MolNFT v1 · #140520 · protein
Crystal structure of the complex of type II dehydroquinate dehydratase from acinetobacter baumannii with dehydroquinic acid at 1.76 ångström resolution
5YDB · 3-dehydroquinate dehydratase: “Crystal structure of the complex of type II dehydroquinate dehydratase from acinetobacter baumannii with…”. X-ray diffraction, 2 ligands (DQA, NA), 6 pockets (best druggability 0.65). MolNFT v1 #140520…
- 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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