+Open data
-Basic information
Entry | Database: PDB / ID: 2xcn | ||||||
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Title | Crystal structure of HCV NS3 protease with a boronate inhibitor | ||||||
Components |
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Keywords | HYDROLASE / SERINE PROTEASE | ||||||
Function / homology | Function and homology information self proteolysis / transformation of host cell by virus / host cell membrane / viral process / serine-type peptidase activity / virion component / symbiont entry into host cell / virion attachment to host cell / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | HEPATITIS C VIRUS | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 3.02 Å | ||||||
Authors | Li, X. / Zhang, Y.-K. / Liu, Y. / Ding, C.Z. / Li, Q. / Zhou, Y. / Plattner, J.J. / Baker, S.J. / Qian, X. / Fan, D. ...Li, X. / Zhang, Y.-K. / Liu, Y. / Ding, C.Z. / Li, Q. / Zhou, Y. / Plattner, J.J. / Baker, S.J. / Qian, X. / Fan, D. / Liao, L. / Ni, Z.-J. / White, G.V. / Mordaunt, J.E. / Lazarides, L.X. / Slater, M.J. / Jarvest, R.L. / Thommes, P. / Ellis, M. / Edge, C.M. / Hubbard, J.A. / Nassau, P. / McDowell, B. / Skarzynski, T.J. / Rowland, P. / Somers, D.O. / Kazmierski, W.M. / Grimes, R.M. / Wright, L.L. / Smith, G.K. / Zou, W. / Wright, J. / Pennicott, L.E. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2010 Title: Synthesis and Evaluation of Novel Alpha-Amino Cyclic Boronates as Inhibitors of Hcv Ns3 Protease. Authors: Li, X. / Zhang, Y.-K. / Liu, Y. / Ding, C.Z. / Li, Q. / Zhou, Y. / Plattner, J.J. / Baker, S.J. / Qian, X. / Fan, D. / Liao, L. / Ni, Z.-J. / White, G.V. / Mordaunt, J.E. / Lazarides, L.X. / ...Authors: Li, X. / Zhang, Y.-K. / Liu, Y. / Ding, C.Z. / Li, Q. / Zhou, Y. / Plattner, J.J. / Baker, S.J. / Qian, X. / Fan, D. / Liao, L. / Ni, Z.-J. / White, G.V. / Mordaunt, J.E. / Lazarides, L.X. / Slater, M.J. / Jarvest, R.L. / Edge, C.M. / Hubbard, J.A. / Nassau, P. / Mcdowell, B. / Skarzynski, T.J. / Thommes, P. / Ellis, M. / Rowland, P. / Somers, D.O. / Kazmierski, W.M. / Grimes, R.M. / Wright, L.L. / Smith, G.K. / Zou, W. / Wright, J. / Pennicott, L.E. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB", "BD" IN EACH CHAIN ON SHEET RECORDS ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB", "BD" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xcn.cif.gz | 82.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xcn.ent.gz | 66.4 KB | Display | PDB format |
PDBx/mmJSON format | 2xcn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xc/2xcn ftp://data.pdbj.org/pub/pdb/validation_reports/xc/2xcn | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Protein/peptide , 2 types, 4 molecules ABCD
#1: Protein | Mass: 21014.949 Da / Num. of mol.: 2 / Fragment: PROTEASE DOMAIN, RESIDUES 1-180 Source method: isolated from a genetically manipulated source Details: TETRAHEDRAL BORATE DERIVATIVE LINKED TO OXYGEN OF S139. Source: (gene. exp.) HEPATITIS C VIRUS / Strain: H / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q91RS4 #2: Protein/peptide | Mass: 2394.039 Da / Num. of mol.: 2 / Fragment: RESIDUES 21-39 / Source method: obtained synthetically / Details: K19, K20, K40 AND K41 ADDED TO FRAGMENT / Source: (synth.) HEPATITIS C VIRUS / References: UniProt: C9WU77 |
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-Non-polymers , 4 types, 60 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.16 Å3/Da / Density % sol: 70.45 % / Description: NONE |
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Crystal grow | pH: 6.5 / Details: pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0723 |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 15, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0723 Å / Relative weight: 1 |
Reflection | Resolution: 3.02→70.71 Å / Num. obs: 15159 / % possible obs: 100 % / Observed criterion σ(I): -10 / Redundancy: 6.9 % / Biso Wilson estimate: 71.7 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 3.02→3.18 Å / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 3.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 3.02→70.71 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.904 / SU B: 14.115 / SU ML: 0.248 / Cross valid method: THROUGHOUT / ESU R: 0.562 / ESU R Free: 0.328 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WERE REFINED INDIVIDUALLY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.462 Å2
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Refinement step | Cycle: LAST / Resolution: 3.02→70.71 Å
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Refine LS restraints |
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