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Crystal structure of a putative glycoside hydrolase (BVU_0362) from bacteroides vulgatus atcc 8482 at 1.80 a resolution
Analyse Crystal structure of a putative glycoside hydrolase (BVU_0362) from bacteroides… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4N0R
- Type
- protein
- Length
- 1,023 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative glycoside hydrolase
- UniProt
- A6KXB7
- Ligands
- UNL, NI
- Pockets
- 9 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative glycoside hydrolase | protein | 512 | 22% helix, 32% strand | A6KXB7 |
| B | Putative glycoside hydrolase | protein | 511 | 22% helix, 32% strand | A6KXB7 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 2 copies · chains A, B
- NI · Nickel (II) ion · metal · 10 copies · chains A, B
- GOL · Glycerol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 335 | 0.60 | 0.77 | 55 | empty |
| 2 | 273 | 0.57 | 0.77 | 39 | UNL, NI |
| 3 | 233 | 0.55 | 0.78 | 40 | UNL, NI |
| 4 | 84 | 0.49 | 0.83 | 17 | empty |
| 5 | 90 | 0.48 | 0.81 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1455 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 modified (engineered).
Compared structures
- 4N0R · Crystal structure of a putative glycoside hydrolase (BVU_0362) 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 A6KXB7
- Elsewhere: RCSB PDB 4N0R · PDBe 4N0R · UniProt A6KXB7
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