MolNFT v1 · #147320 · protein
Bacteroides ovatus mixed-linkage glucan utilization locus (mlgul) sgbp-B in complex with mixed-linkage heptasaccharide
6E9B: “Bacteroides ovatus mixed-linkage glucan utilization locus (mlgul) sgbp-B in complex with mixed-linkage…”. X-ray diffraction, 2 ligands (BGC, SO4), 20 pockets (best druggability 0.79). MolNFT v1 #147320 on GenesisL1: 3D structure…
- PDB
- 6E9B
- Type
- protein
- Length
- 1,514 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mixed-linkage glucan utilization locus (mlgul) sgbp-B
- UniProt
- A7LY28
- Ligands
- BGC, SO4
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mixed-linkage glucan utilization locus (mlgul) sgbp-B | protein | 381 | 5% helix, 43% strand | A7LY28 |
| B | Mixed-linkage glucan utilization locus (mlgul) sgbp-B | protein | 378 | 6% helix, 39% strand | A7LY28 |
| C | Mixed-linkage glucan utilization locus (mlgul) sgbp-B | protein | 387 | 5% helix, 47% strand | A7LY28 |
| D | Mixed-linkage glucan utilization locus (mlgul) sgbp-B | protein | 368 | 7% helix, 35% strand | A7LY28 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 7 copies · chains D
- SO4 · Sulfate ion · ion · 10 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 121 | 0.79 | 0.97 | 28 | empty |
| 2 | 55 | 0.68 | 0.95 | 21 | empty |
| 3 | 427 | 0.65 | 0.78 | 51 | empty |
| 4 | 266 | 0.63 | 0.81 | 33 | empty |
| 5 | 387 | 0.58 | 0.75 | 53 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1539 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1430 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 320 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 288 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6E9B · Bacteroides ovatus mixed-linkage glucan utilization locus (MLGUL) SGBP-B in complex with… · 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 A7LY28
- Elsewhere: RCSB PDB 6E9B · PDBe 6E9B · UniProt A7LY28
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