MolNFT v1 · #116568 · protein
Crystal structure of NAD kinase 1 from listeria monocytogenes in complex with a novel inhibitor
5DHR: “Crystal structure of NAD kinase 1 from listeria monocytogenes in complex with a novel inhibitor”. X-ray diffraction, 1 ligand (5AJ), 11 pockets (best druggability 0.85). MolNFT v1 #116568 on GenesisL1: 3D structure, binding sites…
- PDB
- 5DHR
- Type
- protein
- Length
- 1,043 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
- 5AJ
- Pockets
- 11 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 21% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD kinase 1 (EC 2.7.1.23) | protein | 263 | 22% helix, 42% strand | Q8Y8D7 |
| B | NAD kinase 1 (EC 2.7.1.23) | protein | 262 | 20% helix, 39% strand | Q8Y8D7 |
| C | NAD kinase 1 (EC 2.7.1.23) | protein | 259 | 22% helix, 42% strand | Q8Y8D7 |
| D | NAD kinase 1 (EC 2.7.1.23) | protein | 259 | 20% helix, 41% strand | Q8Y8D7 |
Ligands and binding sites
- 5AJ · 5'-azido-8-[(2-{[2-(1H-benzimidazol-2-yl)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 · chains A, C
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 | 917 | 0.85 | 0.87 | 90 | GOL |
| 2 | 1179 | 0.77 | 0.79 | 99 | 5AJ |
| 3 | 571 | 0.72 | 0.80 | 47 | 5AJ |
| 4 | 522 | 0.68 | 0.78 | 41 | 5AJ |
| 5 | 152 | 0.64 | 0.86 | 23 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1310 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1288 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 779 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 738 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 71 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5DHR · Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with a novel… · 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 5DHR · PDBe 5DHR · UniProt Q8Y8D7
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