MolNFT v1 · #121432 · protein
Crystal structure of thrombin-activatable fibrinolysis inhibitor in complex with two inhibitory nanobodies
5HVH · Carboxypeptidase B2: “Crystal structure of thrombin-activatable fibrinolysis inhibitor in complex with two inhibitory nanobodies”. X-ray diffraction, 2 ligands (NAG, ZN), 6 pockets (best druggability 0.79). MolNFT v1 #121432 on…
- PDB
- 5HVH
- Type
- protein
- Length
- 639 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carboxypeptidase B2; Vhh-A204; Vhh-I83
- EC
- 3.4.17.20
- UniProt
- Q96IY4
- Ligands
- NAG, ZN
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 27% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carboxypeptidase B2 (EC 3.4.17.20) | protein | 401 | 40% helix, 18% strand | Q96IY4 |
| B | Vhh-A204 | protein | 120 | 11% helix, 45% strand | — |
| C | Vhh-I83 | protein | 118 | 3% helix, 58% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, C
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 197 | 0.79 | 0.94 | 41 | empty |
| 2 | 146 | 0.47 | 0.77 | 17 | empty |
| 3 | 141 | 0.41 | 0.74 | 22 | empty |
| 4 | 113 | 0.37 | 0.74 | 24 | empty |
| 5 | 59 | 0.35 | 0.79 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–C · 1078 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 743 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 5HVH · Crystal Structure of Thrombin-activatable Fibrinolysis Inhibitor in Complex with two… · 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 0.98
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 5HVH · PDBe 5HVH · UniProt Q96IY4
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