MolNFT v1 · #27133 · protein
Crystal structure of staphlyococcus aureus 3-dehydroquinate synthase (dhqs) in complex with ZN2+ and NAD+
1XAH: “Crystal structure of staphlyococcus aureus 3-dehydroquinate synthase (dhqs) in complex with ZN2+ and NAD+”. X-ray diffraction, 2 ligands (NAD, ZN), 5 pockets (best druggability 0.80). MolNFT v1 #27133 on GenesisL1: 3D structure…
- PDB
- 1XAH
- Type
- protein
- Length
- 653 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-dehydroquinate synthase
- EC
- 4.2.3.4
- UniProt
- Q6GGU4
- Ligands
- NAD, ZN
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-dehydroquinate synthase (EC 4.2.3.4) | protein | 323 | 53% helix, 18% strand | Q6GGU4 |
| B | 3-dehydroquinate synthase (EC 4.2.3.4) | protein | 330 | 53% helix, 17% strand | Q6GGU4 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1186 | 0.80 | 0.82 | 84 | ZN, NAD |
| 2 | 1070 | 0.78 | 0.80 | 78 | ZN, NAD |
| 3 | 670 | 0.70 | 0.78 | 52 | empty |
| 4 | 188 | 0.56 | 0.79 | 20 | empty |
| 5 | 195 | 0.56 | 0.79 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1446 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 1XAH · Crystal structure of staphlyococcus aureus 3-dehydroquinate synthase (dhqs) in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- Q6GGU4 · AlphaFold monomer V2.0 prediction for 3-dehydroquinate synthase (Q6GGU4) · a predicted model of the same protein · chain A 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 Q6GGU4
- Elsewhere: RCSB PDB 1XAH · PDBe 1XAH · UniProt Q6GGU4
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