6ZUX
Crystal Structure of Thrombin in complex with compound42a
- PDB DOI: https://doi.org/10.2210/pdb6ZUX/pdb
- Classification: BLOOD CLOTTING
- Organism(s): Homo sapiens, Hirudo medicinalis
- Mutation(s): No 
- Deposited: 2020-07-23 Released: 2020-08-26 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.94 Å
- R-Value Free: 0.206 
- R-Value Work: 0.162 
- R-Value Observed: 0.164 
This is version 1.2 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Prothrombin | 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 | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Prothrombin | 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-2 | C [auth I] | 11 | Hirudo medicinalis | Mutation(s): 0  | |
UniProt | |||||
Find proteins for P28504 (Hirudo medicinalis) Explore P28504  Go to UniProtKB:  P28504 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P28504 | ||||
Sequence AnnotationsExpand | |||||
|
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
QQE (Subject of Investigation/LOI) Query on QQE | D [auth H] | [2-[[(1~{R})-1-(3-chlorophenyl)ethyl]amino]-7-methoxy-1,3-benzoxazol-5-yl]-[(2~{S},5~{S})-5-(2-hydroxyethyl)-2-methyl-morpholin-4-yl]methanone C24 H28 Cl N3 O5 DMTPPQGUBJBLMN-KHYOSLBOSA-N | |||
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 I] | L-PEPTIDE LINKING | C9 H11 N O6 S | TYR |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.94 Å
- R-Value Free: 0.206 
- R-Value Work: 0.162 
- R-Value Observed: 0.164 
- Space Group: C 1 2 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 70.26 | α = 90 |
b = 71.3 | β = 100.43 |
c = 72.45 | γ = 90 |
Software Name | Purpose |
---|---|
MOSFLM | data reduction |
SCALA | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
Entry History 
Deposition Data
- Released Date: 2020-08-26  Deposition Author(s): Schafer, M.
Revision History (Full details and data files)
- Version 1.0: 2020-08-26
Type: Initial release - Version 1.1: 2020-11-11
Changes: Database references - Version 1.2: 2020-11-25
Changes: Database references