HEADER VIRAL PROTEIN/INHIBITOR 14-MAR-25 9MA3 TITLE CRYSTAL STRUCTURE OF SARS-COV-2 MAIN PROTEASE (MPRO) MUTANT DEL23T45I TITLE 2 IN COMPLEX WITH NIRMATRELVIR (C2 SPACE GROUP) COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3C-LIKE PROTEINASE NSP5; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 3CL-PRO,3CLP,MAIN PROTEASE,MPRO,NON-STRUCTURAL PROTEIN 5, COMPND 5 NSP5,SARS CORONAVIRUS MAIN PROTEINASE; COMPND 6 EC: 3.4.22.69; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: 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 COMPLEX, INHIBITOR, VIRAL PROTEIN, VIRAL PROTEIN-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.C.SHIN,J.J.SEO,J.M.YOON REVDAT 1 21-JAN-26 9MA3 0 JRNL AUTH S.C.MIN,J.J.SEO,J.H.JEONG,B.K.KIM,J.H.PARK,J.R.LEE,D.G.LEE, JRNL AUTH 2 G.C.LEE,S.H.AN,Y.H.BAEK,Y.K.CHOI,H.CHOO,H.Y.PARK,G.KIM, JRNL AUTH 3 B.JEON,S.C.SHIN,M.S.SONG JRNL TITL A SARS-COV-2 M PRO MUTATION CONFERRING ENSITRELVIR JRNL TITL 2 RESISTANCE PARADOXICALLY INCREASES NIRMATRELVIR JRNL TITL 3 SUSCEPTIBILITY. JRNL REF NAT COMMUN V. 16 10737 2025 JRNL REFN ESSN 2041-1723 JRNL PMID 41274896 JRNL DOI 10.1038/S41467-025-65767-Z REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.19.2_4158: ???) 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.51 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.480 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 3 NUMBER OF REFLECTIONS : 10400 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.211 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1040 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 34.5100 - 4.6000 0.99 1411 157 0.1740 0.1866 REMARK 3 2 4.6000 - 3.6500 1.00 1391 154 0.1757 0.2567 REMARK 3 3 3.6500 - 3.1900 1.00 1372 152 0.2169 0.2466 REMARK 3 4 3.1900 - 2.9000 0.98 1360 152 0.2450 0.2807 REMARK 3 5 2.9000 - 2.6900 0.98 1351 149 0.2553 0.2848 REMARK 3 6 2.6900 - 2.5300 0.96 1295 145 0.2716 0.2913 REMARK 3 7 2.5300 - 2.4000 0.84 1180 131 0.2992 0.3578 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) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.300 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 : 0.002 2413 REMARK 3 ANGLE : 0.493 3287 REMARK 3 CHIRALITY : 0.040 372 REMARK 3 PLANARITY : 0.004 422 REMARK 3 DIHEDRAL : 5.316 326 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 9MA3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-MAR-25. REMARK 100 THE DEPOSITION ID IS D_1300057492. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAR-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 ~ 9.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 5C (4A) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10774 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 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 (%) : 96.6 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 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: 7NF5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200 MM AMMONIUM ACETATE AND 20% (V/V) REMARK 280 PEG 3350, PH 7.5, VAPOR DIFFUSION, HANGING 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 57.52650 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.94400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 57.52650 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 26.94400 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC 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 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 539 LIES ON A SPECIAL POSITION. 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 CYS A 22 -90.00 -122.58 REMARK 500 ASP A 33 -124.88 56.17 REMARK 500 ASN A 51 80.58 -160.68 REMARK 500 ASN A 84 -120.45 54.04 REMARK 500 TYR A 154 -114.04 60.60 REMARK 500 HIS A 164 -43.07 -133.99 REMARK 500 ASN A 221 -158.16 -91.85 REMARK 500 ARG A 279 -160.83 -79.58 REMARK 500 REMARK 500 REMARK: NULL DBREF 9MA3 A 1 301 UNP P0DTC1 R1A_SARS2 3264 3564 SEQADV 9MA3 A UNP P0DTC1 GLY 3286 DELETION SEQADV 9MA3 ILE A 45 UNP P0DTC1 THR 3308 ENGINEERED MUTATION SEQRES 1 A 300 SER GLY PHE ARG LYS MET ALA PHE PRO SER GLY LYS VAL SEQRES 2 A 300 GLU GLY CYS MET VAL GLN VAL THR CYS THR THR THR LEU SEQRES 3 A 300 ASN GLY LEU TRP LEU ASP ASP VAL VAL TYR CYS PRO ARG SEQRES 4 A 300 HIS VAL ILE CYS ILE SER GLU ASP MET LEU ASN PRO ASN SEQRES 5 A 300 TYR GLU ASP LEU LEU ILE ARG LYS SER ASN HIS ASN PHE SEQRES 6 A 300 LEU VAL GLN ALA GLY ASN VAL GLN LEU ARG VAL ILE GLY SEQRES 7 A 300 HIS SER MET GLN ASN CYS VAL LEU LYS LEU LYS VAL ASP SEQRES 8 A 300 THR ALA ASN PRO LYS THR PRO LYS TYR LYS PHE VAL ARG SEQRES 9 A 300 ILE GLN PRO GLY GLN THR PHE SER VAL LEU ALA CYS TYR SEQRES 10 A 300 ASN GLY SER PRO SER GLY VAL TYR GLN CYS ALA MET ARG SEQRES 11 A 300 PRO ASN PHE THR ILE LYS GLY SER PHE LEU ASN GLY SER SEQRES 12 A 300 CYS GLY SER VAL GLY PHE ASN ILE ASP TYR ASP CYS VAL SEQRES 13 A 300 SER PHE CYS TYR MET HIS HIS MET GLU LEU PRO THR GLY SEQRES 14 A 300 VAL HIS ALA GLY THR ASP LEU GLU GLY ASN PHE TYR GLY SEQRES 15 A 300 PRO PHE VAL ASP ARG GLN THR ALA GLN ALA ALA GLY THR SEQRES 16 A 300 ASP THR THR ILE THR VAL ASN VAL LEU ALA TRP LEU TYR SEQRES 17 A 300 ALA ALA VAL ILE ASN GLY ASP ARG TRP PHE LEU ASN ARG SEQRES 18 A 300 PHE THR THR THR LEU ASN ASP PHE ASN LEU VAL ALA MET SEQRES 19 A 300 LYS TYR ASN TYR GLU PRO LEU THR GLN ASP HIS VAL ASP SEQRES 20 A 300 ILE LEU GLY PRO LEU SER ALA GLN THR GLY ILE ALA VAL SEQRES 21 A 300 LEU ASP MET CYS ALA SER LEU LYS GLU LEU LEU GLN ASN SEQRES 22 A 300 GLY MET ASN GLY ARG THR ILE LEU GLY SER ALA LEU LEU SEQRES 23 A 300 GLU ASP GLU PHE THR PRO PHE ASP VAL VAL ARG GLN CYS SEQRES 24 A 300 SER 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 *42(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 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 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 THR A 21 -1 N THR A 21 O LEU A 67 SHEET 4 AA1 7 THR A 26 LEU A 32 -1 O GLY A 29 N VAL A 18 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 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 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 GLU A 166 1 O PHE A 159 N LYS A 102 SHEET 3 AA3 3 HIS A 172 THR A 175 -1 O ALA A 173 N MET A 165 LINK SG CYS A 145 C3 4WI A 401 1555 1555 1.77 CRYST1 115.053 53.888 45.720 90.00 102.29 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 0.008692 0.000000 0.001894 0.00000 SCALE2 0.000000 0.018557 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022386 0.00000 CONECT 1117 2329 CONECT 2328 2336 2352 2356 CONECT 2329 1117 2347 2351 CONECT 2330 2337 2354 2357 CONECT 2331 2348 2353 2358 CONECT 2332 2349 2355 2359 CONECT 2333 2334 2336 CONECT 2334 2333 2352 CONECT 2335 2338 2353 CONECT 2336 2328 2333 2346 CONECT 2337 2330 2339 2353 CONECT 2338 2335 2339 2340 CONECT 2339 2337 2338 2340 CONECT 2340 2338 2339 2341 2342 CONECT 2341 2340 CONECT 2342 2340 CONECT 2343 2350 CONECT 2344 2350 CONECT 2345 2350 CONECT 2346 2336 2347 CONECT 2347 2329 2346 2354 CONECT 2348 2331 2350 2355 CONECT 2349 2332 2360 2361 2362 CONECT 2350 2343 2344 2345 2348 CONECT 2351 2329 CONECT 2352 2328 2334 CONECT 2353 2331 2335 2337 CONECT 2354 2330 2347 CONECT 2355 2332 2348 CONECT 2356 2328 CONECT 2357 2330 CONECT 2358 2331 CONECT 2359 2332 CONECT 2360 2349 CONECT 2361 2349 CONECT 2362 2349 MASTER 226 0 1 11 15 0 0 6 2403 1 36 24 END