MolNFT v1 · #135630 · protein
1.5 ångström resolution crystal structure of NAD-dependent epimerase from klebsiella pneumoniae in complex with NAD.
5U4Q · Dtdp-glucose 4,6-dehydratase: “1.5 ångström resolution crystal structure of NAD-dependent epimerase from klebsiella pneumoniae in complex…”. X-ray diffraction, 2 ligands (NAD, CL), 4 pockets (best druggability 0.77). MolNFT v1…
- PDB
- 5U4Q
- Type
- protein
- Length
- 625 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
- A0A169YGX7
- Ligands
- NAD, CL
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dtdp-glucose 4,6-dehydratase (EC 4.2.1.46) | protein | 321 | 42% helix, 17% strand | A0A169YGX7 |
| B | Dtdp-glucose 4,6-dehydratase (EC 4.2.1.46) | protein | 304 | 44% helix, 15% strand | A0A169YGX7 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 565 | 0.77 | 0.84 | 58 | NAD |
| 2 | 616 | 0.76 | 0.82 | 67 | NAD |
| 3 | 56 | 0.56 | 0.89 | 17 | empty |
| 4 | 109 | 0.37 | 0.74 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 1955 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 23 modified (engineered).
Compared structures
- 5U4Q · 1.5 Angstrom Resolution Crystal Structure of NAD-Dependent Epimerase from Klebsiella… · 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 A0A169YGX7
- Elsewhere: RCSB PDB 5U4Q · PDBe 5U4Q · UniProt A0A169YGX7
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