MolNFT v1 · #121431 · protein
Crystal structure of thrombin-activatable fibrinolysis inhibitor in complex with an inhibitory nanobody (vhh-A204)
5HVG · Carboxypeptidase B2: “Crystal structure of thrombin-activatable fibrinolysis inhibitor in complex with an inhibitory nanobody…”. X-ray diffraction, 4 ligands (NAG, MAN, BMA), 10 pockets (best druggability 0.75). MolNFT v1 #121431 on…
- PDB
- 5HVG
- Type
- protein
- Length
- 1,042 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carboxypeptidase B2; Vhh-A204
- EC
- 3.4.17.20
- UniProt
- Q96IY4
- Ligands
- NAG, MAN, BMA, ZN
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carboxypeptidase B2 (EC 3.4.17.20) | protein | 401 | 40% helix, 19% strand | Q96IY4 |
| B | Vhh-A204 | protein | 122 | 11% helix, 42% strand | — |
| C | Carboxypeptidase B2 (EC 3.4.17.20) | protein | 400 | 40% helix, 19% strand | Q96IY4 |
| D | Vhh-A204 | protein | 119 | 11% helix, 43% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, C
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- BMA · beta-D-mannopyranose · sugar
- ZN · Zinc ion · metal · 2 copies · chains A, C
- ACT · Acetate ion · additive · 2 copies · chains A, 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 223 | 0.75 | 0.90 | 36 | ACT |
| 2 | 359 | 0.71 | 0.83 | 40 | empty |
| 3 | 235 | 0.69 | 0.85 | 41 | ACT |
| 4 | 383 | 0.59 | 0.76 | 40 | empty |
| 5 | 295 | 0.57 | 0.77 | 35 | empty |
Interfaces
5 interfaces between chains.
- A–B · 743 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 720 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 426 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 385 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 104 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 5HVG · 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 C 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 5HVG · PDBe 5HVG · UniProt Q96IY4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.