 159 N LYS D 102 SHEET 3 AA9 3 HIS D 172 THR D 175 -1 O ALA D 173 N MET D 165 SHEET 1 AB1 7 VAL C 73 LEU C 75 0 SHEET 2 AB1 7 LEU C 67 ALA C 70 -1 N ALA C 70 O VAL C 73 SHEET 3 AB1 7 MET C 17 CYS C 22 -1 N THR C 21 O LEU C 67 SHEET 4 AB1 7 THR C 25 LEU C 32 -1 O THR C 25 N CYS C 22 SHEET 5 AB1 7 VAL C 35 PRO C 39 -1 O TYR C 37 N LEU C 30 SHEET 6 AB1 7 VAL C 86 VAL C 91 -1 O LEU C 87 N CYS C 38 SHEET 7 AB1 7 VAL C 77 GLN C 83 -1 N SER C 81 O LYS C 88 SHEET 1 AB2 5 TYR C 101 PHE C 103 0 SHEET 2 AB2 5 CYS C 156 LEU C 167 1 O PHE C 159 N LYS C 102 SHEET 3 AB2 5 VAL C 148 ASP C 153 -1 N ASN C 151 O SER C 158 SHEET 4 AB2 5 THR C 111 TYR C 118 -1 N SER C 113 O PHE C 150 SHEET 5 AB2 5 SER C 121 ALA C 129 -1 O SER C 123 N ALA C 116 SHEET 1 AB3 3 TYR C 101 PHE C 103 0 SHEET 2 AB3 3 CYS C 156 LEU C 167 1 O PHE C 159 N LYS C 102 SHEET 3 AB3 3 VAL C 171 THR C 175 -1 O VAL C 171 N LEU C 167 LINK SG CYS A 145 C57 O6K A 401 1555 1555 1.77 LINK SG CYS B 145 C57 O6K B 401 1555 1555 1.77 LINK SG CYS D 145 C57 O6K D 401 1555 1555 1.77 LINK SG CYS C 145 C57 O6K C 401 1555 1555 1.77 CRYST1 45.488 71.464 85.795 85.61 80.43 78.65 P 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 0.021984 -0.004413 -0.003510 0.00000 SCALE2 0.000000 0.014272 -0.000648 0.00000 SCALE3 0.000000 0.000000 0.011832 0.00000