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Crystal structure of gluconate dehydratase (target efi-501679) from salmonella enterica subsp. enterica serovar enteritidis str. P125109
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
- 3TW9
- Type
- protein
- Length
- 1,607 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative dehydratase
- UniProt
- B5R541
- Ligands
- CL
- Pockets
- 18 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative dehydratase | protein | 394 | 41% helix, 16% strand | B5R541 |
| B | Putative dehydratase | protein | 410 | 42% helix, 15% strand | B5R541 |
| C | Putative dehydratase | protein | 395 | 41% helix, 16% strand | B5R541 |
| D | Putative dehydratase | protein | 408 | 42% helix, 15% strand | B5R541 |
Ligands and binding sites
- CL · Chloride ion · ion · 11 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1062 | 0.84 | 0.85 | 120 | GOL, CL |
| 2 | 1157 | 0.79 | 0.81 | 107 | GOL, CL |
| 3 | 148 | 0.78 | 0.95 | 21 | empty |
| 4 | 91 | 0.77 | 0.98 | 22 | empty |
| 5 | 76 | 0.75 | 0.98 | 21 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2735 Ų buried · 44 hydrogen bonds · protein-protein
- B–C · 1551 Ų buried · 38 hydrogen bonds · protein-protein
- A–D · 1453 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 1302 Ų buried · 22 hydrogen bonds · protein-protein
- B–D · 1294 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 3TW9 · Crystal structure of gluconate dehydratase (TARGET EFI-501679) from Salmonella enterica… · the same entry in another collection · chain D against D, 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 0.99
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 3TW9 · PDBe 3TW9 · UniProt B5R541
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