MolNFT v1 · #5510 · protein
Structure of human udp-galactose 4-epimerase complexed with NADH and udp-glucose
1EK6: “Structure of human udp-galactose 4-epimerase complexed with NADH and udp-glucose”. X-ray diffraction, 3 ligands (NAI, UPG, MG), 4 pockets (best druggability 0.86). MolNFT v1 #5510 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1EK6
- Type
- protein
- Length
- 691 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-galactose 4-epimerase
- EC
- 5.1.3.2
- UniProt
- Q14376
- Ligands
- NAI, UPG, MG
- Pockets
- 4 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-galactose 4-epimerase (EC 5.1.3.2) | protein | 346 | 40% helix, 18% strand | Q14376 |
| B | Udp-galactose 4-epimerase (EC 5.1.3.2) | protein | 345 | 41% helix, 19% strand | Q14376 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 2 copies · chains A, B
- UPG · Uridine-5'-diphosphate-glucose · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- TMA · Tetramethylammonium ion · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 658 | 0.86 | 0.90 | 89 | NAI, UPG |
| 2 | 845 | 0.85 | 0.87 | 86 | NAI, UPG |
| 3 | 57 | 0.30 | 0.75 | 17 | empty |
| 4 | 62 | 0.30 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1067 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 1EK6 · Structure of human udp-galactose 4-epimerase complexed with NADH and udp-glucose · 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 1EK6 · PDBe 1EK6 · UniProt Q14376
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