Research workbench
Inhibitor complex with thrombin activatable fibrinolysis inhibitor (tafia)
Analyse Inhibitor complex with thrombin activatable fibrinolysis inhibitor (tafia) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NEE
- Type
- protein
- Length
- 400 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carboxypeptidase B2
- EC
- 3.4.17.20
- UniProt
- Q96IY4
- Ligands
- U9B, ZN
- Pockets
- 2 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carboxypeptidase B2 (EC 3.4.17.20) | protein | 400 | 38% helix, 18% strand | Q96IY4 |
Ligands and binding sites
- U9B · (1R,3S)-3-(4-ammoniobutyl)-1-benzyl-1,4-azaphosphinan-1-ium-3-carboxylate 4,4-dioxide · ligand · chains A
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 401 | 0.73 | 0.84 | 40 | U9B |
| 2 | 123 | 0.40 | 0.75 | 21 | empty |
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7NEE · Inhibitor Complex with Thrombin Activatable Fibrinolysis inhibitor (TAFIa) · the same entry in another collection · chain A against A, 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 7NEE · PDBe 7NEE · UniProt Q96IY4
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