MolNFT v1 · #180027 · protein
Crystal structure of udp-glucose-4-epimerase (gale) from stenotrophomonas maltophila with bound NAD and formylated udp- arabinopyranose
7KN1 · Udp-glucose 4-epimerase: “Crystal structure of udp-glucose-4-epimerase (gale) from stenotrophomonas maltophila with bound NAD and…”. X-ray diffraction, 2 ligands (NAD, WQD), 6 pockets (best druggability 0.84). MolNFT v1 #180027 on…
- PDB
- 7KN1
- Type
- protein
- Length
- 672 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
- B2FNY6
- Ligands
- NAD, WQD
- Pockets
- 6 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-glucose 4-epimerase (EC 5.1.3.2) | protein | 336 | 43% helix, 17% strand | B2FNY6 |
| B | Udp-glucose 4-epimerase (EC 5.1.3.2) | protein | 336 | 43% helix, 17% strand | B2FNY6 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- WQD · UDP-4-deoxy-4-formamido-beta-L-arabinopyranose · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 15 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 990 | 0.84 | 0.85 | 100 | NAD, EDO, WQD |
| 2 | 950 | 0.83 | 0.85 | 85 | NAD, EDO, WQD |
| 3 | 88 | 0.45 | 0.80 | 16 | empty |
| 4 | 104 | 0.38 | 0.75 | 14 | EDO |
| 5 | 62 | 0.29 | 0.74 | 15 | EDO |
Interfaces
1 interface between chains.
- A–B · 1012 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7KN1 · Crystal structure of UDP-glucose-4-epimerase (galE) from Stenotrophomonas maltophila 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 B2FNY6
- Elsewhere: RCSB PDB 7KN1 · PDBe 7KN1 · UniProt B2FNY6
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