HEADER HYDROLASE/HYDROLASE INHIBITOR 13-SEP-05 2B0F TITLE NMR STRUCTURE OF THE HUMAN RHINOVIRUS 3C PROTEASE (SEROTYPE 14) WITH TITLE 2 COVALENTLY BOUND ACE-LEALFQ-ETHYLPROPIONATE INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEASE 3C; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: HUMAN RHINOVIRUS SEROTYPE 14 3C PROTEASE; COMPND 5 SYNONYM: PICORNAIN 3C,P3C; COMPND 6 EC: 3.4.22.28; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: ACE-LEALFQ-ETHYLPROPIONATE; COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHINOVIRUS B14; SOURCE 3 ORGANISM_TAXID: 12131; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21-DE3; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PLYSS; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630; SOURCE 13 OTHER_DETAILS: PEPTIDYL INHIBITOR SYNTHESIZED VIA SOLID AND SOLUTION SOURCE 14 PHASE PEDTIDE SYNTHESIS KEYWDS BETA BARREL, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR T.C.BJORNDAHL,L.C.ANDREW,D.S.WISHART REVDAT 5 15-NOV-23 2B0F 1 LINK ATOM REVDAT 4 01-MAR-23 2B0F 1 COMPND SOURCE REMARK DBREF REVDAT 4 2 1 SEQRES HET HETNAM FORMUL REVDAT 4 3 1 LINK ATOM REVDAT 3 13-JUL-11 2B0F 1 VERSN REVDAT 2 20-MAY-08 2B0F 1 JRNL VERSN REVDAT 1 05-SEP-06 2B0F 0 JRNL AUTH T.C.BJORNDAHL,L.C.ANDREW,V.SEMENCHENKO,D.S.WISHART JRNL TITL NMR SOLUTION STRUCTURES OF THE APO AND PEPTIDE-INHIBITED JRNL TITL 2 HUMAN RHINOVIRUS 3C PROTEASE (SEROTYPE 14): STRUCTURAL AND JRNL TITL 3 DYNAMIC COMPARISON JRNL REF BIOCHEMISTRY V. 46 12945 2007 JRNL REFN ISSN 0006-2960 JRNL PMID 17944485 JRNL DOI 10.1021/BI7010866 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR XPLOR-NIH V.2.10, CNS 1.1 REMARK 3 AUTHORS : BRUNGER (X-PLOR), BRUNGER (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2B0F COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-SEP-05. REMARK 100 THE DEPOSITION ID IS D_1000034519. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 25; 25 REMARK 210 PH : 6.5; 6.5 REMARK 210 IONIC STRENGTH : 20MM KH2PO4; 20MM KH2PO4 REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 0.75MM HRV14-3C WITH COVALENT REMARK 210 INHIBITOR 20MM KH2PO4 15MM DTT REMARK 210 0.5MM EDTA 0.1MM DSS PH 6.5; 90% REMARK 210 H2O, 10% D2O; 0.75MM HRV14-3C REMARK 210 WITH COVALENT INHIBITOR 20MM REMARK 210 KH2PO4 15MM DTT 0.5MM EDTA 0.1MM REMARK 210 DSS PD 6.5; 99.96% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY; 2D NOESY; HNHA; REMARK 210 15N HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING MOLECULAR REMARK 210 DYNAMICS TORSION ANGLE DYNAMICS REMARK 210 RECOORD WATER REFINEMENT REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : BACK CALCULATED DATA AGREE WITH REMARK 210 EXPERIMENTAL NOESY SPECTRUM, REMARK 210 STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY,STRUCTURES REMARK 210 WITH FAVORABLE NON-BOND ENERGY, REMARK 210 STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS,STRUCTURES REMARK 210 WITH THE LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: H-BOND DONORS DETERMINED FROM 15N HSQC EXCHANGED INTO D2O. REMARK 210 3J HNHA COUPLINGS DETERMINED FROM HNHA. 13C-SEPERATED NOESY REMARK 210 COLLECTED IN 99.96% D2O WITHOUT WET WATER SUPPRESSION TO ACHIEVE REMARK 210 CROSS STRAND BETA-SHEET HA-HA NOES. REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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, B 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (RES=RESIDUE NAME; REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 470 MODELS 1-20 REMARK 470 RES CSSEQI ATOMS REMARK 470 GLN A 182 O REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 REMARK 500 REMARK: NULL 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 1 ASP A 32 -89.21 52.06 REMARK 500 1 GLN A 42 69.07 61.12 REMARK 500 1 ASN A 67 61.98 39.99 REMARK 500 1 GLU A 71 7.89 80.61 REMARK 500 1 GLU A 95 13.48 55.75 REMARK 500 1 ASN A 110 70.40 69.39 REMARK 500 1 TYR A 139 114.70 -163.06 REMARK 500 1 THR A 143 155.68 -45.03 REMARK 500 2 ASP A 32 -90.89 55.12 REMARK 500 2 HIS A 40 4.02 -68.42 REMARK 500 2 GLN A 42 70.97 57.99 REMARK 500 2 PRO A 65 -5.16 -55.88 REMARK 500 2 LEU A 94 -80.78 -74.82 REMARK 500 2 GLU A 95 71.38 45.26 REMARK 500 2 SER A 105 -163.91 -121.63 REMARK 500 2 ASN A 110 71.87 74.44 REMARK 500 2 SER A 128 0.58 81.41 REMARK 500 2 ALA A 140 90.66 -69.85 REMARK 500 2 THR A 143 158.92 -44.30 REMARK 500 3 THR A 20 -162.95 -118.05 REMARK 500 3 ASP A 32 -101.37 44.99 REMARK 500 3 GLN A 42 71.38 62.51 REMARK 500 3 ASP A 58 132.23 -171.96 REMARK 500 3 PRO A 65 -10.21 -48.00 REMARK 500 3 LEU A 94 -68.09 -100.07 REMARK 500 3 GLU A 95 73.87 41.70 REMARK 500 3 SER A 105 -160.67 -109.77 REMARK 500 3 SER A 128 -3.68 85.65 REMARK 500 3 TYR A 139 133.75 -178.42 REMARK 500 3 THR A 143 161.46 -43.30 REMARK 500 4 THR A 20 -157.55 -146.40 REMARK 500 4 ASP A 32 -88.07 58.36 REMARK 500 4 GLN A 42 71.96 56.31 REMARK 500 4 LEU A 94 -72.23 -60.75 REMARK 500 4 ASN A 110 73.36 66.73 REMARK 500 4 ALA A 121 -66.24 -90.07 REMARK 500 4 THR A 143 150.25 -43.10 REMARK 500 4 GLU B 3 71.85 -114.59 REMARK 500 5 ASP A 32 -88.74 57.18 REMARK 500 5 GLN A 42 72.83 60.58 REMARK 500 5 ASN A 67 72.52 71.76 REMARK 500 5 GLU A 71 31.14 71.62 REMARK 500 5 ASN A 110 72.45 77.24 REMARK 500 5 TYR A 139 133.19 -176.12 REMARK 500 5 THR A 143 158.72 -42.24 REMARK 500 6 ASP A 32 -90.49 51.65 REMARK 500 6 ARG A 33 16.36 -140.15 REMARK 500 6 GLN A 42 73.23 62.44 REMARK 500 6 GLU A 71 22.00 84.07 REMARK 500 6 ASP A 85 90.26 -60.64 REMARK 500 REMARK 500 THIS ENTRY HAS 226 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 9 ARG A 133 0.08 SIDE CHAIN REMARK 500 10 ARG A 33 0.09 SIDE CHAIN REMARK 500 15 ARG A 166 0.07 SIDE CHAIN REMARK 500 16 ARG A 55 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN B OF ACE-LEALFQ REMARK 800 -ETHYLPROPIONATE REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1CQQ RELATED DB: PDB REMARK 900 SAME PROTEIN OF A DIFFERENT SEROTYPE (2) SHARES 51% SEQUENCE REMARK 900 IDENTITY REMARK 900 RELATED ID: 1L1N RELATED DB: PDB REMARK 900 POLIO 3C PROTEASE, ANOTHER HOMOLOGUE SHARING 46% SEQENCE IDENTITY. DBREF 2B0F A 1 182 UNP P03303 POLG_HRV14 1538 1719 DBREF 2B0F B 1 7 PDB 2B0F 2B0F 1 7 SEQRES 1 A 182 GLY PRO ASN THR GLU PHE ALA LEU SER LEU LEU ARG LYS SEQRES 2 A 182 ASN ILE MET THR ILE THR THR SER LYS GLY GLU PHE THR SEQRES 3 A 182 GLY LEU GLY ILE HIS ASP ARG VAL CYS VAL ILE PRO THR SEQRES 4 A 182 HIS ALA GLN PRO GLY ASP ASP VAL LEU VAL ASN GLY GLN SEQRES 5 A 182 LYS ILE ARG VAL LYS ASP LYS TYR LYS LEU VAL ASP PRO SEQRES 6 A 182 GLU ASN ILE ASN LEU GLU LEU THR VAL LEU THR LEU ASP SEQRES 7 A 182 ARG ASN GLU LYS PHE ARG ASP ILE ARG GLY PHE ILE SER SEQRES 8 A 182 GLU ASP LEU GLU GLY VAL ASP ALA THR LEU VAL VAL HIS SEQRES 9 A 182 SER ASN ASN PHE THR ASN THR ILE LEU GLU VAL GLY PRO SEQRES 10 A 182 VAL THR MET ALA GLY LEU ILE ASN LEU SER SER THR PRO SEQRES 11 A 182 THR ASN ARG MET ILE ARG TYR ASP TYR ALA THR LYS THR SEQRES 12 A 182 GLY GLN CYS GLY GLY VAL LEU CYS ALA THR GLY LYS ILE SEQRES 13 A 182 PHE GLY ILE HIS VAL GLY GLY ASN GLY ARG GLN GLY PHE SEQRES 14 A 182 SER ALA GLN LEU LYS LYS GLN TYR PHE VAL GLU LYS GLN SEQRES 1 B 7 ACE LEU GLU ALA LEU PHE YTF HET ACE B 1 6 HET YTF B 7 30 HETNAM ACE ACETYL GROUP HETNAM YTF ETHYL (4~{S})-4,7-BIS(AZANYL)-7-OXIDANYLIDENE- HETNAM 2 YTF HEPTANOATE FORMUL 2 ACE C2 H4 O FORMUL 2 YTF C9 H18 N2 O3 HELIX 1 1 GLY A 1 ASN A 14 1 14 HELIX 2 2 ASP A 85 ILE A 90 5 6 HELIX 3 3 LYS A 174 VAL A 179 1 6 SHEET 1 A 7 ILE A 15 THR A 19 0 SHEET 2 A 7 GLU A 24 HIS A 31 -1 O GLY A 27 N MET A 16 SHEET 3 A 7 VAL A 34 ILE A 37 -1 O VAL A 36 N LEU A 28 SHEET 4 A 7 ILE A 68 ASP A 78 -1 O LEU A 75 N CYS A 35 SHEET 5 A 7 GLN A 52 ASP A 64 -1 N LEU A 62 O LEU A 72 SHEET 6 A 7 ASP A 46 VAL A 49 -1 N VAL A 47 O ILE A 54 SHEET 7 A 7 ILE A 15 THR A 19 -1 N THR A 19 O LEU A 48 SHEET 1 B10 THR A 111 LEU A 126 0 SHEET 2 B10 PRO A 130 ASP A 138 -1 O ARG A 136 N THR A 119 SHEET 3 B10 GLN A 167 GLN A 172 -1 O SER A 170 N ILE A 135 SHEET 4 B10 LYS A 155 ASN A 164 -1 N ASN A 164 O GLN A 167 SHEET 5 B10 THR A 111 LEU A 126 0 SHEET 6 B10 ASP A 98 VAL A 103 -1 N LEU A 101 O LEU A 113 SHEET 7 B10 VAL A 149 ALA A 152 -1 O VAL A 149 N VAL A 102 SHEET 8 B10 LYS A 155 ASN A 164 -1 O LYS A 155 N ALA A 152 SHEET 9 B10 GLU B 3 PHE B 6 -1 O LEU B 5 N GLY A 163 SHEET 10 B10 LYS A 155 ASN A 164 -1 N GLY A 163 O LEU B 5 LINK SG CYS A 146 C YTF B 7 1555 1555 1.82 LINK C ACE B 1 N LEU B 2 1555 1555 1.32 LINK C PHE B 6 N YTF B 7 1555 1555 1.33 SITE 1 AC1 19 LYS A 22 HIS A 40 GLU A 71 ILE A 124 SITE 2 AC1 19 ASN A 125 LEU A 126 SER A 127 SER A 128 SITE 3 AC1 19 THR A 141 LYS A 142 THR A 143 GLY A 144 SITE 4 AC1 19 CYS A 146 HIS A 160 VAL A 161 GLY A 162 SITE 5 AC1 19 GLY A 163 ASN A 164 PHE A 169 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1