MolNFT v1 · #146601 · protein
Bacteroides ovatus mixed-linkage glucan utilization locus (mlgul) sgbp-a with cellohexaose
6DMF · Mixed-linkage glucan utilization locus (mlgul) sgbp-B: “Bacteroides ovatus mixed-linkage glucan utilization locus (mlgul) sgbp-a with cellohexaose”. X-ray diffraction, 2 ligands (BGC, MG), 20 pockets (best druggability 0.80). MolNFT…
- PDB
- 6DMF
- Type
- protein
- Length
- 5,139 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mixed-linkage glucan utilization locus (mlgul) sgbp-B
- UniProt
- A7LY27
- Ligands
- BGC, MG
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 10 distinct chains · 52% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mixed-linkage glucan utilization locus (mlgul) sgbp-B | protein | 513 | 53% helix, 5% strand | A7LY27 |
| B | Mixed-linkage glucan utilization locus (mlgul) sgbp-B | protein | 516 | 52% helix, 5% strand | A7LY27 |
| C | Mixed-linkage glucan utilization locus (mlgul) sgbp-B | protein | 512 | 51% helix, 5% strand | A7LY27 |
| D | Mixed-linkage glucan utilization locus (mlgul) sgbp-B | protein | 519 | 52% helix, 5% strand | A7LY27 |
| E | Mixed-linkage glucan utilization locus (mlgul) sgbp-B | protein | 517 | 52% helix, 5% strand | A7LY27 |
| F | Mixed-linkage glucan utilization locus (mlgul) sgbp-B | protein | 514 | 52% helix, 5% strand | A7LY27 |
| G | Mixed-linkage glucan utilization locus (mlgul) sgbp-B | protein | 512 | 53% helix, 5% strand | A7LY27 |
| H | Mixed-linkage glucan utilization locus (mlgul) sgbp-B | protein | 514 | 53% helix, 6% strand | A7LY27 |
| I | Mixed-linkage glucan utilization locus (mlgul) sgbp-B | protein | 510 | 53% helix, 5% strand | A7LY27 |
| J | Mixed-linkage glucan utilization locus (mlgul) sgbp-B | protein | 512 | 53% helix, 5% strand | A7LY27 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 59 copies · chains A, B, C, D, E, F, G, H, I, J
- MG · Magnesium ion · metal · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- EDO · 1,2-ethanediol · additive · 18 copies · chains A, B, C, D, E, G, H, I
- ACT · Acetate ion · additive · 9 copies · chains A, B, C, D, E, F, H, I, J
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains A, B, D, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 599 | 0.80 | 0.85 | 70 | empty |
| 2 | 582 | 0.79 | 0.85 | 71 | empty |
| 3 | 584 | 0.78 | 0.84 | 63 | empty |
| 4 | 568 | 0.77 | 0.84 | 61 | empty |
| 5 | 424 | 0.73 | 0.84 | 53 | MG |
Interfaces
24 interfaces between chains.
- C–E · 837 Ų buried · 9 hydrogen bonds · protein-protein
- G–J · 829 Ų buried · 8 hydrogen bonds · protein-protein
- F–I · 802 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 766 Ų buried · 9 hydrogen bonds · protein-protein
- E–J · 548 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6DMF · Bacteroides ovatus mixed-linkage glucan utilization locus (MLGUL) SGBP-A with cellohexaose · 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 6DMF · PDBe 6DMF · UniProt A7LY27
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