MolNFT v1 · #27137 · protein
Crystal structure of staphlyococcus aureus 3-dehydroquinate synthase (dhqs) in complex with ZN2+, NAD+ and carbaphosphonate (soak)
1XAL: “Crystal structure of staphlyococcus aureus 3-dehydroquinate synthase (dhqs) in complex with ZN2+, NAD+ and…”. X-ray diffraction, 3 ligands (NAD, CRB, ZN), 6 pockets (best druggability 0.79). MolNFT v1 #27137 on GenesisL1: 3D…
- PDB
- 1XAL
- Type
- protein
- Length
- 672 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, CRB, ZN
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3-dehydroquinate synthase (EC 4.2.3.4) | protein | 336 | 47% helix, 20% strand | Q6GGU4 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- CRB · [1R-(1alpha,3beta,4alpha,5beta)]-5-(phosphonomethyl)-1,3,4-trihydroxycyclohexane-1-carboxylic acid · 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
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 | 652 | 0.79 | 0.84 | 67 | ZN, NAD, CRB |
| 2 | 642 | 0.79 | 0.84 | 67 | ZN, NAD, CRB |
| 3 | 640 | 0.68 | 0.77 | 66 | empty |
| 4 | 212 | 0.60 | 0.81 | 27 | empty |
| 5 | 183 | 0.59 | 0.81 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1842 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 1XAL · 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 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 Q6GGU4
- Elsewhere: RCSB PDB 1XAL · PDBe 1XAL · UniProt Q6GGU4
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