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Conservatively refined structure of GAN1D-wt, a putative 6-phospho- beta-galactosidase from geobacillus stearothermophilus, in complex with 6-phospho-beta-galactose
Analyse Conservatively refined structure of GAN1D-wt, a putative 6-phospho… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OKK
- Type
- protein
- Length
- 948 residues
- Chains
- 2
- 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
- BGP
- Pockets
- 7 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative 6-phospho-beta-galactobiosidase (EC 3.2.1.85) | protein | 474 | 41% helix, 17% strand | W8QF82 |
Ligands and binding sites
- BGP · 6-O-phosphono-beta-D-galactopyranose · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 10 copies · chains A, B
- IMD · Imidazole · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 923 | 0.84 | 0.85 | 74 | BGP, GOL |
| 2 | 897 | 0.84 | 0.86 | 74 | BGP, GOL |
| 3 | 162 | 0.82 | 0.98 | 26 | empty |
| 4 | 111 | 0.50 | 0.81 | 23 | GOL |
| 5 | 164 | 0.48 | 0.77 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 1631 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 5OKK · Conservatively refined structure of Gan1D-WT, a putative 6-phospho-beta-galactosidase… · 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 5OKK · PDBe 5OKK · UniProt W8QF82
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