MolNFT v1 · #65995 · protein
Crystal structure of aahiv, a metalloproteinase from venom of agkistrodon acutus
3HDB: “Crystal structure of aahiv, a metalloproteinase from venom of agkistrodon acutus”. X-ray diffraction, 4 ligands (NAG, CA, ZN), 3 pockets (best druggability 0.57). MolNFT v1 #65995 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3HDB
- Type
- protein
- Length
- 420 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aahiv; Knl
- EC
- 3.4.24.-
- Ligands
- NAG, CA, ZN, CL
- Pockets
- 3 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aahiv (EC 3.4.24.-) | protein | 417 | 25% helix, 20% strand | — |
| L | Knl | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- CA · Calcium ion · metal · 7 copies · chains A, L
- ZN · Zinc ion · metal · chains A, L
- CL · Chloride ion · ion · chains A
- 2PE · Nonaethylene glycol · additive · 4 copies · chains A
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 | 372 | 0.57 | 0.75 | 41 | empty |
| 2 | 68 | 0.35 | 0.77 | 17 | empty |
| 3 | 50 | 0.30 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–L · 410 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 3HDB · Crystal structure of AaHIV, A metalloproteinase from venom of Agkistrodon Acutus · the same entry in another collection · 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
- Elsewhere: RCSB PDB 3HDB · PDBe 3HDB
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