Research workbench
Structure of human activated thrombin-activatable fibrinolysis inhibitor, tafia, in complex with tick-derived funnelin inhibitor, tci.
Analyse Structure of human activated thrombin-activatable fibrinolysis inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LMS
- Type
- protein
- Length
- 384 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carboxypeptidase B2; Carboxypeptidase inhibitor
- EC
- 3.4.17.20
- UniProt
- Q96IY4, Q5EPH2
- Ligands
- K, ZN, CA, CL
- Pockets
- 3 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carboxypeptidase B2 (EC 3.4.17.20) | protein | 310 | 39% helix, 17% strand | Q96IY4 |
| B | Carboxypeptidase inhibitor | protein | 74 | 30% helix, 26% strand | Q5EPH2 |
Ligands and binding sites
- K · Potassium ion · metal · 2 copies · chains A
- ZN · Zinc ion · metal · chains A, B
- CA · Calcium ion · metal · chains A
- CL · Chloride ion · ion · 3 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 166 | 0.53 | 0.79 | 27 | GOL |
| 2 | 99 | 0.47 | 0.80 | 24 | empty |
| 3 | 79 | 0.32 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1100 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 3LMS · Structure of human activated thrombin-activatable fibrinolysis inhibitor, TAFIa, in… · 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
- Q5EPH2 · AlphaFold monomer V2.0 prediction for carboxypeptidase inhibitor (Q5EPH2) · a predicted model of the same protein · chain B against A, TM-score 0.95
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
- Every structure of UniProt Q5EPH2
- Elsewhere: RCSB PDB 3LMS · PDBe 3LMS · UniProt Q96IY4 · UniProt Q5EPH2
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