HEADER ANTIVIRAL PROTEIN 24-JAN-23 8CAE TITLE CRYSTAL STRUCTURE OF SARS-COV-2 MPRO-H172Y MUTANT IN COMPLEX WITH TITLE 2 NIRMATRELVIR CAVEAT 8CAE 4WI A 401 HAS WRONG CHIRALITY AT ATOM C11 4WI A 401 HAS CAVEAT 2 8CAE WRONG CHIRALITY AT ATOM C12 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NON-STRUCTURAL PROTEIN 11; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NSP11; COMPND 5 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; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 561 KEYWDS MPRO MUTATION, ANTIVIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.EL KILANI,R.HILGENFELD REVDAT 2 03-SEP-25 8CAE 1 JRNL REVDAT 1 06-AUG-25 8CAE 0 JRNL AUTH H.EL KILANI,X.SUN,M.F.IBRAHIM,U.CURTH,R.HILGENFELD JRNL TITL 13B-K AND NIRMATRELVIR RESISTANCE MUTATIONS OF SARS-COV-2 JRNL TITL 2 MAIN PROTEASE: STRUCTURAL, BIOCHEMICAL, AND BIOPHYSICAL JRNL TITL 3 CHARACTERIZATION OF FREE ENZYMES AND INHIBITOR COMPLEXES JRNL REF CRYSTALS V. 15 2025 JRNL REFN ESSN 2073-4352 JRNL DOI 10.3390/CRYST15090758 REMARK 2 REMARK 2 RESOLUTION. 2.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0419 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.58 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 7973 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NONE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.992 REMARK 3 FREE R VALUE TEST SET COUNT : 398 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.72 REMARK 3 REFLECTION IN BIN (WORKING SET) : 563 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.98 REMARK 3 BIN R VALUE (WORKING SET) : 0.3690 REMARK 3 BIN FREE R VALUE SET COUNT : 18 REMARK 3 BIN FREE R VALUE : 0.2830 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2342 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 35 REMARK 3 SOLVENT ATOMS : 25 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 79.12 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.40200 REMARK 3 B22 (A**2) : -2.43500 REMARK 3 B33 (A**2) : -2.95600 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 3.01700 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.393 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.399 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 20.918 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.935 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2432 ; 0.005 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 2257 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3313 ; 1.373 ; 1.804 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5183 ; 0.490 ; 1.733 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 302 ; 8.745 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 15 ;16.096 ; 6.333 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 384 ;15.818 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 376 ; 0.066 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2880 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 574 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 580 ; 0.242 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 119 ; 0.211 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1226 ; 0.193 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 78 ; 0.191 ; 0.200 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): 1211 ; 6.298 ; 7.725 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1211 ; 6.286 ; 7.724 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1512 ; 9.619 ;13.841 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1513 ; 9.616 ;13.846 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1221 ; 6.423 ; 8.344 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1222 ; 6.420 ; 8.345 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1798 ;10.236 ;15.069 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1799 ;10.234 ;15.069 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL 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 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT 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 THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 8CAE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-JAN-23. REMARK 100 THE DEPOSITION ID IS D_1292128131. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-OCT-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 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) : 1.033 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7973 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.650 REMARK 200 RESOLUTION RANGE LOW (A) : 48.583 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.72 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.86 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: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M MMT PH8.0, 25% W/VPEG 1500, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 57.60400 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.88050 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 57.60400 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 26.88050 REMARK 290 SMTRY3 4 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 -9.14762 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 44.62303 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 510 LIES ON A SPECIAL POSITION. 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 THR A 199 CA - CB - OG1 ANGL. DEV. = -13.1 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 PHE A 3 112.10 -163.92 REMARK 500 CYS A 22 83.73 -157.55 REMARK 500 ASP A 33 -114.01 47.39 REMARK 500 ASN A 51 78.07 -169.42 REMARK 500 ASN A 63 -47.15 -23.31 REMARK 500 ILE A 78 28.84 -143.49 REMARK 500 ASN A 84 -129.83 54.90 REMARK 500 SER A 139 86.26 -150.43 REMARK 500 TYR A 154 -75.78 58.78 REMARK 500 THR A 169 -30.26 141.90 REMARK 500 PRO A 184 53.26 -93.38 REMARK 500 PHE A 223 -161.79 -124.98 REMARK 500 MET A 235 -60.99 -20.23 REMARK 500 CYS A 300 47.47 -109.38 REMARK 500 SER A 301 -72.43 -150.88 REMARK 500 REMARK 500 REMARK: NULL DBREF 8CAE A 1 303 UNP P0DTC1 R1A_SARS2 3264 3566 SEQADV 8CAE TYR A 172 UNP P0DTC1 HIS 3435 ENGINEERED MUTATION SEQRES 1 A 303 SER GLY PHE ARG LYS MET ALA PHE PRO SER GLY LYS VAL SEQRES 2 A 303 GLU GLY CYS MET VAL GLN VAL THR CYS GLY THR THR THR SEQRES 3 A 303 LEU ASN GLY LEU TRP LEU ASP ASP VAL VAL TYR CYS PRO SEQRES 4 A 303 ARG HIS VAL ILE CYS THR SER GLU ASP MET LEU ASN PRO SEQRES 5 A 303 ASN TYR GLU ASP LEU LEU ILE ARG LYS SER ASN HIS ASN SEQRES 6 A 303 PHE LEU VAL GLN ALA GLY ASN VAL GLN LEU ARG VAL ILE SEQRES 7 A 303 GLY HIS SER MET GLN ASN CYS VAL LEU LYS LEU LYS VAL SEQRES 8 A 303 ASP THR ALA ASN PRO LYS THR PRO LYS TYR LYS PHE VAL SEQRES 9 A 303 ARG ILE GLN PRO GLY GLN THR PHE SER VAL LEU ALA CYS SEQRES 10 A 303 TYR ASN GLY SER PRO SER GLY VAL TYR GLN CYS ALA MET SEQRES 11 A 303 ARG PRO ASN PHE THR ILE LYS GLY SER PHE LEU ASN GLY SEQRES 12 A 303 SER CYS GLY SER VAL GLY PHE ASN ILE ASP TYR ASP CYS SEQRES 13 A 303 VAL SER PHE CYS TYR MET HIS HIS MET GLU LEU PRO THR SEQRES 14 A 303 GLY VAL TYR ALA GLY THR ASP LEU GLU GLY ASN PHE TYR SEQRES 15 A 303 GLY PRO PHE VAL ASP ARG GLN THR ALA GLN ALA ALA GLY SEQRES 16 A 303 THR ASP THR THR ILE THR VAL ASN VAL LEU ALA TRP LEU SEQRES 17 A 303 TYR ALA ALA VAL ILE ASN GLY ASP ARG TRP PHE LEU ASN SEQRES 18 A 303 ARG PHE THR THR THR LEU ASN ASP PHE ASN LEU VAL ALA SEQRES 19 A 303 MET LYS TYR ASN TYR GLU PRO LEU THR GLN ASP HIS VAL SEQRES 20 A 303 ASP ILE LEU GLY PRO LEU SER ALA GLN THR GLY ILE ALA SEQRES 21 A 303 VAL LEU ASP MET CYS ALA SER LEU LYS GLU LEU LEU GLN SEQRES 22 A 303 ASN GLY MET ASN GLY ARG THR ILE LEU GLY SER ALA LEU SEQRES 23 A 303 LEU GLU ASP GLU PHE THR PRO PHE ASP VAL VAL ARG GLN SEQRES 24 A 303 CYS SER GLY VAL HET 4WI A 401 35 HETNAM 4WI (1R,2S,5S)-N-{(1E,2S)-1-IMINO-3-[(3S)-2-OXOPYRROLIDIN- HETNAM 2 4WI 3-YL]PROPAN-2-YL}-6,6-DIMETHYL-3-[3-METHYL-N- HETNAM 3 4WI (TRIFLUOROACETYL)-L-VALYL]-3-AZABICYCLO[3.1.0]HEXANE- HETNAM 4 4WI 2-CARBOXAMIDE HETSYN 4WI PF-07321332, BOUND FORM; NIRMATRELVIR, BOUND FORM; HETSYN 2 4WI PAXLOVID, BOUND FORM FORMUL 2 4WI C23 H34 F3 N5 O4 FORMUL 3 HOH *25(H2 O) HELIX 1 AA1 SER A 10 GLY A 15 1 6 HELIX 2 AA2 HIS A 41 CYS A 44 5 4 HELIX 3 AA3 GLU A 47 ASN A 51 5 5 HELIX 4 AA4 ASN A 53 ARG A 60 1 8 HELIX 5 AA5 LYS A 61 PHE A 66 5 6 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 GLY A 258 1 16 HELIX 9 AA9 ALA A 260 GLY A 275 1 16 HELIX 10 AB1 THR A 292 CYS A 300 1 9 SHEET 1 AA1 7 VAL A 73 LEU A 75 0 SHEET 2 AA1 7 LEU A 67 ALA A 70 -1 N ALA A 70 O VAL A 73 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 GLY A 29 N VAL A 18 SHEET 5 AA1 7 VAL A 35 PRO A 39 -1 O VAL A 35 N LEU A 32 SHEET 6 AA1 7 VAL A 86 VAL A 91 -1 O LEU A 87 N CYS A 38 SHEET 7 AA1 7 VAL A 77 GLN A 83 -1 N GLN A 83 O VAL A 86 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 ASP A 153 O CYS A 156 SHEET 4 AA2 5 THR A 111 CYS A 117 -1 N SER A 113 O PHE A 150 SHEET 5 AA2 5 PRO A 122 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 LINK SG CYS A 145 C3 4WI A 401 1555 1555 1.77 CRYST1 115.208 53.761 45.551 90.00 101.59 90.00 C 1 2 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 0.008680 0.000000 0.001779 0.00000 SCALE2 0.000000 0.018601 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022410 0.00000 TER 2343 VAL A 303 HETATM 2344 C8 4WI A 401 -10.737 1.356 4.210 0.90115.17 C0 HETATM 2345 C3 4WI A 401 -11.975 -2.255 2.818 0.90112.88 C0 HETATM 2346 C1 4WI A 401 -14.443 -0.671 0.648 0.90 86.28 C0 HETATM 2347 C13 4WI A 401 -15.097 2.559 0.500 0.90 92.56 C0 HETATM 2348 C21 4WI A 401 -17.576 4.670 -0.171 0.90 95.84 C0 HETATM 2349 C6 4WI A 401 -10.849 1.364 1.852 0.90102.70 C0 HETATM 2350 C7 4WI A 401 -9.664 2.194 2.315 0.90104.80 C0 HETATM 2351 C10 4WI A 401 -16.600 1.324 -1.051 0.90 94.80 C0 HETATM 2352 C5 4WI A 401 -11.745 1.279 3.082 0.90104.86 C0 HETATM 2353 C9 4WI A 401 -15.648 0.216 0.916 0.90 84.01 C0 HETATM 2354 C11 4WI A 401 -17.606 0.322 -0.546 0.90 95.33 C0 HETATM 2355 C12 4WI A 401 -16.942 -0.491 0.554 0.90 89.75 C0 HETATM 2356 C18 4WI A 401 -17.274 -1.101 -0.784 0.90 92.88 C0 HETATM 2357 C19 4WI A 401 -16.236 -1.394 -1.843 0.90104.19 C0 HETATM 2358 C20 4WI A 401 -18.458 -2.039 -0.817 0.90 92.98 C0 HETATM 2359 C16 4WI A 401 -14.313 5.497 -1.918 0.90 92.85 C0 HETATM 2360 C17 4WI A 401 -12.879 3.642 -1.099 0.90 87.44 C0 HETATM 2361 C23 4WI A 401 -13.526 5.470 0.442 0.90 91.12 C0 HETATM 2362 C4 4WI A 401 -12.725 0.112 3.262 0.90105.97 C0 HETATM 2363 C2 4WI A 401 -12.639 -1.019 2.235 0.90103.69 C0 HETATM 2364 C14 4WI A 401 -15.291 3.806 -0.370 0.90 96.54 C0 HETATM 2365 C22 4WI A 401 -18.583 5.391 0.729 0.90106.60 C0 HETATM 2366 C15 4WI A 401 -14.013 4.596 -0.717 0.90 90.24 C0 HETATM 2367 N5 4WI A 401 -11.449 -2.290 4.002 0.90131.60 N0 HETATM 2368 N2 4WI A 401 -9.665 1.990 3.759 0.90113.86 N0 HETATM 2369 N3 4WI A 401 -15.709 1.437 0.108 0.90 89.84 N0 HETATM 2370 N1 4WI A 401 -13.965 -1.317 1.719 0.90 92.86 N0 HETATM 2371 N4 4WI A 401 -16.312 4.635 0.255 0.90 97.76 N0 HETATM 2372 O1 4WI A 401 -10.891 0.903 5.363 0.90130.62 O0 HETATM 2373 O2 4WI A 401 -13.880 -0.670 -0.444 0.90 92.86 O0 HETATM 2374 O3 4WI A 401 -14.464 2.572 1.547 0.90100.43 O0 HETATM 2375 O4 4WI A 401 -17.963 4.182 -1.212 0.90 88.89 O0 HETATM 2376 F1 4WI A 401 -18.327 5.167 2.010 0.90123.66 F0 HETATM 2377 F2 4WI A 401 -19.828 4.989 0.512 0.90106.54 F0 HETATM 2378 F3 4WI A 401 -18.564 6.706 0.543 0.90103.44 F0 HETATM 2379 O HOH A 501 -34.443 9.978 32.484 1.00 68.57 O0 HETATM 2380 O HOH A 502 -23.411 -7.326 16.792 1.00 51.75 O0 HETATM 2381 O HOH A 503 -14.223 6.763 17.194 1.00 52.59 O0 HETATM 2382 O HOH A 504 -27.369 -8.102 16.604 1.00 71.59 O0 HETATM 2383 O HOH A 505 -20.592 -5.020 2.610 1.00 64.30 O0 HETATM 2384 O HOH A 506 -11.961 -17.571 -5.600 1.00 74.85 O0 HETATM 2385 O HOH A 507 -4.260 20.577 38.962 1.00 53.89 O0 HETATM 2386 O HOH A 508 -26.571 -18.353 -4.509 1.00 63.44 O0 HETATM 2387 O HOH A 509 -26.416 -17.734 11.990 1.00 57.05 O0 HETATM 2388 O HOH A 510 -4.574 17.202 22.312 0.50 39.20 O0 HETATM 2389 O HOH A 511 -31.939 -10.154 5.052 1.00 57.98 O0 HETATM 2390 O HOH A 512 -25.778 9.496 10.545 1.00 61.18 O0 HETATM 2391 O HOH A 513 -19.049 0.449 26.475 1.00 60.16 O0 HETATM 2392 O HOH A 514 -28.203 1.735 17.187 1.00 65.71 O0 HETATM 2393 O HOH A 515 -21.788 -18.897 23.910 1.00 56.90 O0 HETATM 2394 O HOH A 516 -21.307 3.001 30.892 1.00 57.22 O0 HETATM 2395 O HOH A 517 -29.893 -4.268 2.734 1.00 58.21 O0 HETATM 2396 O HOH A 518 -24.406 -20.096 14.815 1.00 66.64 O0 HETATM 2397 O HOH A 519 -22.699 -15.105 26.775 1.00 63.07 O0 HETATM 2398 O HOH A 520 -30.886 4.199 -6.075 1.00 69.80 O0 HETATM 2399 O HOH A 521 -24.159 10.670 24.946 1.00 52.09 O0 HETATM 2400 O HOH A 522 -26.643 17.825 16.077 1.00 67.26 O0 HETATM 2401 O HOH A 523 -25.932 -20.061 7.396 1.00 52.78 O0 HETATM 2402 O HOH A 524 -25.683 -16.870 18.081 1.00 62.92 O0 HETATM 2403 O HOH A 525 -25.515 -18.698 20.134 1.00 58.73 O0 CONECT 1120 2345 CONECT 2344 2352 2368 2372 CONECT 2345 1120 2363 2367 CONECT 2346 2353 2370 2373 CONECT 2347 2364 2369 2374 CONECT 2348 2365 2371 2375 CONECT 2349 2350 2352 CONECT 2350 2349 2368 CONECT 2351 2354 2369 CONECT 2352 2344 2349 2362 CONECT 2353 2346 2355 2369 CONECT 2354 2351 2355 2356 CONECT 2355 2353 2354 2356 CONECT 2356 2354 2355 2357 2358 CONECT 2357 2356 CONECT 2358 2356 CONECT 2359 2366 CONECT 2360 2366 CONECT 2361 2366 CONECT 2362 2352 2363 CONECT 2363 2345 2362 2370 CONECT 2364 2347 2366 2371 CONECT 2365 2348 2376 2377 2378 CONECT 2366 2359 2360 2361 2364 CONECT 2367 2345 CONECT 2368 2344 2350 CONECT 2369 2347 2351 2353 CONECT 2370 2346 2363 CONECT 2371 2348 2364 CONECT 2372 2344 CONECT 2373 2346 CONECT 2374 2347 CONECT 2375 2348 CONECT 2376 2365 CONECT 2377 2365 CONECT 2378 2365 MASTER 300 0 1 10 15 0 0 6 2402 1 36 24 END