MolNFT v1 · #121430 · protein
Crystal structure of thrombin-activatable fibrinolysis inhibitor in complex with an inhibitory nanobody (vhh-I83)
5HVF · Carboxypeptidase B2: “Crystal structure of thrombin-activatable fibrinolysis inhibitor in complex with an inhibitory nanobody…”. X-ray diffraction, 4 ligands (NAG, BMA, MAN), 4 pockets (best druggability 0.71). MolNFT v1 #121430 on…
- PDB
- 5HVF
- Type
- protein
- Length
- 490 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carboxypeptidase B2; Vhh-I83
- EC
- 3.4.17.20
- UniProt
- Q96IY4
- Ligands
- NAG, BMA, MAN, ZN
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carboxypeptidase B2 (EC 3.4.17.20) | protein | 372 | 39% helix, 18% strand | Q96IY4 |
| B | Vhh-I83 | protein | 118 | 5% helix, 56% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar
- MAN · alpha-D-mannopyranose · sugar
- ZN · Zinc ion · metal · chains A
- FLC · Citrate anion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 322 | 0.71 | 0.84 | 53 | FLC |
| 2 | 191 | 0.47 | 0.75 | 34 | empty |
| 3 | 72 | 0.32 | 0.75 | 15 | empty |
| 4 | 51 | 0.31 | 0.77 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1090 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 5HVF · Crystal Structure of Thrombin-activatable Fibrinolysis Inhibitor in Complex with an… · 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 1.00
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 5HVF · PDBe 5HVF · UniProt Q96IY4
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