MolNFT v1 · #93169 · protein
1.78 ångström crystal structure of the salmonella enterica 3- dehydroquinate dehydratase (arod) in complex with quinate
4GUI · 3-dehydroquinate dehydratase: “1.78 ångström crystal structure of the salmonella enterica 3- dehydroquinate dehydratase (arod) in complex…”. X-ray diffraction, 2 ligands (QIC, NI), 5 pockets (best druggability 0.68). MolNFT v1…
- PDB
- 4GUI
- Type
- protein
- Length
- 502 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
- QIC, NI
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 251 | 46% helix, 22% strand | P58687 |
Ligands and binding sites
- QIC · (1S,3R,4S,5R)-1,3,4,5-tetrahydroxycyclohexanecarboxylic acid · ligand · 2 copies · chains A, B
- NI · Nickel (II) ion · metal · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 72 | 0.68 | 0.94 | 19 | QIC |
| 2 | 252 | 0.61 | 0.80 | 31 | QIC |
| 3 | 91 | 0.41 | 0.78 | 21 | empty |
| 4 | 69 | 0.36 | 0.78 | 19 | empty |
| 5 | 51 | 0.35 | 0.79 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1123 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4GUI · 1.78 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 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 4GUI · PDBe 4GUI · UniProt P58687
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