MolNFT v1 · #129443 · protein
Non-conservatively refined structure of GAN1D-wt, a putative 6- phospho-beta-galactosidase from geobacillus stearothermophilus, in the C2 spacegroup
5OKJ · Putative 6-phospho-beta-galactobiosidase: “Non-conservatively refined structure of GAN1D-wt, a putative 6- phospho-beta-galactosidase from geobacillus…”. X-ray diffraction, 6 pockets (best druggability 0.84). MolNFT v1 #129443 on…
- PDB
- 5OKJ
- 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
- Pockets
- 6 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 16% 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, 16% strand | W8QF82 |
Ligands and binding sites
- IMD · Imidazole · additive · 2 copies · chains A
- GOL · Glycerol · additive · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1034 | 0.84 | 0.85 | 77 | TRS |
| 2 | 1030 | 0.84 | 0.84 | 76 | empty |
| 3 | 153 | 0.82 | 0.98 | 28 | empty |
| 4 | 182 | 0.49 | 0.77 | 28 | empty |
| 5 | 179 | 0.48 | 0.76 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 1593 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 5OKJ · Non-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 5OKJ · PDBe 5OKJ · UniProt W8QF82
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