Research workbench
Crystal structure of thrombin activatable fibrinolysis inhibitor (tafi)
Analyse Crystal structure of thrombin activatable fibrinolysis inhibitor (tafi) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DGV
- Type
- protein
- Length
- 1,181 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carboxypeptidase B2
- EC
- 3.4.17.20
- UniProt
- Q2KIG3
- Ligands
- NAG, NDG, FUL, BMA, ZN, SO4
- Pockets
- 16 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Carboxypeptidase B2 (EC 3.4.17.20) | protein | 401 | 38% helix, 19% strand | Q2KIG3 |
| C | Carboxypeptidase B2 (EC 3.4.17.20) | protein | 379 | 35% helix, 14% strand | Q2KIG3 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains A, B, C
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 2 copies · chains A
- FUL · beta-L-fucopyranose · sugar · 2 copies · chains A
- BMA · beta-D-mannopyranose · sugar
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 22 copies · chains A, B, C
- MLI · Malonate ion · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 631 | 0.81 | 0.87 | 62 | ZN, SO4, MLI |
| 2 | 649 | 0.81 | 0.86 | 61 | SO4, MLI |
| 3 | 271 | 0.70 | 0.85 | 38 | empty |
| 4 | 184 | 0.70 | 0.88 | 26 | MLI |
| 5 | 429 | 0.61 | 0.76 | 50 | SO4 |
Interfaces
2 interfaces between chains.
- A–B · 1425 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 744 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 9 glycan (disulfide, N-glycosylation).
Compared structures
- 3DGV · Crystal structure of thrombin activatable fibrinolysis inhibitor (TAFI) · the same entry in another collection · chain A against A, TM-score 1.00
- Q2KIG3 · AlphaFold monomer V2.0 prediction for carboxypeptidase B2 (Q2KIG3) · a predicted model of the same protein · chain B 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 Q2KIG3
- Elsewhere: RCSB PDB 3DGV · PDBe 3DGV · UniProt Q2KIG3
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