HEADER VIRAL PROTEIN 22-AUG-24 9DAJ TITLE HUMAN NOROVIRUS GII.4 SYDNEY 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 S.H.PHAM,N.NEETU,B.SANKARAN,B.V.V.PRASAD REVDAT 1 19-FEB-25 9DAJ 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) : 48.86 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 8664 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.226 REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.271 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 438 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 48.8600 - 3.6100 1.00 2818 156 0.1964 0.2506 REMARK 3 2 3.6000 - 2.8600 1.00 2730 147 0.2400 0.2859 REMARK 3 3 2.8600 - 2.5000 0.99 2678 135 0.2977 0.3162 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) : 0.301 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.678 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 42.93 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.98 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 : 0.003 1276 REMARK 3 ANGLE : 0.644 1727 REMARK 3 CHIRALITY : 0.049 191 REMARK 3 PLANARITY : 0.007 218 REMARK 3 DIHEDRAL : 18.487 455 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -31.7908 -26.1145 2.4636 REMARK 3 T TENSOR REMARK 3 T11: 0.1642 T22: 0.2024 REMARK 3 T33: 0.1892 T12: 0.0005 REMARK 3 T13: 0.0431 T23: -0.0324 REMARK 3 L TENSOR REMARK 3 L11: 4.1687 L22: 2.4820 REMARK 3 L33: 2.7701 L12: -0.6357 REMARK 3 L13: 0.9809 L23: -0.6848 REMARK 3 S TENSOR REMARK 3 S11: 0.0137 S12: -0.2018 S13: 0.1265 REMARK 3 S21: 0.0495 S22: -0.0128 S23: -0.1643 REMARK 3 S31: -0.0294 S32: 0.0334 S33: -0.0192 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 9DAJ 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_1000287715. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-AUG-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97946 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16516 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 48.960 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.11220 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.6600 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) : 2.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.640 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 (%): 61.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.3 M SODIUM IODIDE, 0.1 M POTASSIUM REMARK 280 NITRATE:NAOH, 22.5 % (V/V) PUREPEGS COCKTAIL, PH 7, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 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+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 29.74667 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 14.87333 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 14.87333 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 29.74667 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 I IOD A 203 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 316 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: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 SG CYS A 139 H191 AG7 A 209 1.03 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 323 DISTANCE = 6.08 ANGSTROMS DBREF 9DAJ A 1 181 UNP K4L8Z7 K4L8Z7_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 SER ALA LYS GLU PHE SEQRES 4 A 181 PHE GLY VAL PRO ILE LYS GLN ILE GLN ILE 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 ALA THR LEU LEU ILE LYS ARG PRO 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 IOD A 201 1 HET IOD A 202 1 HET IOD A 203 1 HET IOD A 204 1 HET IOD A 205 1 HET IOD A 206 1 HET IOD A 207 1 HET IOD A 208 1 HET AG7 A 209 84 HETNAM IOD IODIDE ION 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 IOD 8(I 1-) FORMUL 10 AG7 C31 H41 F N4 O7 FORMUL 11 HOH *23(H2 O) HELIX 1 AA1 SER A 4 SER A 7 5 4 HELIX 2 AA2 LYS A 45 ILE A 47 5 3 HELIX 3 AA3 THR A 135 CYS A 139 5 5 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 15 N PHE A 12 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 VAL A 167 ALA A 170 -1 O ALA A 170 N VAL A 156 SHEET 4 AA3 8 ARG A 112 LEU A 121 -1 N GLN A 117 O CYS A 169 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 ALA A 83 O ALA A 99 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 ASP A 150 N ARG A 147 LINK SG CYS A 139 C19 AG7 A 209 1555 1555 1.77 CRYST1 97.722 97.722 44.620 90.00 90.00 120.00 P 32 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 0.010233 0.005908 0.000000 0.00000 SCALE2 0.000000 0.011816 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022411 0.00000