MolNFT v1 · #164952 · protein
Crystal structure of a galactokinase from bifidobacterium infantis in complex with 2-deoxy-2-fluoro-galactose
6TEQ: “Crystal structure of a galactokinase from bifidobacterium infantis in complex with 2-deoxy-2-fluoro-galactose”. X-ray diffraction, 3 ligands (GAF, 2FG, CL), 17 pockets (best druggability 0.77). MolNFT v1 #164952 on GenesisL1: 3D…
- PDB
- 6TEQ
- Type
- protein
- Length
- 1,672 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Galactokinase
- UniProt
- B7GUI0
- Ligands
- GAF, 2FG, CL
- Pockets
- 17 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Galactokinase | protein | 418 | 45% helix, 21% strand | B7GUI0 |
Ligands and binding sites
- GAF · 2-deoxy-2-fluoro-alpha-D-galactopyranose · ligand · 4 copies · chains A, B, C, D
- 2FG · 2-deoxy-2-fluoro-beta-D-galactopyranose · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 7 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 17 copies · chains A, B, C, D
- GOL · Glycerol · additive · 14 copies · chains A, B, C, D
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains B, C
- PGE · Triethylene glycol · additive · 2 copies · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 410 | 0.77 | 0.86 | 55 | MES, GAF, 2FG |
| 2 | 414 | 0.76 | 0.85 | 52 | PEG, GOL, PGE, GAF, 2FG, CL |
| 3 | 1006 | 0.75 | 0.78 | 90 | empty |
| 4 | 524 | 0.75 | 0.83 | 53 | PEG, 2FG, GAF |
| 5 | 1006 | 0.74 | 0.77 | 85 | GOL |
Interfaces
5 interfaces between chains.
- A–D · 922 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 911 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 530 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 508 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 38 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6TEQ · 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 6TEQ · PDBe 6TEQ · UniProt B7GUI0
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