Research workbench
Crystal structure of thrombin-activatable fibrinolysis inhibitor (tafi) in complex with 2-guanidino-ethyl-mercaptosuccinic acid (gemsa)
Analyse Crystal structure of thrombin-activatable fibrinolysis inhibitor (tafi) in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3D67
- Type
- protein
- Length
- 1,203 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carboxypeptidase B2
- EC
- 3.4.17.20
- UniProt
- Q96IY4
- Ligands
- GEM, NAG, ZN
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Carboxypeptidase B2 (EC 3.4.17.20) | protein | 401 | 39% helix, 18% strand | Q96IY4 |
Ligands and binding sites
- GEM · (2-guanidinoethylmercapto)succinic acid · ligand · 3 copies · chains A, B, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, B, C
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 790 | 0.77 | 0.81 | 78 | empty |
| 2 | 235 | 0.74 | 0.89 | 35 | GEM |
| 3 | 232 | 0.72 | 0.87 | 38 | GEM |
| 4 | 270 | 0.70 | 0.85 | 44 | ZN, GEM |
| 5 | 275 | 0.55 | 0.76 | 28 | empty |
Interfaces
3 interfaces between chains.
- A–C · 833 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 574 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 115 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 glycan, 9 disulfide (N-glycosylation, disulfide).
Compared structures
- 3D67 · Crystal structure of Thrombin-Activatable Fibrinolysis Inhibitor (TAFI) in complex with… · the same entry in another collection · chain B against B, TM-score 1.00
- Q96IY4 · AlphaFold monomer V2.0 prediction for carboxypeptidase B2 (Q96IY4) · a predicted model of the same protein · chain A against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q96IY4
- Elsewhere: RCSB PDB 3D67 · PDBe 3D67 · UniProt Q96IY4
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