MolNFT v1 · #171941 · protein
Equilibrium structure of udp-glucuronic acid 4-epimerase from bacillus cereus in complex with udp-glucuronic ACID/UDP-galacturonic acid and NAD
6ZLK · Epimerase domain-containing protein: “Equilibrium structure of udp-glucuronic acid 4-epimerase from bacillus cereus in complex with udp-glucuronic…”. X-ray diffraction, 3 ligands (NAD, UGA, UGB), 12 pockets (best druggability 0.88).…
- PDB
- 6ZLK
- Type
- protein
- Length
- 1,259 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epimerase domain-containing protein
- UniProt
- J8BY31
- Ligands
- NAD, UGA, UGB
- Pockets
- 12 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Epimerase domain-containing protein | protein | 315 | 42% helix, 17% strand | J8BY31 |
| C | Epimerase domain-containing protein | protein | 314 | 41% helix, 18% strand | J8BY31 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- UGA · Uridine-5'-diphosphate-glucuronic acid · ligand · 4 copies · chains A, B, C, D
- UGB · (2S,3R,4S,5R,6R)-6-[[[(2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]oxy-3,4,5-trihydroxy-oxane-2-carboxylic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 529 | 0.88 | 0.94 | 71 | NAD, UGA, UGB |
| 2 | 529 | 0.87 | 0.93 | 74 | NAD, UGA, UGB |
| 3 | 519 | 0.87 | 0.93 | 73 | NAD, UGA, UGB |
| 4 | 487 | 0.87 | 0.93 | 63 | NAD, UGA, UGB |
| 5 | 774 | 0.76 | 0.80 | 61 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1359 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 1256 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 540 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6ZLK · Equilibrium Structure of UDP-Glucuronic acid 4-epimerase from Bacillus cereus in complex… · 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 J8BY31
- Elsewhere: RCSB PDB 6ZLK · PDBe 6ZLK · UniProt J8BY31
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