Research workbench
Molecular basis for severe epimerase-deficiency galactosemia: X-ray structure of the human V94M-substituted udp-galactose 4-epimerase
Analyse Molecular basis for severe epimerase-deficiency galactosemia: X-ray structure… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1I3L
- Type
- protein
- Length
- 692 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-glucose 4-epimerase
- EC
- 5.1.3.2
- UniProt
- Q14376
- Ligands
- GDU, NAD, MG, CL
- Pockets
- 3 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-glucose 4-epimerase (EC 5.1.3.2) | protein | 347 | 39% helix, 18% strand | Q14376 |
| B | Udp-glucose 4-epimerase (EC 5.1.3.2) | protein | 345 | 39% helix, 19% strand | Q14376 |
Ligands and binding sites
- GDU · Galactose-uridine-5'-diphosphate · ligand · 2 copies · chains A, B
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 954 | 0.86 | 0.87 | 90 | GDU, NAD |
| 2 | 1074 | 0.85 | 0.86 | 87 | GDU, NAD |
| 3 | 99 | 0.37 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1038 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 1I3L · Molecular basis for severe epimerase-deficiency galactosemia: X-ray structure of the… · the same entry in another collection · chain A against A, TM-score 1.00
- Q14376 · AlphaFold monomer V2.0 prediction for udp-glucose 4-epimerase (Q14376) · a predicted model of the same protein · 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 Q14376
- Elsewhere: RCSB PDB 1I3L · PDBe 1I3L · UniProt Q14376
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