MolNFT v1 · #16322 · protein
Crystal structure of 3-dehydroquinate synthase (dhqs) in complex with ZN2+ and NAD
1NVE: “Crystal structure of 3-dehydroquinate synthase (dhqs) in complex with ZN2+ and NAD”. X-ray diffraction, 3 ligands (NAD, ZN, CL), 12 pockets (best druggability 0.74). MolNFT v1 #16322 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1NVE
- Type
- protein
- Length
- 1,519 residues
- Chains
- 4
- 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, ZN, CL
- Pockets
- 12 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-dehydroquinate synthase (EC 4.2.3.4) | protein | 378 | 52% helix, 17% strand | P07547 |
| B | 3-dehydroquinate synthase (EC 4.2.3.4) | protein | 383 | 52% helix, 17% strand | P07547 |
| C | 3-dehydroquinate synthase (EC 4.2.3.4) | protein | 377 | 52% helix, 16% strand | P07547 |
| D | 3-dehydroquinate synthase (EC 4.2.3.4) | protein | 381 | 52% helix, 17% strand | P07547 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1033 | 0.74 | 0.77 | 83 | NAD |
| 2 | 808 | 0.72 | 0.77 | 63 | NAD |
| 3 | 746 | 0.71 | 0.78 | 59 | ZN, NAD |
| 4 | 732 | 0.71 | 0.78 | 58 | ZN, NAD |
| 5 | 71 | 0.57 | 0.88 | 16 | CL |
Interfaces
2 interfaces between chains.
- C–D · 984 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 943 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 1NVE · Crystal structure of 3-dehydroquinate synthase (DHQS) in complex with ZN2+ and NAD · the same entry in another collection · chain D against D, TM-score 1.00
- P07547 · AlphaFold monomer V2.0 prediction for pentafunctional arom polypeptide (P07547) · a predicted model of the same protein · chain A 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 1NVE · PDBe 1NVE · UniProt P07547
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