+Open data
-Basic information
Entry | Database: PDB / ID: 1zzz | ||||||
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Title | Trypsin inhibitors with rigid tripeptidyl aldehydes | ||||||
Components | TRYPSIN | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / SERINE PROTEASE / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Krishnan, R. / Zhang, E. / Hakansson, K. / Arni, R.K. / Tulinsky, A. / Lim-Wilby, M.S.L. / Levy, O.E. / Semple, J.E. / Brunck, T.K. | ||||||
Citation | Journal: Biochemistry / Year: 1998 Title: Highly selective mechanism-based thrombin inhibitors: structures of thrombin and trypsin inhibited with rigid peptidyl aldehydes. Authors: Krishnan, R. / Zhang, E. / Hakansson, K. / Arni, R.K. / Tulinsky, A. / Lim-Wilby, M.S. / Levy, O.E. / Semple, J.E. / Brunck, T.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zzz.cif.gz | 61.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zzz.ent.gz | 42.8 KB | Display | PDB format |
PDBx/mmJSON format | 1zzz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1zzz_validation.pdf.gz | 455.7 KB | Display | wwPDB validaton report |
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Full document | 1zzz_full_validation.pdf.gz | 468.3 KB | Display | |
Data in XML | 1zzz_validation.xml.gz | 8.4 KB | Display | |
Data in CIF | 1zzz_validation.cif.gz | 12.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zz/1zzz ftp://data.pdbj.org/pub/pdb/validation_reports/zz/1zzz | HTTPS FTP |
-Related structure data
Related structure data | 1ba8C 1bb0C 1ca8C 1yyyC 1ppcS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 24739.814 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00760 |
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#2: Chemical | ChemComp-0IV / |
#3: Chemical | ChemComp-CA / |
#4: Water | ChemComp-HOH / |
Has protein modification | Y |
Nonpolymer details | THE ACTIVE SITE INHIBITOR IS IN ITS R CHIRAL FORM. THE ACTIVE SITE SER 195 IS CLOSE TO THE CARBONYL ...THE ACTIVE SITE INHIBITOR IS IN ITS R CHIRAL FORM. THE ACTIVE SITE SER 195 IS CLOSE TO THE CARBONYL CARBON (C9) OF THE ALDEHYDE GROUP OF THE INHIBITOR FORMING A TRANSITION |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.28 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 300 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Sep 1, 1995 |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 1.9 Å / Num. obs: 16355 / % possible obs: 72 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Rmerge(I) obs: 0.043 / Rsym value: 0.12 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 2 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.25 / % possible all: 43 |
Reflection | *PLUS Redundancy: 2.5 % / Num. measured all: 41525 |
Reflection shell | *PLUS % possible obs: 43 % / Rmerge(I) obs: 0.103 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PPC Resolution: 1.9→7 Å / Cross valid method: THROUGHOUT / σ(F): 4
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Displacement parameters | Biso mean: 20.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.2 Å / Luzzati d res low obs: 7 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→7 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 9 Å / Rfactor obs: 0.157 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |