MolNFT v1 · #117814 · protein
Crystal structure of NAD kinase P252D mutant from listeria monocytogenes
5EJG · NAD kinase 1: “Crystal structure of NAD kinase P252D mutant from listeria monocytogenes”. X-ray diffraction, 11 pockets (best druggability 0.82). MolNFT v1 #117814 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5EJG
- Type
- protein
- Length
- 977 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
- 11 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 19% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD kinase 1 (EC 2.7.1.23) | protein | 253 | 21% helix, 37% strand | Q8Y8D7 |
| B | NAD kinase 1 (EC 2.7.1.23) | protein | 254 | 21% helix, 41% strand | Q8Y8D7 |
| C | NAD kinase 1 (EC 2.7.1.23) | protein | 218 | 14% helix, 39% strand | Q8Y8D7 |
| D | NAD kinase 1 (EC 2.7.1.23) | protein | 252 | 18% helix, 33% strand | Q8Y8D7 |
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 736 | 0.82 | 0.86 | 81 | empty |
| 2 | 640 | 0.69 | 0.77 | 44 | empty |
| 3 | 670 | 0.66 | 0.75 | 47 | empty |
| 4 | 143 | 0.60 | 0.84 | 28 | empty |
| 5 | 306 | 0.60 | 0.77 | 32 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1331 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1299 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 628 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 594 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 68 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5EJG · Crystal structure of NAD kinase P252D 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 5EJG · PDBe 5EJG · UniProt Q8Y8D7
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