+Open data
-Basic information
Entry | Database: PDB / ID: 1gvx | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Endothiapepsin complexed with H256 | |||||||||
Components |
| |||||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / HYDROLASE / ASPARTIC PROTEINASE MECHANISM / TETRAHEDRAL INTERMEDIATE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | ENDOTHIA PARASITICA (chestnut blight fungus) SYNTHETIC CONSTRUCT (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å | |||||||||
Authors | Coates, L. / Erskine, P.T. / Crump, M.P. / Wood, S.P. / Cooper, J.B. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Five Atomic Resolution Structures of Endothiapepsin Inhibitor Complexes: Implications for the Aspartic Proteinase Mechanism Authors: Coates, L. / Erskine, P.T. / Crump, M.P. / Wood, S.P. / Cooper, J.B. | |||||||||
History |
| |||||||||
Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1gvx.cif.gz | 152.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1gvx.ent.gz | 119.1 KB | Display | PDB format |
PDBx/mmJSON format | 1gvx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gv/1gvx ftp://data.pdbj.org/pub/pdb/validation_reports/gv/1gvx | HTTPS FTP |
---|
-Related structure data
Related structure data | 1gvtC 1gvuC 1gvvC 1gvwC 3er5S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 33795.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ENDOTHIA PARASITICA (chestnut blight fungus) References: UniProt: P11838, endothiapepsin | ||
---|---|---|---|
#2: Protein/peptide | Type: Peptide-like / Class: Inhibitor / Mass: 912.019 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) References: N-{(2R)-3-phenyl-2-[(L-prolyl-L-threonyl-L-alpha-glutamyl)amino]propyl}-L-phenylalanyl-N~5~-[amino(iminio)methyl]- L-ornithyl-L-glutamic acid | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.83 % | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 4.5 / Details: PH 4.50 | |||||||||||||||
Crystal grow | *PLUS Method: unknown | |||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 130 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 1, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1→10 Å / Num. obs: 136765 / % possible obs: 96.9 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 1→1.05 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.163 / Mean I/σ(I) obs: 3.6 / % possible all: 94.3 |
Reflection | *PLUS Lowest resolution: 10 Å |
Reflection shell | *PLUS % possible obs: 94.3 % |
-Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ER5 Resolution: 1→10 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
| |||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: MOEWS AND KRETSINGER | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1→10 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 10 Å / Rfactor Rfree: 0.1647 / Rfactor Rwork: 0.1393 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |