1TMU
Changes in interactions in complexes of hirudin derivatives and human alpha-thrombin due to different crystal forms
- PDB DOI: https://doi.org/10.2210/pdb1TMU/pdb
- Classification: HYDROLASE/HYDROLASE INHIBITOR
- Organism(s): Homo sapiens, Hirudo medicinalis
- Mutation(s): No 
- Deposited: 1994-05-26 Released: 1994-09-30 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 Å
- R-Value Observed: 0.202 
wwPDB Validation   3D Report Full Report
This is version 1.7 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Thrombin light chain | A [auth L] | 28 | 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:
(by identity cutoff) | 3D Structure
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 J] | 11 | 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 | |||||
|
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
0G6 Query on 0G6 | D [auth H] | D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide C21 H34 Cl N6 O3 DVFLYEYCMMLBTQ-VSZNYVQBSA-O | |||
NAG Query on NAG | E [auth H] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Modified Residues 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Type | Formula | 2D Diagram | Parent |
TYS Query on TYS | C [auth J] | 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_000020 (0G6) Query on PRD_000020 | D [auth H] | D-Phe-Pro-Arg-CH2Cl | Peptide-like / Inhibitor |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 Å
- R-Value Observed: 0.202 
- Space Group: P 21 21 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 80.9 | α = 90 |
b = 107.5 | β = 90 |
c = 45.9 | γ = 90 |
Software Name | Purpose |
---|---|
X-PLOR | model building |
TNT | refinement |
X-PLOR | refinement |
X-PLOR | phasing |
Entry History 
Deposition Data
- Released Date: 1994-09-30  Deposition Author(s): Priestle, J.P., Gruetter, M.G.
Revision History (Full details and data files)
- Version 1.0: 1994-09-30
Type: Initial release - Version 1.1: 2008-03-07
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 1.3: 2012-12-12
Changes: Other - Version 1.4: 2013-02-27
Changes: Other - Version 1.5: 2013-03-13
Changes: Other - Version 1.6: 2017-11-29
Changes: Derived calculations, Other - Version 1.7: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary