2PGQ
Human thrombin mutant C191A-C220A in complex with the inhibitor PPACK
- PDB DOI: https://doi.org/10.2210/pdb2PGQ/pdb
- Classification: HYDROLASE/HYDROLASE INHIBITOR
- Organism(s): Homo sapiens
- Expression System: Cricetulus griseus
- Mutation(s): Yes 
- Deposited: 2007-04-10 Released: 2007-07-17 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.222 
- R-Value Work: 0.198 
- R-Value Observed: 0.198 
wwPDB Validation   3D Report Full Report
This is version 1.8 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 |
Thrombin light chain | 45 | Homo sapiens | Mutation(s): 0  Gene Names: F2 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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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Thrombin heavy chain | 259 | Homo sapiens | Mutation(s): 2  Gene Names: F2 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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Small Molecules
Ligands 3 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
0G6 Query on 0G6 | E [auth B] | 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 | F [auth B] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
ZN Query on ZN | C [auth A], D [auth A], G [auth B] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |
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 | E [auth B] | D-Phe-Pro-Arg-CH2Cl | Peptide-like / Inhibitor |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.222 
- R-Value Work: 0.198 
- R-Value Observed: 0.198 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 53.945 | α = 90 |
b = 75.327 | β = 90 |
c = 80.984 | γ = 90 |
Software Name | Purpose |
---|---|
CNS | refinement |
ADSC | data collection |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
MOLREP | phasing |
Entry History 
Deposition Data
- Released Date: 2007-07-17  Deposition Author(s): Bush-Pelc, L.A., Marino, F., Chen, Z., Pineda, A.O., Mathews, F.S., Di Cera, E.
Revision History (Full details and data files)
- Version 1.0: 2007-07-17
Type: Initial release - Version 1.1: 2008-04-21
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: 2013-02-27
Changes: Other - Version 1.4: 2013-09-25
Changes: Derived calculations - Version 1.5: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 1.6: 2021-10-20
Changes: Database references, Source and taxonomy, Structure summary - Version 1.7: 2023-08-30
Changes: Data collection, Refinement description - Version 1.8: 2024-03-13
Changes: Source and taxonomy, Structure summary