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- PDB-4tmn: SLOW-AND FAST-BINDING INHIBITORS OF THERMOLYSIN DISPLAY DIFFERENT... -
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Basic information
Entry | Database: PDB / ID: 4tmn | |||||||||
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Title | SLOW-AND FAST-BINDING INHIBITORS OF THERMOLYSIN DISPLAY DIFFERENT MODES OF BINDING. CRYSTALLOGRAPHIC ANALYSIS OF EXTENDED PHOSPHONAMIDATE TRANSITION-STATE ANALOGUES | |||||||||
![]() | THERMOLYSIN | |||||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex / METALLOPROTEINASE | |||||||||
Function / homology | ![]() thermolysin / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() | |||||||||
![]() | Holden, H.M. / Tronrud, D.E. / Monzingo, A.F. / Weaver, L.H. / Matthews, B.W. | |||||||||
![]() | ![]() Title: Slow- and fast-binding inhibitors of thermolysin display different modes of binding: crystallographic analysis of extended phosphonamidate transition-state analogues. Authors: Holden, H.M. / Tronrud, D.E. / Monzingo, A.F. / Weaver, L.H. / Matthews, B.W. #1: ![]() 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: ![]() Title: Crystallographic Structural Analysis of Phosphoramidates as Inhibitors and Transition-State Analogs of Thermolysin Authors: Tronrud, D.E. / Monzingo, A.F. / Matthews, B.W. #3: ![]() 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: ![]() 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. #5: ![]() 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. #6: ![]() 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. #7: ![]() Title: Structure of Thermolysin Refined at 1.6 Angstroms Resolution Authors: Holmes, M.A. / Matthews, B.W. #8: ![]() Title: Binding of Hydroxamic Acid Inhibitors to Crystalline Thermolysin Suggests a Pentacoordinate Zinc Intermediate in Catalysis Authors: Holmes, M.A. / Matthews, B.W. #9: ![]() Title: Binding of the Biproduct Analog L-Benzylsuccinic Acid to Thermolysin Determined by X-Ray Crystallography Authors: Bolognesi, M.C. / Matthews, B.W. #10: ![]() Title: Comparison of the Structures of Carboxypeptidase a and Thermolysin Authors: Kester, W.R. / Matthews, B.W. #11: ![]() 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. #12: ![]() Title: Crystallographic Study of the Binding of Dipeptide Inhibitors to Thermolysin. Implications for the Mechanism of Catalysis Authors: Kester, W.R. / Matthews, B.W. #13: ![]() Title: Role of Calcium in the Thermal Stability of Thermolysin Authors: Dahlquist, F.W. / Long, J.W. / Bigbee, W.L. #14: ![]() 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. #15: ![]() Title: The Structure and Stability of Thermolysin Authors: Weaver, L.H. / Kester, W.R. / Teneyck, L.F. / Matthews, B.W. #16: ![]() Title: The Conformation of Thermolysin Authors: Matthews, B.W. / Weaver, L.H. / Kester, W.R. #17: ![]() Title: Binding of Lanthanide Ions to Thermolysin Authors: Matthews, B.W. / Weaver, L.H. #18: ![]() Title: The Structure of Thermolysin. An Electron Density Map at 2.3 Angstroms Resolution Authors: Colman, P.M. / Jansonius, J.N. / Matthews, B.W. #19: ![]() Title: Amino-Acid Sequence of Thermolysin Authors: Titani, K. / Hermodson, M.A. / Ericsson, L.H. / Walsh, K.A. / Neurath, H. #20: ![]() Title: Three Dimensional Structure of Thermolysin Authors: Matthews, B.W. / Jansonius, J.N. / Colman, P.M. / Schoenborn, B.P. / Duporque, D. #21: ![]() Title: Structure of Thermolysin Authors: Matthews, B.W. / Colman, P.M. / Jansonius, J.N. / Titani, K. / Walsh, K.A. / Neurath, H. #22: ![]() Title: The Gamma Turn. Evidence for a New Folded Conformation in Proteins Authors: Matthews, B.W. #23: ![]() 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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 84 KB | Display | ![]() |
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PDB format | ![]() | 61.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 752.1 KB | Display | ![]() |
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Full document | ![]() | 768.1 KB | Display | |
Data in XML | ![]() | 17.4 KB | Display | |
Data in CIF | ![]() | 24.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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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 2615 - 2621 LIE IN SUBSITE S1. / 3: ATOMS 2626 - 2629 LIE IN SUBSITE S1(PRIME). / 4: ATOM 2634 LIES IN SUBSITE S2(PRIME). / 5: ATOMS 2613 AND 2614 ARE BONDED TO THE ZINC ATOM. |
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Components
#1: Protein | Mass: 34362.305 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: P00800, thermolysin | ||||||
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#2: Chemical | ChemComp-0PK / | ||||||
#3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-ZN / | #5: Water | ChemComp-HOH / | Compound details | THE ACTIVE SITE CLEFT OF THERMOLYSIN CONTAINS AT LEAST FOUR SUBSITES S1, S1(PRIME), S2, AND ...THE ACTIVE SITE CLEFT OF THERMOLYSI | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.94 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7.2 / Method: unknown / Details: Holmes, M.A., (1982) J.Mol.Biol., 160, 623. | ||||||||||||||||||||||||||||||
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 | *PLUS Highest resolution: 1.7 Å / Num. obs: 28875 / Num. measured all: 58214 / Rmerge(I) obs: 0.042 |
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Processing
Software | Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
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Refinement | Rfactor obs: 0.17 / Highest resolution: 1.7 Å | ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 1.7 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 10 Å / Num. reflection obs: 28691 / Rfactor obs: 0.17 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: t_dihedral_angle_deg / Dev ideal: 16.5 |