MolNFT v1 · #16884 · protein
The structure of NADH in the dtdp-D-glucose dehydratase (rmlb) enzyme
1OC2 · Dtdp-glucose 4,6-dehydratase: “The structure of NADH in the dtdp-D-glucose dehydratase (rmlb) enzyme”. X-ray diffraction, 3 ligands (TDX, NAD, SO4), 6 pockets (best druggability 0.87). MolNFT v1 #16884 on GenesisL1: 3D structure…
- PDB
- 1OC2
- Type
- protein
- Length
- 692 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dtdp-glucose 4,6-dehydratase
- EC
- 4.2.1.46
- UniProt
- Q8GIP9
- Ligands
- TDX, NAD, SO4
- Pockets
- 6 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dtdp-glucose 4,6-dehydratase (EC 4.2.1.46) | protein | 346 | 45% helix, 17% strand | Q8GIP9 |
| B | Dtdp-glucose 4,6-dehydratase (EC 4.2.1.46) | protein | 346 | 45% helix, 17% strand | Q8GIP9 |
Ligands and binding sites
- TDX · Thymidine-5'-diphospho-beta-D-xylose · ligand · 2 copies · chains A, B
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A
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 | 460 | 0.87 | 0.94 | 63 | NAD, TDX |
| 2 | 444 | 0.87 | 0.94 | 64 | TDX, NAD |
| 3 | 110 | 0.44 | 0.78 | 25 | empty |
| 4 | 131 | 0.42 | 0.76 | 29 | empty |
| 5 | 112 | 0.40 | 0.76 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 1359 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 1OC2 · The structure of NADH in the dTDP-D-glucose dehydratase (RmlB) enzyme · 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 Q8GIP9
- Elsewhere: RCSB PDB 1OC2 · PDBe 1OC2 · UniProt Q8GIP9
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