MolNFT v1 · #117813 · protein
Crystal structure of NAD kinase P101A mutant from listeria monocytogenes
5EJF · NAD kinase 1: “Crystal structure of NAD kinase P101A mutant from listeria monocytogenes”. X-ray diffraction, 8 pockets (best druggability 0.81). MolNFT v1 #117813 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5EJF
- Type
- protein
- Length
- 1,008 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
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 23% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD kinase 1 (EC 2.7.1.23) | protein | 254 | 24% helix, 42% strand | Q8Y8D7 |
| B | NAD kinase 1 (EC 2.7.1.23) | protein | 253 | 22% helix, 42% strand | Q8Y8D7 |
| C | NAD kinase 1 (EC 2.7.1.23) | protein | 251 | 22% helix, 42% strand | Q8Y8D7 |
| D | NAD kinase 1 (EC 2.7.1.23) | protein | 250 | 24% helix, 42% strand | Q8Y8D7 |
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 649 | 0.81 | 0.86 | 76 | empty |
| 2 | 265 | 0.71 | 0.86 | 44 | empty |
| 3 | 191 | 0.67 | 0.86 | 33 | empty |
| 4 | 242 | 0.64 | 0.82 | 29 | empty |
| 5 | 104 | 0.57 | 0.85 | 23 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1299 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1274 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 639 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 566 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 73 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5EJF · Crystal structure of NAD kinase P101A mutant from Listeria monocytogenes · 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 5EJF · PDBe 5EJF · UniProt Q8Y8D7
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