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Crystal structure of type I 3-dehydroquinate dehydratase (arod) from salmonella typhimurium with close loop conformation.
Analyse Crystal structure of type I 3-dehydroquinate dehydratase (arod) from salmonella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OEX
- Type
- protein
- Length
- 1,006 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-dehydroquinate dehydratase
- EC
- 4.2.1.10
- UniProt
- P58687
- Ligands
- CL
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 251 | 46% helix, 21% strand | P58687 |
| B | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 253 | 46% helix, 21% strand | P58687 |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 632 | 0.81 | 0.86 | 75 | CL |
| 2 | 409 | 0.73 | 0.84 | 51 | empty |
| 3 | 414 | 0.70 | 0.81 | 45 | empty |
| 4 | 76 | 0.48 | 0.83 | 16 | empty |
| 5 | 78 | 0.43 | 0.79 | 18 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1158 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 1128 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 1051 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 198 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 178 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3OEX · Crystal Structure of Type I 3-Dehydroquinate Dehydratase (aroD) from Salmonella… · the same entry in another collection · chain D against D, TM-score 1.00
- P58687 · AlphaFold monomer V2.0 prediction for 3-dehydroquinate dehydratase (P58687) · 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 P58687
- Elsewhere: RCSB PDB 3OEX · PDBe 3OEX · UniProt P58687
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