MolNFT v1 · #16179 · protein
Crystal structure of 3-dehydroquinate synthase (dhqs) in complex with ZN2+, NAD and carbaphosphonate
1NR5: “Crystal structure of 3-dehydroquinate synthase (dhqs) in complex with ZN2+, NAD and carbaphosphonate”. X-ray diffraction, 5 ligands (NAD, CRB, ZN), 7 pockets (best druggability 0.78). MolNFT v1 #16179 on GenesisL1: 3D structure…
- PDB
- 1NR5
- Type
- protein
- Length
- 780 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
- P07547
- Ligands
- NAD, CRB, ZN, CO, CL
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-dehydroquinate synthase (EC 4.2.3.4) | protein | 390 | 52% helix, 17% strand | P07547 |
| B | 3-dehydroquinate synthase (EC 4.2.3.4) | protein | 390 | 52% helix, 17% strand | P07547 |
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
- CO · Cobalt (II) ion · metal · chains B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 545 | 0.78 | 0.85 | 60 | ZN, NAD, CRB |
| 2 | 545 | 0.77 | 0.84 | 63 | NAD, CRB |
| 3 | 267 | 0.67 | 0.83 | 41 | empty |
| 4 | 145 | 0.44 | 0.76 | 26 | empty |
| 5 | 58 | 0.35 | 0.77 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 594 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 1NR5 · Crystal structure of 3-dehydroquinate synthase (DHQS) in complex with ZN2+, NAD and… · the same entry in another collection · chain A against A, TM-score 1.00
- P07547 · AlphaFold monomer V2.0 prediction for pentafunctional arom polypeptide (P07547) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P07547
- Elsewhere: RCSB PDB 1NR5 · PDBe 1NR5 · UniProt P07547
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