MolNFT v1 · #50979 · protein
Udp-galactose 4-epimerase complexed with udp-phenol
2UDP: “Udp-galactose 4-epimerase complexed with udp-phenol”. X-ray diffraction, 3 ligands (NAD, UPP, NA), 5 pockets (best druggability 0.84). MolNFT v1 #50979 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2UDP
- Type
- protein
- Length
- 676 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
- P09147
- Ligands
- NAD, UPP, NA
- Pockets
- 5 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Udp-galactose 4-epimerase (EC 5.1.3.2) | protein | 338 | 42% helix, 18% strand | P09147 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- UPP · Phenyl-uridine-5'-diphosphate · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 802 | 0.84 | 0.87 | 82 | NAD, UPP |
| 2 | 866 | 0.84 | 0.86 | 84 | NAD, UPP |
| 3 | 85 | 0.53 | 0.85 | 16 | empty |
| 4 | 79 | 0.33 | 0.74 | 15 | empty |
| 5 | 70 | 0.30 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 969 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
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 P09147
- Elsewhere: RCSB PDB 2UDP · PDBe 2UDP · UniProt P09147
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