HEADER VIRAL PROTEIN 01-DEC-25 9ZFQ TITLE TULANE VIRUS PROTEASE COMPLEXED WITH RUPINTRIVIR COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3C-LIKE PROTEASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TULANE VIRUS; SOURCE 3 ORGANISM_TAXID: 512169; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI B; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 37762 KEYWDS VIRAL PROTEASE INHIBITOR COMPLEX, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.H.PHAM,B.SANKARAN,B.V.V.PRASAD REVDAT 1 25-FEB-26 9ZFQ 0 JRNL AUTH S.PHAM,N.SHARMA,B.SANKARAN,J.NGUYEN,M.K.ESTES,J.M.HYSER, JRNL AUTH 2 B.V.V.PRASAD JRNL TITL TULANE VIRUS PROTEASE AS A STRUCTURAL SURROGATE FOR JRNL TITL 2 INHIBITOR SCREENING OF HUMAN NOROVIRUS PROTEASES. JRNL REF J.VIROL. 17625 2026 JRNL REFN ESSN 1098-5514 JRNL PMID 41670373 JRNL DOI 10.1128/JVI.02176-25 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21RC1_5156 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.91 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.440 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 14833 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.100 REMARK 3 FREE R VALUE TEST SET COUNT : 905 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 45.9100 - 3.4500 1.00 2455 159 0.1643 0.1781 REMARK 3 2 3.4500 - 2.7400 1.00 2332 152 0.1797 0.2386 REMARK 3 3 2.7400 - 2.3900 1.00 2298 149 0.1926 0.2379 REMARK 3 4 2.3900 - 2.1800 1.00 2276 148 0.1915 0.2260 REMARK 3 5 2.1700 - 2.0200 1.00 2281 149 0.1688 0.2177 REMARK 3 6 2.0200 - 1.9000 1.00 2286 148 0.2025 0.2327 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) : 0.167 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.133 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.29 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.50 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 : 0.007 1294 REMARK 3 ANGLE : 0.998 1754 REMARK 3 CHIRALITY : 0.066 205 REMARK 3 PLANARITY : 0.011 224 REMARK 3 DIHEDRAL : 13.315 459 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 9ZFQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-DEC-25. REMARK 100 THE DEPOSITION ID IS D_1000300151. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-OCT-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00013 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 S 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : DIALS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14834 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 45.910 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 10.40 REMARK 200 R MERGE (I) : 0.08300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.94 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.40 REMARK 200 R MERGE FOR SHELL (I) : 0.23200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.600 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 (%): 45.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.3M AMMONIUM CITRATE DIBASIC, 0.1M REMARK 280 MAGNEISUM FORMATE, PH 6, 22.5% (V/V) PUREPEGS COCKTAIL, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 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,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.24100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 45.90650 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.24100 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 45.90650 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 362 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 389 LIES ON A SPECIAL POSITION. 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 GLY A -2 REMARK 465 PRO A -1 REMARK 465 ARG A 170 REMARK 465 PHE A 171 REMARK 465 ASN A 172 REMARK 465 LEU A 173 REMARK 465 GLU A 174 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 24 122.20 -171.72 REMARK 500 GLN A 66 -167.85 -121.41 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 430 DISTANCE = 5.89 ANGSTROMS REMARK 525 HOH A 431 DISTANCE = 6.01 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 9ZFN RELATED DB: PDB DBREF 9ZFQ A 1 174 UNP B2Y6C9 B2Y6C9_9CALI 803 976 SEQADV 9ZFQ GLY A -2 UNP B2Y6C9 EXPRESSION TAG SEQADV 9ZFQ PRO A -1 UNP B2Y6C9 EXPRESSION TAG SEQADV 9ZFQ GLY A 0 UNP B2Y6C9 EXPRESSION TAG SEQRES 1 A 177 GLY PRO GLY GLY TYR VAL CYS SER PHE VAL PHE PRO ALA SEQRES 2 A 177 THR SER GLY GLY VAL LYS LYS GLY CYS ALA THR GLN ILE SEQRES 3 A 177 SER GLY SER LYS PHE LEU THR ALA THR HIS VAL ALA LYS SEQRES 4 A 177 SER CYS ASP LYS ILE ARG GLY LEU PRO PHE LYS ILE ILE SEQRES 5 A 177 LYS ILE ASP GLY GLU LEU CYS LEU VAL ASP VAL PRO GLY SEQRES 6 A 177 VAL LYS SER GLN THR LYS LEU GLU VAL SER PHE PRO ALA SEQRES 7 A 177 ILE GLY ASP VAL VAL ASN LEU CYS PRO SER ARG GLY SER SEQRES 8 A 177 GLN ARG PRO ASN ILE PRO VAL VAL VAL ARG SER ILE GLY SEQRES 9 A 177 ASN THR ASN ILE ALA GLY LYS PHE LEU ASN VAL PHE THR SEQRES 10 A 177 GLY THR VAL VAL ALA ALA GLY LYS LYS SER ASP GLY LEU SEQRES 11 A 177 GLY SER GLU PRO GLY ASP CYS GLY SER PRO TYR LEU LYS SEQRES 12 A 177 PHE VAL ASN GLY LYS PRO THR LEU VAL GLY ILE HIS THR SEQRES 13 A 177 ALA GLY SER TYR THR THR ASN GLN VAL ALA GLY LEU VAL SEQRES 14 A 177 ILE PRO SER ARG PHE ASN LEU GLU HET AG7 A 201 43 HETNAM AG7 4-{2-(4-FLUORO-BENZYL)-6-METHYL-5-[(5-METHYL-ISOXAZOLE- HETNAM 2 AG7 3-CARBONYL)-AMINO]-4-OXO-HEPTANOYLAMINO}-5-(2-OXO- HETNAM 3 AG7 PYRROLIDIN-3-YL)-PENTANOIC ACID ETHYL ESTER HETSYN AG7 RUPINTRIVIR, BOUND FORM FORMUL 2 AG7 C31 H41 F N4 O7 FORMUL 3 HOH *131(H2 O) HELIX 1 AA1 THR A 32 CYS A 38 1 7 HELIX 2 AA2 LYS A 122 GLY A 126 5 5 HELIX 3 AA3 GLU A 130 CYS A 134 5 5 SHEET 1 AA1 6 LYS A 40 ILE A 41 0 SHEET 2 AA1 6 VAL A 7 SER A 12 -1 N THR A 11 O LYS A 40 SHEET 3 AA1 6 VAL A 15 SER A 24 -1 O GLY A 18 N ALA A 10 SHEET 4 AA1 6 LYS A 27 ALA A 31 -1 O LEU A 29 N THR A 21 SHEET 5 AA1 6 LEU A 55 ASP A 59 -1 O VAL A 58 N PHE A 28 SHEET 6 AA1 6 LYS A 47 ASP A 52 -1 N LYS A 50 O LEU A 57 SHEET 1 AA2 7 VAL A 79 LEU A 82 0 SHEET 2 AA2 7 ILE A 93 ILE A 105 -1 O VAL A 95 N VAL A 80 SHEET 3 AA2 7 LYS A 108 VAL A 117 -1 O LYS A 108 N ILE A 105 SHEET 4 AA2 7 GLN A 161 LEU A 165 -1 O GLY A 164 N PHE A 113 SHEET 5 AA2 7 LYS A 145 GLY A 155 -1 N ILE A 151 O LEU A 165 SHEET 6 AA2 7 PRO A 137 VAL A 142 -1 N VAL A 142 O LYS A 145 SHEET 7 AA2 7 VAL A 79 LEU A 82 -1 N ASN A 81 O LEU A 139 LINK SG CYS A 134 C19 AG7 A 201 1555 1555 1.77 CRYST1 38.792 50.482 91.813 90.00 90.00 90.00 P 2 21 21 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 0.025779 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019809 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010892 0.00000 CONECT 973 1246 CONECT 1228 1229 1230 1255 CONECT 1229 1228 1231 CONECT 1230 1228 CONECT 1231 1229 1232 1251 CONECT 1232 1231 1233 CONECT 1233 1232 1234 1238 CONECT 1234 1233 1235 CONECT 1235 1234 1236 CONECT 1236 1235 1237 1261 CONECT 1237 1236 1238 CONECT 1238 1233 1237 CONECT 1239 1240 1251 CONECT 1240 1239 1241 1246 CONECT 1241 1240 1242 CONECT 1242 1241 1243 1264 CONECT 1243 1242 1244 1245 CONECT 1244 1243 1263 CONECT 1245 1243 CONECT 1246 973 1240 1247 CONECT 1247 1246 1248 CONECT 1248 1247 1249 1250 CONECT 1249 1248 1253 CONECT 1250 1248 CONECT 1251 1231 1239 1252 CONECT 1252 1251 CONECT 1253 1249 1254 CONECT 1254 1253 CONECT 1255 1228 1256 1259 CONECT 1256 1255 1257 CONECT 1257 1256 1258 1265 CONECT 1258 1257 CONECT 1259 1255 1260 1262 CONECT 1260 1259 CONECT 1261 1236 CONECT 1262 1259 CONECT 1263 1244 1264 CONECT 1264 1242 1263 CONECT 1265 1257 1266 1269 CONECT 1266 1265 1267 CONECT 1267 1266 1268 1270 CONECT 1268 1267 1269 CONECT 1269 1265 1268 CONECT 1270 1267 MASTER 252 0 1 3 13 0 0 6 1400 1 44 14 END