MolNFT v1 · #164953 · protein
Crystal structure of a galactokinase from bifidobacterium infantis in complex with galactose
6TER: “Crystal structure of a galactokinase from bifidobacterium infantis in complex with galactose”. X-ray diffraction, 4 ligands (GLA, GAL, NA), 15 pockets (best druggability 0.76). MolNFT v1 #164953 on GenesisL1: 3D structure, binding…
- PDB
- 6TER
- Type
- protein
- Length
- 1,668 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Galactokinase
- UniProt
- B7GUI0
- Ligands
- GLA, GAL, NA, CL
- Pockets
- 15 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Galactokinase | protein | 418 | 45% helix, 19% strand | B7GUI0 |
| C, D | Galactokinase | protein | 416 | 43% helix, 19% strand | B7GUI0 |
Ligands and binding sites
- GLA · alpha-D-galactopyranose · sugar · 4 copies · chains A, B, C, D
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B
- NA · Sodium ion · metal · 6 copies · chains B, C, D
- CL · Chloride ion · ion · 3 copies · chains A, C
- GOL · Glycerol · additive · 27 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 26 copies · chains A, B, D, C
- PGE · Triethylene glycol · additive · 4 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 494 | 0.76 | 0.84 | 56 | PEG, GOL, GLA, GAL |
| 2 | 441 | 0.76 | 0.85 | 48 | TRS, GLA |
| 3 | 471 | 0.76 | 0.84 | 56 | PEG, GOL, GLA, GAL |
| 4 | 441 | 0.75 | 0.85 | 55 | GLA |
| 5 | 1005 | 0.75 | 0.78 | 86 | PEG, GOL |
Interfaces
5 interfaces between chains.
- A–D · 929 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 920 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 582 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 541 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 41 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6TER · Crystal structure of a galactokinase from Bifidobacterium infantis 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 B7GUI0
- Elsewhere: RCSB PDB 6TER · PDBe 6TER · UniProt B7GUI0
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