Research workbench
Crystal structure of 3-dehydroquinate dehydratase I from klebsiella oxytoca (I222 form)
Analyse Crystal structure of 3-dehydroquinate dehydratase I from klebsiella oxytoca… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8DQC
- Type
- protein
- Length
- 726 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-dehydroquinate dehydratase I
- UniProt
- A0A8F3UXX5
- Ligands
- ZN
- Pockets
- 9 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-dehydroquinate dehydratase I | protein | 361 | 32% helix, 25% strand | A0A8F3UXX5 |
| B | 3-dehydroquinate dehydratase I | protein | 365 | 33% helix, 25% strand | A0A8F3UXX5 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 634 | 0.70 | 0.78 | 64 | ACT |
| 2 | 248 | 0.63 | 0.82 | 30 | empty |
| 3 | 200 | 0.62 | 0.83 | 28 | empty |
| 4 | 356 | 0.62 | 0.78 | 35 | ACT |
| 5 | 175 | 0.56 | 0.80 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1550 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 8DQC · Crystal structure of 3-dehydroquinate dehydratase I from Klebsiella oxytoca (I222 Form) · the same entry in another collection · 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 A0A8F3UXX5
- Elsewhere: RCSB PDB 8DQC · PDBe 8DQC · UniProt A0A8F3UXX5
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