MolNFT v1 · #82525 · protein
Structure of a novel NAD dependent-ndp-hexosamine 5,6-dehydratase, tuna, involved in tunicamycin biosynthesis
3VPS · NAD-dependent EPIMERASE/DEHYDRATASE: “Structure of a novel NAD dependent-ndp-hexosamine 5,6-dehydratase, tuna, involved in tunicamycin biosynthesis”. X-ray diffraction, 2 ligands (UD1, NAD), 4 pockets (best druggability 0.86).…
- PDB
- 3VPS
- Type
- protein
- Length
- 604 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent EPIMERASE/DEHYDRATASE
- EC
- 4.2.1.-
- UniProt
- E5KJ94
- Ligands
- UD1, NAD
- Pockets
- 4 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent EPIMERASE/DEHYDRATASE (EC 4.2.1.-) | protein | 303 | 38% helix, 19% strand | E5KJ94 |
| B | NAD-dependent EPIMERASE/DEHYDRATASE (EC 4.2.1.-) | protein | 301 | 39% helix, 20% strand | E5KJ94 |
Ligands and binding sites
- UD1 · Uridine-diphosphate-N-acetylglucosamine · ligand · 2 copies · chains A, B
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 562 | 0.86 | 0.92 | 64 | UD1, NAD |
| 2 | 586 | 0.86 | 0.91 | 65 | UD1, NAD |
| 3 | 957 | 0.78 | 0.80 | 80 | empty |
| 4 | 204 | 0.62 | 0.83 | 35 | empty |
Interfaces
1 interface between chains.
- A–B · 383 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3VPS · Structure of a novel NAD dependent-NDP-hexosamine 5,6-dehydratase, TunA, involved in… · 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 E5KJ94
- Elsewhere: RCSB PDB 3VPS · PDBe 3VPS · UniProt E5KJ94
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