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1.62 ångström crystal structure of the salmonella enterica 3- dehydroquinate dehydratase (arod) E86A mutant in complex with dehydroshikimate (crystal form #1)
Analyse 1.62 ångström crystal structure of the salmonella enterica 3- dehydroquinate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GUG
- Type
- protein
- Length
- 492 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
- 3DS, CL
- Pockets
- 10 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 247 | 46% helix, 21% strand | P58687 |
| B | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 245 | 46% helix, 20% strand | P58687 |
Ligands and binding sites
- 3DS · (4S,5R)-4,5-dihydroxy-3-oxocyclohex-1-ene-1-carboxylic acid · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 87 | 0.54 | 0.85 | 24 | 3DS |
| 2 | 145 | 0.51 | 0.80 | 30 | 3DS |
| 3 | 68 | 0.45 | 0.82 | 20 | empty |
| 4 | 120 | 0.45 | 0.77 | 19 | CL |
| 5 | 70 | 0.43 | 0.81 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1061 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4GUG · 1.62 Angstrom Crystal Structure of the Salmonella enterica 3-Dehydroquinate Dehydratase… · the same entry in another collection · chain A against A, TM-score 1.00
- P58687 · AlphaFold monomer V2.0 prediction for 3-dehydroquinate dehydratase (P58687) · a predicted model of the same protein · chain B 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 P58687
- Elsewhere: RCSB PDB 4GUG · PDBe 4GUG · UniProt P58687
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