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Crystal structure of the 3-dehydroquinate dehydratase (arod) from salmonella enterica typhimurium LT2 with malonate and boric acid at the active site
Analyse Crystal structure of the 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
- 3S42
- Type
- protein
- Length
- 526 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-dehydroquinate dehydratase
- EC
- 4.2.1.10
- UniProt
- P58687
- Ligands
- NI, BO3
- Pockets
- 6 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 266 | 44% helix, 20% strand | P58687 |
| A | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 260 | 45% helix, 22% strand | P58687 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · chains B
- BO3 · Boric acid · ion · chains A
- DMS · Dimethyl sulfoxide · additive · 6 copies · chains B, A
- MLA · Malonic acid · additive · 2 copies · chains B, A
- IMD · Imidazole · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 56 | 0.65 | 0.95 | 19 | MLA, BO3 |
| 2 | 55 | 0.63 | 0.94 | 18 | MLA |
| 3 | 54 | 0.44 | 0.84 | 15 | DMS |
| 4 | 98 | 0.43 | 0.78 | 20 | DMS |
| 5 | 99 | 0.42 | 0.78 | 20 | empty |
Interfaces
1 interface between chains.
- B–A · 1092 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 3S42 · Crystal Structure of the 3-Dehydroquinate Dehydratase (aroD) from Salmonella enterica… · the same entry in another collection · chain B against B, 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 0.96
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 3S42 · PDBe 3S42 · UniProt P58687
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