- FASTA Sequence
- PDBx/mmCIF Format
- PDBx/mmCIF Format (gz)
- BinaryCIF Format (gz)
- Legacy PDB Format
- Legacy PDB Format (gz)
- PDBML/XML Format (gz)
- Structure Factors (CIF)
- Structure Factors (CIF - gz)
- Validation Full (PDF - gz)
- Validation (XML - gz)
- Validation (CIF - gz)
- Validation 2fo-fc coefficients (CIF - gz)
- Validation fo-fc coefficients (CIF - gz)
- Biological Assembly 1 (CIF - gz)
- Biological Assembly 1 (PDB - gz)
2ZIQ|pdb_00002ziq
Thrombin Inhibition
- PDB DOI: https://doi.org/10.2210/pdb2ZIQ/pdb
- Classification: Hydrolase/Hydrolase Inhibitor
- Organism(s): Homo sapiens,Hirudo medicinalis
- Mutation(s): No
- Deposited: 2008-02-20 Released: 2009-01-13
- Deposition Author(s): Baum, B.,Heine, A.,Klebe, G.
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.65 Å
- R-Value Free: 0.225 (Depositor), 0.190 (DCC)
- R-Value Work: 0.181 (Depositor), 0.180 (DCC)
- R-Value Observed: 0.187 (Depositor)
Starting Model:experimental
View more details
This is version 1.7 of the entry. See complete history.
Literature
Download MendeleyExplore in 3D: Structure |Sequence Annotations |Electron Density |Validation Report |Ligand Interaction (26U)
Global Symmetry: Asymmetric - C1
Global Stoichiometry: Hetero 3-mer - A1B1C1
Find Similar Assemblies
Biological assembly 1 assigned by authors and generated by PISA (software)
Macromolecule Content
- Total Structure Weight: 35.81 kDa
- Atom Count: 2,557
- Modeled Residue Count: 289
- Deposited Residue Count: 306
- Unique protein chains: 3
Macromolecules
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 | |||||
| |||||
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-1 | C [auth I] | 11 | Hirudo medicinalis | Mutation(s): 0 |  |
UniProt | |||||
Find proteins for P01050 (Hirudo medicinalis) Explore P01050 Go to UniProtKB: P01050 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P01050 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| 26U Query on 26U Download Ideal Coordinates CCD File | D [auth H] | N-(4-carbamimidoylbenzyl)-1-(4-methylpentanoyl)-L-prolinamide C19 H28 N4 O2 AEKJCSNKYXWOAQ-INIZCTEOSA-N |  | ||
| BEN Query on BEN Download Ideal Coordinates CCD File | G [auth H] | BENZAMIDINE C7 H8 N2 PXXJHWLDUBFPOL-UHFFFAOYSA-N |  | ||
| NA Query on NA Download Ideal Coordinates CCD File | E [auth H], F [auth H] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
| 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 |
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 4 | |||||
|---|---|---|---|---|---|
| ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
| PRD_000596 (26U) Query on PRD_000596 | D [auth H] | N-(4-carbamimidoylbenzyl)-1-(4-methylpentanoyl)-L-prolinamide | Peptide-like / Thrombin inhibitor | | |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.65 Å
- R-Value Free: 0.225 (Depositor), 0.190 (DCC)
- R-Value Work: 0.181 (Depositor), 0.180 (DCC)
- R-Value Observed: 0.187 (Depositor)
Space Group: C 1 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 70.2 | α = 90 |
| b = 71.6 | β = 100.3 |
| c = 72.3 | γ = 90 |
| Software Name | Purpose |
|---|---|
| SHELX | model building |
| SHELXL-97 | refinement |
| MAR345 | data collection |
| HKL-2000 | data reduction |
| HKL-3000 | data scaling |
| CNS | phasing |
Entry History
Revision History (Full details and data files)
- Version 1.0: 2009-01-13
Type: Initial release - Version 1.1: 2011-07-13
Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance - Version 1.2: 2012-12-12
Changes: Other - Version 1.3: 2016-05-25
Changes: Source and taxonomy - Version 1.4: 2017-10-11
Changes: Refinement description - Version 1.5: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description - Version 1.6: 2023-11-15
Changes: Data collection - Version 1.7: 2024-10-30
Changes: Structure summary
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RCSB PDB Core Operations are funded by theU.S. National Science Foundation (DBI-2321666), theUS Department of Energy (DE-SC0019749), and theNational Cancer Institute,National Institute of Allergy and Infectious Diseases, andNational Institute of General Medical Sciences of theNational Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.