HEADER HYDROLASE 05-FEB-25 9N6L TITLE ROOM TEMPERATURE X-RAY STRUCTURE OF SARS-COV-2 MAIN PROTEASE MUTANT TITLE 2 D48Y, P168 DELETION IN COMPLEX WITH GC373 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 GENE: REP, 1A-1B; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CYSTEINE PROTEASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR D.BHANDARI,A.KOVALEVSKY REVDAT 1 30-JUL-25 9N6L 0 JRNL AUTH D.BHANDARI,O.GERLITS,S.KEABLE,L.COATES,A.ANIANA,R.GHIRLANDO, JRNL AUTH 2 N.T.NASHED,A.KOVALEVSKY,J.M.LOUIS JRNL TITL CHARACTERIZATION OF AN UNUSUAL SARS-COV-2 MAIN PROTEASE JRNL TITL 2 NATURAL VARIANT EXHIBITING RESISTANCE TO NIRMATRELVIR AND JRNL TITL 3 ENSITRELVIR. JRNL REF COMMUN BIOL V. 8 1061 2025 JRNL REFN ESSN 2399-3642 JRNL PMID 40676153 JRNL DOI 10.1038/S42003-025-08487-W REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.21.1_5286: ???) 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.53 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 19347 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 948 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 28.5300 - 4.2000 0.98 2682 139 0.1615 0.1814 REMARK 3 2 4.2000 - 3.3400 0.99 2645 155 0.1592 0.2097 REMARK 3 3 3.3400 - 2.9200 0.98 2645 134 0.1937 0.2269 REMARK 3 4 2.9200 - 2.6500 0.98 2608 141 0.2037 0.2678 REMARK 3 5 2.6500 - 2.4600 0.98 2635 131 0.2054 0.2759 REMARK 3 6 2.4600 - 2.3200 0.97 2594 120 0.2002 0.2974 REMARK 3 7 2.3200 - 2.2000 0.96 2590 128 0.2046 0.2430 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.530 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 : 0.008 2447 REMARK 3 ANGLE : 0.879 3323 REMARK 3 CHIRALITY : 0.049 373 REMARK 3 PLANARITY : 0.008 430 REMARK 3 DIHEDRAL : 14.769 867 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 9N6L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-FEB-25. REMARK 100 THE DEPOSITION ID IS D_1000292601. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JUN-24 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER R 4M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSALISPRO REMARK 200 DATA SCALING SOFTWARE : CRYSALISPRO REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19382 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 60.960 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.08200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.7400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.3 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : 0.27400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.730 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 (%): 57.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15-17 % PEG3350, 0.1 M BIS-TRIS PH REMARK 280 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 287K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 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+1/2 REMARK 290 4555 -X+1/2,Y+1/2,-Z+1/2 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 22.18187 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.94750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 45.64945 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 22.18187 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 40.94750 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 45.64945 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 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 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 19.14796 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 365.19564 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 540 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 ASP A 33 -128.45 51.14 REMARK 500 ASN A 51 79.10 -157.67 REMARK 500 ASN A 84 -117.83 50.59 REMARK 500 TYR A 154 -107.68 53.44 REMARK 500 LEU A 167 -129.30 -94.78 REMARK 500 SER A 301 -37.15 -137.48 REMARK 500 REMARK 500 REMARK: NULL REMARK 630 REMARK 630 MOLECULE TYPE: NULL REMARK 630 MOLECULE NAME: (1S,2S)-2-({N-[(BENZYLOXY)CARBONYL]-L-LEUCYL}AMINO)- REMARK 630 1-HYDROXY-3-[(3S)-2-OXOPYRROLIDIN-3-YL]PROPANE-1-SULFONIC ACID REMARK 630 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 630 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 630 REMARK 630 M RES C SSSEQI REMARK 630 K36 A 401 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: PHQ LEU 04F REMARK 630 DETAILS: NULL DBREF 9N6L A 1 306 UNP P0DTD1 R1AB_SARS2 3264 3569 SEQADV 9N6L TYR A 48 UNP P0DTD1 ASP 3311 ENGINEERED MUTATION SEQADV 9N6L A UNP P0DTD1 PRO 3431 DELETION SEQRES 1 A 305 SER GLY PHE ARG LYS MET ALA PHE PRO SER GLY LYS VAL SEQRES 2 A 305 GLU GLY CYS MET VAL GLN VAL THR CYS GLY THR THR THR SEQRES 3 A 305 LEU ASN GLY LEU TRP LEU ASP ASP VAL VAL TYR CYS PRO SEQRES 4 A 305 ARG HIS VAL ILE CYS THR SER GLU TYR MET LEU ASN PRO SEQRES 5 A 305 ASN TYR GLU ASP LEU LEU ILE ARG LYS SER ASN HIS ASN SEQRES 6 A 305 PHE LEU VAL GLN ALA GLY ASN VAL GLN LEU ARG VAL ILE SEQRES 7 A 305 GLY HIS SER MET GLN ASN CYS VAL LEU LYS LEU LYS VAL SEQRES 8 A 305 ASP THR ALA ASN PRO LYS THR PRO LYS TYR LYS PHE VAL SEQRES 9 A 305 ARG ILE GLN PRO GLY GLN THR PHE SER VAL LEU ALA CYS SEQRES 10 A 305 TYR ASN GLY SER PRO SER GLY VAL TYR GLN CYS ALA MET SEQRES 11 A 305 ARG PRO ASN PHE THR ILE LYS GLY SER PHE LEU ASN GLY SEQRES 12 A 305 SER CYS GLY SER VAL GLY PHE ASN ILE ASP TYR ASP CYS SEQRES 13 A 305 VAL SER PHE CYS TYR MET HIS HIS MET GLU LEU THR GLY SEQRES 14 A 305 VAL HIS ALA GLY THR ASP LEU GLU GLY ASN PHE TYR GLY SEQRES 15 A 305 PRO PHE VAL ASP ARG GLN THR ALA GLN ALA ALA GLY THR SEQRES 16 A 305 ASP THR THR ILE THR VAL ASN VAL LEU ALA TRP LEU TYR SEQRES 17 A 305 ALA ALA VAL ILE ASN GLY ASP ARG TRP PHE LEU ASN ARG SEQRES 18 A 305 PHE THR THR THR LEU ASN ASP PHE ASN LEU VAL ALA MET SEQRES 19 A 305 LYS TYR ASN TYR GLU PRO LEU THR GLN ASP HIS VAL ASP SEQRES 20 A 305 ILE LEU GLY PRO LEU SER ALA GLN THR GLY ILE ALA VAL SEQRES 21 A 305 LEU ASP MET CYS ALA SER LEU LYS GLU LEU LEU GLN ASN SEQRES 22 A 305 GLY MET ASN GLY ARG THR ILE LEU GLY SER ALA LEU LEU SEQRES 23 A 305 GLU ASP GLU PHE THR PRO PHE ASP VAL VAL ARG GLN CYS SEQRES 24 A 305 SER GLY VAL THR PHE GLN HET K36 A 401 29 HETNAM K36 (1S,2S)-2-({N-[(BENZYLOXY)CARBONYL]-L-LEUCYL}AMINO)-1- HETNAM 2 K36 HYDROXY-3-[(3S)-2-OXOPYRROLIDIN-3-YL]PROPANE-1- HETNAM 3 K36 SULFONIC ACID HETSYN K36 GC376 FORMUL 2 K36 C21 H31 N3 O8 S FORMUL 3 HOH *74(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 TYR A 237 1 12 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 SHEET 1 AA1 7 VAL A 73 LEU A 75 0 SHEET 2 AA1 7 PHE A 66 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 GLY A 79 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 ASP A 153 O CYS A 156 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 C21 K36 A 401 1555 1555 1.86 CRYST1 52.769 81.895 91.685 90.00 95.26 90.00 I 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 0.018950 0.000000 0.001746 0.00000 SCALE2 0.000000 0.012211 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010953 0.00000 CONECT 1124 2386 CONECT 2366 2367 2370 CONECT 2367 2366 2368 CONECT 2368 2367 2369 2376 CONECT 2369 2368 CONECT 2370 2366 2371 2375 CONECT 2371 2370 2372 CONECT 2372 2371 2373 CONECT 2373 2372 2374 CONECT 2374 2373 2375 CONECT 2375 2370 2374 CONECT 2376 2368 2377 CONECT 2377 2376 2378 2380 CONECT 2378 2377 2379 2384 CONECT 2379 2378 CONECT 2380 2377 2381 CONECT 2381 2380 2382 2383 CONECT 2382 2381 CONECT 2383 2381 CONECT 2384 2378 2385 CONECT 2385 2384 2386 2388 CONECT 2386 1124 2385 2387 CONECT 2387 2386 CONECT 2388 2385 2389 CONECT 2389 2388 2390 2393 CONECT 2390 2389 2391 CONECT 2391 2390 2392 CONECT 2392 2391 2393 CONECT 2393 2389 2392 2394 CONECT 2394 2393 MASTER 241 0 1 10 15 0 0 6 2467 1 30 24 END