MolNFT v1 · #1175 · protein
Structural interaction of natural and synthetic inhibitors with the venom metalloproteinase, atrolysin C (form-D)
1ATL · Snake venom metalloproteinase atrolysin-D: “Structural interaction of natural and synthetic inhibitors with the venom metalloproteinase, atrolysin C…”. X-ray diffraction, 3 ligands (0QI, ZN, CA), 4 pockets (best druggability 0.62).…
- PDB
- 1ATL
- Type
- protein
- Length
- 400 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Snake venom metalloproteinase atrolysin-D
- EC
- 3.4.24.42
- UniProt
- P15167
- Ligands
- 0QI, ZN, CA
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Snake venom metalloproteinase atrolysin-D (EC 3.4.24.42) | protein | 200 | 40% helix, 20% strand | P15167 |
Ligands and binding sites
- 0QI · O-methyl-N-[(2S)-4-methyl-2-(sulfanylmethyl)pentanoyl]-L-tyrosine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 378 | 0.62 | 0.77 | 42 | empty |
| 2 | 75 | 0.51 | 0.85 | 22 | 0QI |
| 3 | 75 | 0.47 | 0.82 | 19 | ZN, 0QI |
| 4 | 60 | 0.33 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 444 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1ATL · Structural interaction of natural and synthetic inhibitors with the VENOM… · the same entry in another collection · chain B against B, TM-score 1.00
- P15167 · AlphaFold monomer V2.0 prediction for snake venom metalloproteinase atrolysin-D (P15167) · a predicted model of the same protein · chain B 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 P15167
- Elsewhere: RCSB PDB 1ATL · PDBe 1ATL · UniProt P15167
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