MolNFT v1 · #104364 · protein
Glycosyl hydrolase family 88 from bacteroides vulgatus
4Q88 · Uncharacterized protein: “Glycosyl hydrolase family 88 from bacteroides vulgatus”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.64). MolNFT v1 #104364 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4Q88
- Type
- protein
- Length
- 698 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- A6L195
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 57% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein | protein | 350 | 57% helix, 3% strand | A6L195 |
| B | Uncharacterized protein | protein | 348 | 57% helix, 3% strand | A6L195 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 276 | 0.64 | 0.81 | 39 | empty |
| 2 | 284 | 0.62 | 0.80 | 41 | empty |
| 3 | 272 | 0.60 | 0.79 | 38 | empty |
| 4 | 338 | 0.55 | 0.74 | 38 | SO4 |
| 5 | 106 | 0.43 | 0.77 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 513 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 4Q88 · Glycosyl hydrolase family 88 from Bacteroides vulgatus · 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 A6L195
- Elsewhere: RCSB PDB 4Q88 · PDBe 4Q88 · UniProt A6L195
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