MolNFT v1 · #60493 · protein
Crystal structure of a putative zinc peptidase (NP_812461.1) from bacteroides thetaiotaomicron vpi-5482 at 2.31 a resolution
3CT9 · Acetylornithine deacetylase: “Crystal structure of a putative zinc peptidase (NP_812461.1) from bacteroides thetaiotaomicron vpi-5482 at…”. X-ray diffraction, 2 ligands (IOD, CL), 6 pockets (best druggability 0.66). MolNFT v1 #60493…
- PDB
- 3CT9
- Type
- protein
- Length
- 693 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetylornithine deacetylase
- UniProt
- Q8A1V9
- Ligands
- IOD, CL
- Pockets
- 6 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetylornithine deacetylase | protein | 346 | 32% helix, 25% strand | Q8A1V9 |
| B | Acetylornithine deacetylase | protein | 347 | 29% helix, 25% strand | Q8A1V9 |
Ligands and binding sites
- IOD · Iodide ion · ion · 8 copies · chains A, B
- CL · Chloride ion · ion · 6 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 375 | 0.66 | 0.80 | 53 | CL, IOD |
| 2 | 278 | 0.55 | 0.77 | 39 | IOD, EDO, CL |
| 3 | 81 | 0.49 | 0.83 | 22 | empty |
| 4 | 96 | 0.38 | 0.76 | 19 | empty |
| 5 | 80 | 0.37 | 0.77 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1432 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 3CT9 · Crystal structure of a putative zinc peptidase (NP_812461.1) from Bacteroides… · 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
- Every structure of UniProt Q8A1V9
- Elsewhere: RCSB PDB 3CT9 · PDBe 3CT9 · UniProt Q8A1V9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.