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Download EndnoteExploring thrombin S3 pocket
Brandt, T., Baum, B., Hangauer, D., Heine, A., Klebe, G.To be published.
2ZHW
Exploring thrombin S3 pocket
- DOI: 10.2210/pdb2ZHW/pdb
- Classification: HYDROLASE/HYDROLASE INHIBITOR
- Organism(s): Hirudo medicinalis, Homo sapiens
- Deposited: 2008-02-08 Released: 2009-02-10
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.02 Å
- R-Value Free: 0.292
- R-Value Work: 0.188
wwPDB Validation 3D Report Full Report
This is version 1.3 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by: Sequence | Structure
Entity ID: 1 | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details |
| Thrombin light chain | L | 36 | Homo sapiens | Mutation(s): 0 Gene Names: F2 EC: 3.4.21.5 |
Find proteins for P00734 (Homo sapiens) Go to Gene View: F2 Go to UniProtKB: P00734 | ||||
Entity ID: 2 | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details |
| Thrombin heavy chain | H | 259 | Homo sapiens | Mutation(s): 0 Gene Names: F2 EC: 3.4.21.5 |
Find proteins for P00734 (Homo sapiens) Go to Gene View: F2 Go to UniProtKB: P00734 | ||||
Entity ID: 3 | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details |
| Hirudin variant-2 | I | 12 | Hirudo medicinalis | Mutation(s): 0 |
Find proteins for P09945 (Hirudo medicinalis) Go to UniProtKB: P09945 | ||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| 12U Query on 12U | H | N-cycloheptylglycyl-N-(4-carbamimidoylbenzyl)-L-prolinamide (2S)-N-[(4-carbamimidoylphenyl)methyl]-1-[2-(cycloheptylamino)ethanoyl]pyrrolidine-2-carboxamide C22 H33 N5 O2 BYTJPDBCLWUEBU-IBGZPJMESA-N |  | Ligand Interaction | |
| NA Query on NA | H | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | Ligand Interaction | |
| Biologically Interesting Molecules 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
| PRD_000588 (12U) Query on PRD_000588 | H | N-cycloheptylglycyl-N-(4-carbamimidoylbenzyl)-L-prolinamide | Peptide-like / Thrombin inhibitor | | -- |
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| TYS Query on TYS | I | L-PEPTIDE LINKING | C9 H11 N O6 S |  | TYR |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.02 Å
- R-Value Free: 0.292
- R-Value Work: 0.188
- Space Group: C 1 2 1
Unit Cell:
| Length (Å) | Angle (°) |
|---|---|
| a = 68.900 | α = 90.00 |
| b = 71.500 | β = 99.10 |
| c = 71.300 | γ = 90.00 |
| Software Name | Purpose |
|---|---|
| SHELX | model building |
| SHELXL-97 | refinement |
| CrystalClear | data collection |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| CNS | phasing |
Entry History
Deposition Data
- Deposited Date: 2008-02-08
- Released Date: 2009-02-10
- Deposition Author(s): Brandt, T., Baum, B., Heine, A., Klebe, G.
Revision History
- Version 1.0: 2009-02-10
Type: Initial release - Version 1.1: 2011-07-13
Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance - Version 1.2: 2012-12-12
Type: Other - Version 1.3: 2016-05-25
Type: Source and taxonomy
