MolNFT v1 · #104657 · protein
Crystal structure of a putative hydrolase (BVU_2763) from bacteroides vulgatus atcc 8482 at 2.44 a resolution
4QHB · Uncharacterized protein: “Crystal structure of a putative hydrolase (BVU_2763) from bacteroides vulgatus atcc 8482 at 2.44 a resolution”. X-ray diffraction, 1 ligand (SO4), 13 pockets (best druggability 0.74). MolNFT v1 #104657 on…
- PDB
- 4QHB
- Type
- protein
- Length
- 1,551 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- A6L3Z9
- Ligands
- SO4
- Pockets
- 13 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein | protein | 387 | 8% helix, 45% strand | A6L3Z9 |
| B, C | Uncharacterized protein | protein | 390 | 9% helix, 45% strand | A6L3Z9 |
| D | Uncharacterized protein | protein | 384 | 8% helix, 45% strand | A6L3Z9 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · 6 copies · chains A, B, C
- PG4 · Tetraethylene glycol · additive · chains A, B
- PGE · Triethylene glycol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 871 | 0.74 | 0.78 | 94 | SO4 |
| 2 | 219 | 0.52 | 0.77 | 29 | PG4 |
| 3 | 176 | 0.51 | 0.78 | 26 | empty |
| 4 | 131 | 0.45 | 0.76 | 30 | empty |
| 5 | 121 | 0.41 | 0.75 | 26 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1837 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1733 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 416 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 326 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 303 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 modified, 6 disulfide (engineered, disulfide).
Compared structures
- 4QHB · Crystal structure of a putative hydrolase (BVU_2763) from Bacteroides vulgatus ATCC 8482… · 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 A6L3Z9
- Elsewhere: RCSB PDB 4QHB · PDBe 4QHB · UniProt A6L3Z9
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