3D67
Crystal structure of Thrombin-Activatable Fibrinolysis Inhibitor (TAFI) in complex with 2-guanidino-ethyl-mercaptosuccinic acid (GEMSA)
- PDB DOI: https://doi.org/10.2210/pdb3D67/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Expression System: Homo sapiens
- Mutation(s): No 
- Deposited: 2008-05-19 Released: 2008-07-01 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.40 Å
- R-Value Free: 0.252 
- R-Value Work: 0.198 
- R-Value Observed: 0.200 
This is version 1.4 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 |
Carboxypeptidase B2 | 424 | Homo sapiens | Mutation(s): 0  Gene Names: CPB2 EC: 3.4.17.20 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q96IY4 (Homo sapiens) Explore Q96IY4  Go to UniProtKB:  Q96IY4 | |||||
PHAROS:  Q96IY4 GTEx:  ENSG00000080618  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q96IY4 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
Ligands 3 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
GEM Query on GEM | I [auth A], O [auth B], T [auth C] | (2-GUANIDINOETHYLMERCAPTO)SUCCINIC ACID C7 H13 N3 O4 S VKVCLXDFOQQABP-BYPYZUCNSA-N | |||
NAG Query on NAG | D [auth A] E [auth A] F [auth A] G [auth A] J [auth B] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
ZN Query on ZN | H [auth A], N [auth B], S [auth C] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 3.40 Å
- R-Value Free: 0.252 
- R-Value Work: 0.198 
- R-Value Observed: 0.200 
- Space Group: P 31 2 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 161.05 | α = 90 |
b = 161.05 | β = 90 |
c = 138.99 | γ = 120 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
XDS | data scaling |
XDS | data reduction |
SCALA | data scaling |
PHASER | phasing |
Entry History 
Deposition Data
- Released Date: 2008-07-01  Deposition Author(s): Brondijk, T.H.C., Huizinga, E.G.
Revision History (Full details and data files)
- Version 1.0: 2008-07-01
Type: Initial release - Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance - Version 1.2: 2018-06-20
Changes: Data collection, Source and taxonomy - Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary - Version 1.4: 2023-11-01
Changes: Data collection, Database references, Refinement description, Structure summary