MolNFT v1 · #117859 · protein
Structure of 3-dehydroquinate synthase from acinetobacter baumannii in complex with NAD
5EKS: “Structure of 3-dehydroquinate synthase from acinetobacter baumannii in complex with NAD”. X-ray diffraction, 2 ligands (NAD, MG), 4 pockets (best druggability 0.80). MolNFT v1 #117859 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5EKS
- Type
- protein
- Length
- 709 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
- V5V8R5
- Ligands
- NAD, MG
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-dehydroquinate synthase (EC 4.2.3.4) | protein | 355 | 54% helix, 20% strand | V5V8R5 |
| B | 3-dehydroquinate synthase (EC 4.2.3.4) | protein | 354 | 54% helix, 20% strand | V5V8R5 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 933 | 0.80 | 0.82 | 83 | NAD |
| 2 | 929 | 0.73 | 0.77 | 80 | NAD |
| 3 | 340 | 0.56 | 0.75 | 39 | empty |
| 4 | 176 | 0.42 | 0.73 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 435 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5EKS · Structure of 3-dehydroquinate synthase from Acinetobacter baumannii in complex with NAD · the same entry in another collection · 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 V5V8R5
- Elsewhere: RCSB PDB 5EKS · PDBe 5EKS · UniProt V5V8R5
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