MolNFT v1 · #123581 · protein
Bacteroides ovatus xyloglucan pul GH31 with bound 5FIDOF
5JOV · Alpha-xylosidase BOGH31A: “Bacteroides ovatus xyloglucan pul GH31 with bound 5FIDOF”. X-ray diffraction, 2 ligands (B9D, NI), 10 pockets (best druggability 0.74). MolNFT v1 #123581 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5JOV
- Type
- protein
- Length
- 949 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-xylosidase BOGH31A
- EC
- 3.2.1.177
- UniProt
- A7LXT0
- Ligands
- B9D, NI
- Pockets
- 10 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 22% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-xylosidase BOGH31A (EC 3.2.1.177) | protein | 949 | 22% helix, 33% strand | A7LXT0 |
Ligands and binding sites
- B9D · 5-fluoro-alpha-L-idopyranose · ligand · chains A
- NI · Nickel (II) ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 5 copies · chains A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 231 | 0.74 | 0.89 | 33 | empty |
| 2 | 259 | 0.63 | 0.81 | 32 | EPE, B9D |
| 3 | 122 | 0.59 | 0.85 | 31 | empty |
| 4 | 125 | 0.49 | 0.80 | 25 | empty |
| 5 | 183 | 0.47 | 0.75 | 28 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- A7LXT0 · AlphaFold monomer V2.0 prediction for alpha-xylosidase BOGH31A (A7LXT0) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 A7LXT0
- Elsewhere: RCSB PDB 5JOV · PDBe 5JOV · UniProt A7LXT0
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