MolNFT v1 · #171931 · protein
Crystal structure of udp-glucuronic acid 4-epimerase from bacillus cereus in complex with NAD
6ZLA · Epimerase domain-containing protein: “Crystal structure of udp-glucuronic acid 4-epimerase from bacillus cereus in complex with NAD”. X-ray diffraction, 1 ligand (NAD), 9 pockets (best druggability 0.80). MolNFT v1 #171931 on…
- PDB
- 6ZLA
- Type
- protein
- Length
- 1,233 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epimerase domain-containing protein
- UniProt
- J8BY31
- Ligands
- NAD
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epimerase domain-containing protein | protein | 311 | 42% helix, 18% strand | J8BY31 |
| B | Epimerase domain-containing protein | protein | 306 | 44% helix, 20% strand | J8BY31 |
| C | Epimerase domain-containing protein | protein | 305 | 43% helix, 20% strand | J8BY31 |
| D | Epimerase domain-containing protein | protein | 311 | 41% helix, 18% strand | J8BY31 |
Ligands and binding sites
- 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
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 934 | 0.80 | 0.82 | 82 | NAD |
| 2 | 683 | 0.80 | 0.84 | 77 | NAD |
| 3 | 847 | 0.79 | 0.82 | 69 | NAD |
| 4 | 746 | 0.78 | 0.82 | 70 | NAD |
| 5 | 209 | 0.55 | 0.79 | 33 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1323 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 535 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 173 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6ZLA · Crystal Structure of UDP-Glucuronic acid 4-epimerase from Bacillus cereus in complex 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 J8BY31
- Elsewhere: RCSB PDB 6ZLA · PDBe 6ZLA · UniProt J8BY31
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