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Crystal structure of NAD bound dtdp-glucose 4,6-dehydratase from elizabethkingia anophelis
Analyse Crystal structure of NAD bound dtdp-glucose 4,6-dehydratase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8DU1
- Type
- protein
- Length
- 1,432 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dtdp-glucose 4,6-dehydratase
- EC
- 4.2.1.46
- UniProt
- A0A077ELH2
- Ligands
- NAD, MG, CL
- Pockets
- 18 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dtdp-glucose 4,6-dehydratase (EC 4.2.1.46) | protein | 361 | 44% helix, 17% strand | A0A077ELH2 |
| B | Dtdp-glucose 4,6-dehydratase (EC 4.2.1.46) | protein | 359 | 45% helix, 17% strand | A0A077ELH2 |
| C | Dtdp-glucose 4,6-dehydratase (EC 4.2.1.46) | protein | 353 | 44% helix, 17% strand | A0A077ELH2 |
| D | Dtdp-glucose 4,6-dehydratase (EC 4.2.1.46) | protein | 359 | 44% helix, 17% strand | A0A077ELH2 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies · chains C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 12 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 945 | 0.82 | 0.83 | 79 | empty |
| 2 | 1078 | 0.78 | 0.80 | 91 | EDO, NAD, CL |
| 3 | 905 | 0.78 | 0.80 | 79 | EDO, NAD, CL |
| 4 | 844 | 0.78 | 0.81 | 81 | EDO, NAD, CL |
| 5 | 718 | 0.77 | 0.81 | 64 | EDO, NAD |
Interfaces
3 interfaces between chains.
- B–D · 1328 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 1287 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 489 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 8DU1 · Crystal Structure of NAD bound dTDP-glucose 4,6-dehydratase from Elizabethkingia anophelis · 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 A0A077ELH2
- Elsewhere: RCSB PDB 8DU1 · PDBe 8DU1 · UniProt A0A077ELH2
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