MolNFT v1 · #171942 · protein
Crystal structure of udp-glucuronic acid 4-epimerase from bacillus cereus in complex with udp-galacturonic acid and NAD
6ZLL · Epimerase domain-containing protein: “Crystal structure of udp-glucuronic acid 4-epimerase from bacillus cereus in complex with udp-galacturonic…”. X-ray diffraction, 2 ligands (UGB, NAD), 8 pockets (best druggability 0.88). MolNFT…
- PDB
- 6ZLL
- Type
- protein
- Length
- 1,272 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epimerase domain-containing protein
- UniProt
- J8BY31
- Ligands
- UGB, NAD
- Pockets
- 8 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Epimerase domain-containing protein | protein | 321 | 42% helix, 18% strand | J8BY31 |
| B, C | Epimerase domain-containing protein | protein | 315 | 43% helix, 17% strand | J8BY31 |
Ligands and binding sites
- 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
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 515 | 0.88 | 0.94 | 70 | UGB, NAD |
| 2 | 465 | 0.87 | 0.94 | 60 | UGB, NAD |
| 3 | 538 | 0.87 | 0.92 | 84 | UGB, NAD |
| 4 | 491 | 0.87 | 0.93 | 70 | UGB, NAD |
| 5 | 276 | 0.60 | 0.79 | 31 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1350 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 1296 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 558 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 136 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 63 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6ZLL · Crystal Structure of UDP-Glucuronic acid 4-epimerase from Bacillus cereus in complex with… · the same entry in another collection · chain D against D, 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 6ZLL · PDBe 6ZLL · UniProt J8BY31
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