Research workbench
Crystal structure of the complex of type II dehydroquinate dehydratase from acinetobacter baumannii with dehydroquinic acid at 1.76 ångström resolution
Analyse Crystal structure of the complex of type II dehydroquinate dehydratase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YDB
- Type
- protein
- Length
- 580 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
- A3M692
- Ligands
- DQA, NA
- Pockets
- 6 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 145 | 48% helix, 17% strand | A3M692 |
Ligands and binding sites
- DQA · 1,3,4-trihydroxy-5-oxo-cyclohexanecarboxylic acid · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 124 | 0.65 | 0.88 | 33 | NA |
| 2 | 123 | 0.63 | 0.87 | 29 | NA |
| 3 | 255 | 0.62 | 0.80 | 26 | DQA |
| 4 | 204 | 0.58 | 0.80 | 24 | DQA |
| 5 | 205 | 0.50 | 0.76 | 27 | DQA |
Interfaces
3 interfaces between chains.
- A–B · 900 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 893 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 733 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5YDB · Crystal structure of the complex of type II dehydroquinate dehydratase from Acinetobacter… · the same entry in another collection · chain D against D, TM-score 1.00
- A3M692 · AlphaFold monomer V2.0 prediction for 3-dehydroquinate dehydratase (A3M692) · a predicted model of the same protein · chain C 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 A3M692
- Elsewhere: RCSB PDB 5YDB · PDBe 5YDB · UniProt A3M692
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