Research workbench
Crystal structure of gluconate dehydratase (target efi-501679) from salmonella enterica subsp. enterica serovar enteritidis str. P125109 complexed with magnesium and gluconic acid
Analyse Crystal structure of gluconate dehydratase (target efi-501679) from salmonella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TWB
- Type
- protein
- Length
- 2,079 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative dehydratase
- UniProt
- B5R541
- Ligands
- GCO, MG, CL
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Putative dehydratase | protein | 415 | 40% helix, 16% strand | B5R541 |
| B, D | Putative dehydratase | protein | 416 | 40% helix, 16% strand | B5R541 |
| C | Putative dehydratase | protein | 417 | 40% helix, 16% strand | B5R541 |
Ligands and binding sites
- GCO · D-gluconic acid · ligand · 5 copies · chains A, B, C, D, E
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, D, E
- CL · Chloride ion · ion · 3 copies · chains A, B, C, D, E
- GOL · Glycerol · additive · 7 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 865 | 0.79 | 0.82 | 114 | GOL, GCO |
| 2 | 272 | 0.67 | 0.83 | 54 | GOL, GCO |
| 3 | 264 | 0.67 | 0.83 | 47 | GOL, GCO |
| 4 | 280 | 0.67 | 0.83 | 38 | GCO |
| 5 | 51 | 0.65 | 0.96 | 23 | GCO |
Interfaces
6 interfaces between chains.
- C–D · 2673 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 2667 Ų buried · 43 hydrogen bonds · protein-protein
- B–C · 338 Ų buried · 1 hydrogen bond · protein-protein
- C–E · 209 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 196 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3TWB · Crystal structure of gluconate dehydratase (TARGET EFI-501679) from Salmonella enterica… · the same entry in another collection · chain E against E, TM-score 1.00
- B5R541 · AlphaFold monomer V2.0 prediction for D-galactonate dehydratase family member SEN1436… · a predicted model of the same protein · 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 B5R541
- Elsewhere: RCSB PDB 3TWB · PDBe 3TWB · UniProt B5R541
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