HEADER VIRAL PROTEIN 21-AUG-24 9DA7 TITLE HUMAN NOROVIRUS GII.4 HOUSTON PROTEASE IN COMPLEX WITH RUPINTRIVIR COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDASE C37; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NOROVIRUS; SOURCE 3 ORGANISM_TAXID: 142786; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI B; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 37762 KEYWDS VIRAL PROTEASE WITH INHIBITOR, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR B.ZHAO,S.H.PHAM,N.NEETU,B.SANKARAN,B.V.V.PRASAD REVDAT 1 19-FEB-25 9DA7 0 JRNL AUTH S.PHAM,B.ZHAO,N.NEETU,B.SANKARAN,K.PATIL,S.RAMANI,Y.SONG, JRNL AUTH 2 M.K.ESTES,T.PALZKILL,B.V.V.PRASAD JRNL TITL CONFORMATIONAL FLEXIBILITY IS A CRITICAL FACTOR IN DESIGNING JRNL TITL 2 BROAD-SPECTRUM HUMAN NOROVIRUS PROTEASE INHIBITORS. JRNL REF J.VIROL. 75724 2025 JRNL REFN ESSN 1098-5514 JRNL PMID 39873493 JRNL DOI 10.1128/JVI.01757-24 REMARK 2 REMARK 2 RESOLUTION. 2.50 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.99 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 6439 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.254 REMARK 3 R VALUE (WORKING SET) : 0.252 REMARK 3 FREE R VALUE : 0.292 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 326 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 48.9900 - 3.1500 0.99 3104 166 0.2271 0.2574 REMARK 3 2 3.1500 - 2.5000 1.00 3009 160 0.3204 0.3897 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) : 0.157 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 35.128 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 43.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.21 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 1273 REMARK 3 ANGLE : 1.050 1722 REMARK 3 CHIRALITY : 0.060 191 REMARK 3 PLANARITY : 0.009 217 REMARK 3 DIHEDRAL : 15.641 452 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 9DA7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-AUG-24. REMARK 100 THE DEPOSITION ID IS D_1000287674. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-FEB-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97936 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12340 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 48.990 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 12.40 REMARK 200 R MERGE (I) : 0.10850 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.0500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.15 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 12.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.340 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 (%): 45.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PH 5.5, 2.0 M AMMONIUM REMARK 280 SULFATE, PH 4.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.68800 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 63.37600 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 63.37600 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 31.68800 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 313 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 ALA A 1 REMARK 465 PRO A 2 REMARK 465 PRO A 3 REMARK 465 THR A 123 REMARK 465 GLY A 124 REMARK 465 SER A 125 REMARK 465 ASN A 126 REMARK 465 ALA A 127 REMARK 465 LYS A 128 REMARK 465 SER A 129 REMARK 465 MET A 130 REMARK 465 ASP A 131 REMARK 465 LEU A 132 REMARK 465 GLY A 173 REMARK 465 SER A 174 REMARK 465 GLU A 175 REMARK 465 GLY A 176 REMARK 465 GLU A 177 REMARK 465 ALA A 178 REMARK 465 THR A 179 REMARK 465 LEU A 180 REMARK 465 GLU A 181 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 GLN A 110 38.23 73.16 REMARK 500 REMARK 500 REMARK: NULL DBREF 9DA7 A 1 181 UNP Q6REV3 Q6REV3_9CALI 1009 1189 SEQRES 1 A 181 ALA PRO PRO SER ILE TRP SER ARG ILE VAL ASN PHE GLY SEQRES 2 A 181 SER GLY TRP GLY PHE TRP VAL SER PRO SER LEU PHE ILE SEQRES 3 A 181 THR SER THR HIS VAL ILE PRO GLN GLY ALA LYS GLU PHE SEQRES 4 A 181 PHE GLY VAL PRO ILE LYS GLN ILE GLN VAL HIS LYS SER SEQRES 5 A 181 GLY GLU PHE CYS ARG LEU ARG PHE PRO LYS PRO ILE ARG SEQRES 6 A 181 THR ASP VAL THR GLY MET ILE LEU GLU GLU GLY ALA PRO SEQRES 7 A 181 GLU GLY THR VAL VAL THR LEU LEU ILE LYS ARG SER THR SEQRES 8 A 181 GLY GLU LEU MET PRO LEU ALA ALA ARG MET GLY THR HIS SEQRES 9 A 181 ALA THR MET LYS ILE GLN GLY ARG THR VAL GLY GLY GLN SEQRES 10 A 181 MET GLY MET LEU LEU THR GLY SER ASN ALA LYS SER MET SEQRES 11 A 181 ASP LEU GLY THR THR PRO GLY ASP CYS GLY CYS PRO TYR SEQRES 12 A 181 ILE TYR LYS ARG GLY ASN ASP TYR VAL VAL ILE GLY VAL SEQRES 13 A 181 HIS THR ALA ALA ALA ARG GLY GLY ASN THR VAL ILE CYS SEQRES 14 A 181 ALA THR GLN GLY SER GLU GLY GLU ALA THR LEU GLU HET AG7 A 201 84 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 *17(H2 O) HELIX 1 AA1 SER A 4 SER A 7 5 4 HELIX 2 AA2 HIS A 30 ILE A 32 5 3 HELIX 3 AA3 LYS A 45 ILE A 47 5 3 SHEET 1 AA1 5 ILE A 9 PHE A 12 0 SHEET 2 AA1 5 GLY A 15 TRP A 19 -1 O GLY A 17 N VAL A 10 SHEET 3 AA1 5 LEU A 24 SER A 28 -1 O ILE A 26 N PHE A 18 SHEET 4 AA1 5 PHE A 55 ARG A 59 -1 O LEU A 58 N PHE A 25 SHEET 5 AA1 5 GLN A 48 SER A 52 -1 N SER A 52 O PHE A 55 SHEET 1 AA2 2 GLU A 38 PHE A 39 0 SHEET 2 AA2 2 VAL A 42 PRO A 43 -1 O VAL A 42 N PHE A 39 SHEET 1 AA3 8 ILE A 72 LEU A 73 0 SHEET 2 AA3 8 ASP A 150 ALA A 160 1 O VAL A 153 N ILE A 72 SHEET 3 AA3 8 THR A 166 THR A 171 -1 O ILE A 168 N THR A 158 SHEET 4 AA3 8 ARG A 112 LEU A 121 -1 N GLY A 119 O VAL A 167 SHEET 5 AA3 8 LEU A 94 ILE A 109 -1 N GLY A 102 O MET A 118 SHEET 6 AA3 8 VAL A 82 LYS A 88 -1 N LEU A 85 O LEU A 97 SHEET 7 AA3 8 PRO A 142 ARG A 147 -1 O ILE A 144 N THR A 84 SHEET 8 AA3 8 ASP A 150 ALA A 160 -1 O VAL A 152 N TYR A 145 LINK SG CYS A 139 C19 AG7 A 201 1555 1555 1.77 CRYST1 56.569 56.569 95.064 90.00 90.00 120.00 P 31 2 1 6 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 0.017678 0.010206 0.000000 0.00000 SCALE2 0.000000 0.020412 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010519 0.00000