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The crystal structure of dtdp-D-glucose 4,6-dehydratase (RMLB)FROM salmonella enterica serovar typhimurium
Analyse The crystal structure of dtdp-D-glucose 4,6-dehydratase (RMLB)FROM salmonella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1G1A
- Type
- protein
- Length
- 1,408 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dtdp-D-glucose 4,6-dehydratase
- EC
- 4.2.1.46
- UniProt
- P26391
- Ligands
- NAD, SO4
- Pockets
- 14 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Dtdp-D-glucose 4,6-dehydratase (EC 4.2.1.46) | protein | 352 | 44% helix, 15% strand | P26391 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 9 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 879 | 0.79 | 0.82 | 77 | SO4, NAD |
| 2 | 902 | 0.79 | 0.81 | 75 | SO4, NAD |
| 3 | 887 | 0.79 | 0.81 | 77 | SO4, NAD |
| 4 | 839 | 0.78 | 0.81 | 74 | SO4, NAD |
| 5 | 910 | 0.73 | 0.77 | 69 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1359 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1338 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 637 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 1G1A · The crystal structure of dtdp-D-glucose 4,6-dehydratase (RMLB)FROM salmonella enterica… · the same entry in another collection · chain A against A, TM-score 1.00
- P26391 · AlphaFold monomer V2.0 prediction for dtdp-glucose 4,6-dehydratase (P26391) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P26391
- Elsewhere: RCSB PDB 1G1A · PDBe 1G1A · UniProt P26391
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