MolNFT v1 · #183417 · protein
Structure of sgbp BO2743 from bacteroides ovatus in complex with mixed-linked gluco-nonasaccharide
7NOX · Surface glycan-binding protein BO2743: “Structure of sgbp BO2743 from bacteroides ovatus in complex with mixed-linked gluco-nonasaccharide”. X-ray diffraction, 5 ligands (TAM, BGC, NA), 10 pockets (best druggability 0.72). MolNFT v1…
- PDB
- 7NOX
- Type
- protein
- Length
- 1,040 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Surface glycan-binding protein BO2743
- UniProt
- A7LY27
- Ligands
- TAM, BGC, NA, MG, AZI
- Pockets
- 10 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Surface glycan-binding protein BO2743 | protein | 520 | 53% helix, 5% strand | A7LY27 |
| B | Surface glycan-binding protein BO2743 | protein | 520 | 54% helix, 5% strand | A7LY27 |
Ligands and binding sites
- TAM · Tris(hydroxyethyl)aminomethane · ligand · chains B
- BGC · beta-D-glucopyranose · sugar · 18 copies · chains A, B
- NA · Sodium ion · metal · 3 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- AZI · Azide ion · ion · 14 copies · chains A, B
- PGE · Triethylene glycol · additive · 8 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
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 | 863 | 0.72 | 0.77 | 65 | PGE |
| 2 | 136 | 0.53 | 0.81 | 23 | AZI |
| 3 | 86 | 0.51 | 0.84 | 23 | empty |
| 4 | 191 | 0.48 | 0.75 | 28 | empty |
| 5 | 160 | 0.48 | 0.77 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 263 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 7NOX · Structure of SGBP BO2743 from Bacteroides ovatus in complex with mixed-linked… · 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 A7LY27
- Elsewhere: RCSB PDB 7NOX · PDBe 7NOX · UniProt A7LY27
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