MolNFT v1 · #129438 · protein
Conservatively refined structure of GAN1D-E170Q, a catalytic mutant of a putative 6-phospho-beta-galactosidase from geobacillus stearothermophilus, in complex with cellobiose-6-phosphate
5OKE · Putative 6-phospho-beta-galactobiosidase: “Conservatively refined structure of GAN1D-E170Q, a catalytic mutant of a putative…”. X-ray diffraction, 2 ligands (BG6, BGC), 9 pockets (best druggability 0.77). MolNFT v1 #129438 on…
- PDB
- 5OKE
- Type
- protein
- Length
- 1,847 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative 6-phospho-beta-galactobiosidase
- EC
- 3.2.1.85
- UniProt
- W8QF82
- Ligands
- BG6, BGC
- Pockets
- 9 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Putative 6-phospho-beta-galactobiosidase (EC 3.2.1.85) | protein | 462 | 42% helix, 17% strand | W8QF82 |
| D | Putative 6-phospho-beta-galactobiosidase (EC 3.2.1.85) | protein | 461 | 42% helix, 17% strand | W8QF82 |
Ligands and binding sites
- BG6 · 6-O-phosphono-beta-D-glucopyranose · sugar · 4 copies · chains C, D, A, B
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains C, D
- GOL · Glycerol · additive · 12 copies · chains A, B, C, D
- IMD · Imidazole · additive · 3 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 742 | 0.77 | 0.81 | 84 | BG6, GOL |
| 2 | 812 | 0.74 | 0.79 | 62 | BG6 |
| 3 | 690 | 0.74 | 0.80 | 69 | BGC, BG6 |
| 4 | 791 | 0.73 | 0.78 | 62 | BGC, BG6 |
| 5 | 530 | 0.71 | 0.80 | 66 | empty |
Interfaces
4 interfaces between chains.
- C–D · 335 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 320 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 317 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 273 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5OKE · Conservatively refined structure of Gan1D-E170Q, a catalytic mutant of a putative… · 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 W8QF82
- Elsewhere: RCSB PDB 5OKE · PDBe 5OKE · UniProt W8QF82
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