MolNFT v1 · #81953 · protein
Crystal structure of NAD kinase 1 from listeria monocytogenes in complex with 5'-N-propargylamino-5'-deoxyadenosine
3V7Y · Probable inorganic POLYPHOSPHATE/ATP-NAD kinase 1: “Crystal structure of NAD kinase 1 from listeria monocytogenes in complex with…”. X-ray diffraction, 1 ligand (A3N), 1 pocket (best druggability 0.55). MolNFT v1 #81953 on…
- PDB
- 3V7Y
- Type
- protein
- Length
- 258 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable inorganic POLYPHOSPHATE/ATP-NAD kinase 1
- EC
- 2.7.1.23
- UniProt
- Q8Y8D7
- Ligands
- A3N
- Pockets
- 1 · best druggability 0.55
Structure
x-ray diffraction · 1 distinct chain · 22% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable inorganic POLYPHOSPHATE/ATP-NAD kinase 1 (EC 2.7.1.23) | protein | 258 | 22% helix, 42% strand | Q8Y8D7 |
Ligands and binding sites
- A3N · 5'-deoxy-5'-(prop-2-yn-1-ylamino)adenosine · ligand · 2 copies · 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 | 106 | 0.55 | 0.84 | 23 | CIT |
Compared structures
- 3V7Y · Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8Y8D7 · AlphaFold monomer V2.0 prediction for NAD kinase 1 (Q8Y8D7) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 3V7Y · PDBe 3V7Y · UniProt Q8Y8D7
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