MolNFT v1 · #162681 · protein
Crystal structure of NAD kinase 1 from listeria monocytogenes in complexe with an inhibitor
6RG6: “Crystal structure of NAD kinase 1 from listeria monocytogenes in complexe with an inhibitor”. X-ray diffraction, 1 ligand (K3B), 1 pocket (best druggability 0.59). MolNFT v1 #162681 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6RG6
- Type
- protein
- Length
- 258 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD kinase 1
- EC
- 2.7.1.23
- UniProt
- Q8Y8D7
- Ligands
- K3B
- Pockets
- 1 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 20% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD kinase 1 (EC 2.7.1.23) | protein | 258 | 20% helix, 39% strand | Q8Y8D7 |
Ligands and binding sites
- K3B · (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-[3-(6-azanyl-9~{H}-purin-8-yl)prop-2-ynoxymethyl]oxolane-3,4-diol · ligand · chains A
- CIT · Citric acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 121 | 0.59 | 0.85 | 21 | CIT |
Compared structures
- 6RG6 · Crystal structure of NAD kinase 1 from Listeria monocytogenes in complexe with an… · 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 Q8Y8D7
- Elsewhere: RCSB PDB 6RG6 · PDBe 6RG6 · UniProt Q8Y8D7
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