MolNFT v1 · #116570 · protein
Crystal structure of NAD kinase 1 from listeria monocytogenes in complex with a novel inhibitor
5DHT: “Crystal structure of NAD kinase 1 from listeria monocytogenes in complex with a novel inhibitor”. X-ray diffraction, 1 ligand (5A9), 11 pockets (best druggability 0.84). MolNFT v1 #116570 on GenesisL1: 3D structure, binding sites…
- PDB
- 5DHT
- Type
- protein
- Length
- 1,032 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD kinase 1
- EC
- 2.7.1.23
- UniProt
- Q8Y8D7
- Ligands
- 5A9
- Pockets
- 11 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 22% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD kinase 1 (EC 2.7.1.23) | protein | 263 | 22% helix, 40% strand | Q8Y8D7 |
| B | NAD kinase 1 (EC 2.7.1.23) | protein | 259 | 22% helix, 41% strand | Q8Y8D7 |
| C | NAD kinase 1 (EC 2.7.1.23) | protein | 260 | 22% helix, 42% strand | Q8Y8D7 |
| D | NAD kinase 1 (EC 2.7.1.23) | protein | 250 | 22% helix, 38% strand | Q8Y8D7 |
Ligands and binding sites
- 5A9 · 5'-azido-8-[(2-{[2-(3-bromophenyl)ethyl]amino}-2-oxoethyl)sulfanyl]-5'-deoxyadenosine · ligand · 4 copies · chains A, C, B, D
- CIT · Citric acid · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 883 | 0.84 | 0.86 | 93 | GOL |
| 2 | 283 | 0.73 | 0.87 | 38 | 5A9 |
| 3 | 243 | 0.71 | 0.86 | 38 | 5A9 |
| 4 | 498 | 0.67 | 0.78 | 47 | 5A9 |
| 5 | 161 | 0.65 | 0.86 | 29 | 5A9 |
Interfaces
6 interfaces between chains.
- A–B · 1285 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1274 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 804 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 800 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 105 Ų buried · 1 hydrogen bond · protein-protein
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 5DHT · PDBe 5DHT · UniProt Q8Y8D7
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