3HAT|pdb_00003hat
ACTIVE SITE MIMETIC INHIBITION OF THROMBIN
- PDB DOI: https://doi.org/10.2210/pdb3HAT/pdb
- Entry: 3HAT supersedes: 2HAT
- Classification: HYDROLASE/HYDROLASE INHIBITOR
- Organism(s): Homo sapiens,Hirudo medicinalis,synthetic construct
- Mutation(s): No
- Deposited: 1994-10-16 Released: 1995-02-27
- Deposition Author(s): Tulinsky, A.,Mathews, I.I.
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 Å
- R-Value Observed: 0.140 (Depositor)
wwPDB Validation 3D Report Full Report
Download MendeleyActive-site mimetic inhibition of thrombin.
Mathews, I.I., Tulinsky, A.(1995) Acta Crystallogr D Biol Crystallogr 51: 550-559
- PubMed: 15299843 Search on PubMed
- DOI: https://doi.org/10.1107/S0907444994013132
- Primary Citation of Related Structures:
1FPC,3HAT - PubMed Abstract:
The structures of two mimetic inhibitor complexes of human alpha-thrombin have been determined by X-ray crystallography. One mimics a beta-turn with a bicyclic ring system; the other mimics two different active-site binding modes. The beta-turn mimetic is used to approximate a turn found in the conformation of fibrinopeptide A, which is catalytically released by thrombin in the activation of fibrinogen to fibrin. The binding of the second mimetic is a hybrid between normal substrate and the abnormal binding of the potent natural leech inhibitor hirudin. The binding of the beta-turn mimetic is tenuous, because it is like a substrate, while that of the substrate-hirudin hybrid is that of a tenacious inhibitor (which it is). Structurally retrospect modifications for rational design and improvement of both mimetic inhibitors are proposed.
- Department of Chemistry, Michigan State University, East Lansing 48824, USA.
Organizational Affiliation:
Explore in 3D: Structure |Sequence Annotations |Validation Report
Global Symmetry: Asymmetric - C1
Global Stoichiometry: Hetero 4-mer - A1B1C1D1
Find Similar Assemblies
Biological assembly 1 assigned by authors and generated by PISA (software)
Macromolecule Content
- Total Structure Weight: 35.96 kDa
- Atom Count: 2,575
- Modeled Residue Count: 301
- Deposited Residue Count: 311
- Unique protein chains: 4
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Thrombin light chain | A [auth L] | 36 | Homo sapiens | Mutation(s): 0 EC: 3.4.21.5 |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P00734 (Homo sapiens) Explore P00734 Go to UniProtKB: P00734 | |||||
PHAROS: P00734 GTEx: ENSG00000180210 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P00734 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Thrombin heavy chain | B [auth H] | 259 | Homo sapiens | Mutation(s): 0 EC: 3.4.21.5 |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P00734 (Homo sapiens) Explore P00734 Go to UniProtKB: P00734 | |||||
PHAROS: P00734 GTEx: ENSG00000180210 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P00734 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by: Sequence | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Hirudin variant-2 | C [auth I] | 12 | Hirudo medicinalis | Mutation(s): 0 |  |
UniProt | |||||
Find proteins for P09945 (Hirudo medicinalis) Explore P09945 Go to UniProtKB: P09945 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P09945 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by: Sequence | 3D Structure
Entity ID: 4 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| FPAM (FIBRINOPEPTIDE A MIMIC) | D [auth T] | 4 | synthetic construct | Mutation(s): 0 |  |
Sequence AnnotationsExpand | |||||
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| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| TYS Query on TYS | C [auth I] | L-PEPTIDE LINKING | C9 H11 N O6 S |  | TYR |
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 Å
- R-Value Observed: 0.140 (Depositor)
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 71.1 | α = 90 |
| b = 72.4 | β = 101 |
| c = 73 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PROLSQ | refinement |
Deposition Data
- Released Date: 1995-02-27 Deposition Author(s): Tulinsky, A.,Mathews, I.I.
- This entry supersedes: 2HAT
Revision History (Full details and data files)
- Version 1.0: 1995-02-27
Type: Initial release - Version 1.1: 2008-05-22
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance - Version 2.0: 2024-04-24
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Other, Polymer sequence, Source and taxonomy, Structure summary - Version 3.0: 2024-07-10
Changes: Data collection, Non-polymer description, Structure summary - Version 3.1: 2024-10-30
Changes: Structure summary
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