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Yorodumi- PDB-1tlp: CRYSTALLOGRAPHIC STRUCTURAL ANALYSIS OF PHOSPHORAMIDATES AS INHIB... -
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-Basic information
Entry | Database: PDB / ID: 1tlp | |||||||||
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Title | CRYSTALLOGRAPHIC STRUCTURAL ANALYSIS OF PHOSPHORAMIDATES AS INHIBITORS AND TRANSITION-STATE ANALOGS OF THERMOLYSIN | |||||||||
Components | THERMOLYSIN | |||||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / METALLOPROTEINASE / HYDROLASE-HYDROLASE INHIBITOR complex | |||||||||
Function / homology | Function and homology information thermolysin / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding Similarity search - Function | |||||||||
Biological species | Bacillus thermoproteolyticus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 2.3 Å | |||||||||
Authors | Tronrud, D.E. / Monzingo, A.F. / Matthews, B.W. | |||||||||
Citation | Journal: Eur.J.Biochem. / Year: 1986 Title: Crystallographic structural analysis of phosphoramidates as inhibitors and transition-state analogs of thermolysin. Authors: Tronrud, D.E. / Monzingo, A.F. / Matthews, B.W. #1: Journal: Science / Year: 1987 Title: Structures of Two Thermolysin-Inhibitor Complexes that Differ by a Single Hydrogen Bond Authors: Tronrud, D.E. / Holden, H.M. / Matthews, B.W. #2: Journal: Biochemistry / Year: 1984 Title: An Interactive Computer Graphics Study of Thermolysin-Catalyzed Peptide Cleavage and Inhibition by N-Carboxymethyl Dipeptides Authors: Hangauer, D.G. / Monzingo, A.F. / Matthews, B.W. #3: Journal: Biochemistry / Year: 1984 Title: Binding of N-Carboxymethyl Dipepetide Inhibitors to Thermolysin Determined by X-Ray Crystallography. A Novel Class of Transition-State Analogues for Zinc Peptidases Authors: Monzingo, A.F. / Matthews, B.W. #4: Journal: Biochemistry / Year: 1983 Title: Structural Analysis of the Inhibition of Thermolysin by an Active-Site-Directed Irreversible Inhibitor Authors: Holmes, M.A. / Tronrud, D.E. / Matthews, B.W. #5: Journal: Biochemistry / Year: 1982 Title: Structure of a Mercaptan-Thermolysin Complex Illustrates Mode of Inhibition of Zinc Proteases by Substrate-Analogue Mercaptans Authors: Monzingo, A.F. / Matthews, B.W. #6: Journal: J.Mol.Biol. / Year: 1982 Title: Structure of Thermolysin Refined at 1.6 Angstroms Resolution Authors: Holmes, M.A. / Matthews, B.W. #7: Journal: Biochemistry / Year: 1981 Title: Binding of Hydroxamic Acid Inhibitors to Crystalline Thermolysin Suggests a Pentacoordinate Zinc Intermediate in Catalysis Authors: Holmes, M.A. / Matthews, B.W. #8: Journal: J.Biol.Chem. / Year: 1979 Title: Binding of the Biproduct Analog L-Benzylsuccinic Acid to Thermolysin Determined by X-Ray Crystallography Authors: Bolognesi, M.C. / Matthews, B.W. #9: Journal: J.Biol.Chem. / Year: 1977 Title: Comparison of the Structures of Carboxypeptidase a and Thermolysin Authors: Kester, W.R. / Matthews, B.W. #10: Journal: J.Mol.Biol. / Year: 1977 Title: A Crystallographic Study of the Complex of Phosphoramidon with Thermolysin. A Model for the Presumed Catalytic Transition State and for the Binding of Extended Substrates Authors: Weaver, L.H. / Kester, W.R. / Matthews, B.W. #11: Journal: Biochemistry / Year: 1977 Title: Crystallographic Study of the Binding of Dipeptide Inhibitors to Thermolysin. Implications for the Mechanism of Catalysis Authors: Kester, W.R. / Matthews, B.W. #12: Journal: Biochemistry / Year: 1976 Title: Role of Calcium in the Thermal Stability of Thermolysin Authors: Dahlquist, F.W. / Long, J.W. / Bigbee, W.L. #13: Journal: Proc.Natl.Acad.Sci.USA / Year: 1975 Title: Evidence of Homologous Relationship between Thermolysin and Neutral Protease a of Bacillus Subtilis Authors: Levy, P.L. / Pangburn, M.K. / Burstein, Y. / Ericsson, L.H. / Neurath, H. / Walsh, K.A. #14: Journal: Experientia,Suppl. / Year: 1976 Title: The Structure and Stability of Thermolysin Authors: Weaver, L.H. / Kester, W.R. / Teneyck, L.F. / Matthews, B.W. #15: Journal: J.Biol.Chem. / Year: 1974 Title: The Conformation of Thermolysin Authors: Matthews, B.W. / Weaver, L.H. / Kester, W.R. #16: Journal: Biochemistry / Year: 1974 Title: Binding of Lanthanide Ions to Thermolysin Authors: Matthews, B.W. / Weaver, L.H. #17: Journal: J.Mol.Biol. / Year: 1972 Title: The Structure of Thermolysin. An Electron Density Map at 2.3 Angstroms Resolution Authors: Colman, P.M. / Jansonius, J.N. / Matthews, B.W. #18: Journal: Nature New Biol. / Year: 1972 Title: Amino-Acid Sequence of Thermolysin Authors: Titani, K. / Hermodson, M.A. / Ericsson, L.H. / Walsh, K.A. / Neurath, H. #19: Journal: Nature New Biol. / Year: 1972 Title: Three Dimensional Structure of Thermolysin Authors: Matthews, B.W. / Jansonius, J.N. / Colman, P.M. / Schoenborn, B.P. / Duporque, D. #20: Journal: Nature New Biol. / Year: 1972 Title: Structure of Thermolysin Authors: Matthews, B.W. / Colman, P.M. / Jansonius, J.N. / Titani, K. / Walsh, K.A. / Neurath, H. #21: Journal: Macromolecules / Year: 1972 Title: The Gamma Turn. Evidence for a New Folded Conformation in Proteins Authors: Matthews, B.W. #22: Journal: Biochem.Biophys.Res.Commun. / Year: 1972 Title: Rare Earths as Isomorphous Calcium Replacements for Protein Crystallography Authors: Colman, P.M. / Weaver, L.H. / Matthews, B.W. | |||||||||
History |
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Remark 700 | SHEET THE *ACTIVE-SITE* SHEET SUBSTRUCTURE OF THIS MOLECULE HAS ONE EDGE-STRAND COMPRISED OF TWO ...SHEET THE *ACTIVE-SITE* SHEET SUBSTRUCTURE OF THIS MOLECULE HAS ONE EDGE-STRAND COMPRISED OF TWO DISTINCT SEQUENCES OF THE POLYPEPTIDE CHAIN. TO REPRESENT THIS FEATURE AN EXTRA SHEET IS DEFINED. STRANDS 2,3,4,5 OF S1 ARE IDENTICAL TO STRANDS 2,3,4,5 OF S2. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tlp.cif.gz | 82.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tlp.ent.gz | 61 KB | Display | PDB format |
PDBx/mmJSON format | 1tlp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tl/1tlp ftp://data.pdbj.org/pub/pdb/validation_reports/tl/1tlp | 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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Atom site foot note | 1: RESIDUE 51 IS A CIS-PROLINE. / 2: ATOMS 2601 - 2611 LIE IN SUBSITE S1. / 3: ATOMS 2619 - 2622 LIE IN SUBSITE S1(PRIME). / 4: ATOMS 2627 - 2636 LIE IN SUBSITE S2(PRIME). / 5: ATOM 2613 IS BONDED TO THE ZINC ATOM. |
-Components
#1: Protein | Mass: 34362.305 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus thermoproteolyticus (bacteria) References: UniProt: P00800, thermolysin | ||||
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#2: Chemical | ChemComp-RDF / | ||||
#3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-ZN / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.87 % | ||||||||||||||||||||
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Crystal grow | *PLUS pH: 7.2 / Method: unknown | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.3→23.3 Å |
Reflection | *PLUS |
-Processing
Software | Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.3→23.3 Å /
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Refinement step | Cycle: LAST / Resolution: 2.3→23.3 Å
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Refine LS restraints |
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Refinement | *PLUS Num. reflection obs: 13523 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |