MolNFT v1 · #100999 · protein
Pantothenamide-bound pantothenate kinase from klebsiella pneumoniae
4NE2: “Pantothenamide-bound pantothenate kinase from klebsiella pneumoniae”. X-ray diffraction, 3 ligands (ADP, SH2, MG), 5 pockets (best druggability 0.80). MolNFT v1 #100999 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4NE2
- Type
- protein
- Length
- 605 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pantothenate kinase
- EC
- 2.7.1.33
- UniProt
- B5XYG3
- Ligands
- ADP, SH2, MG
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pantothenate kinase (EC 2.7.1.33) | protein | 304 | 49% helix, 17% strand | B5XYG3 |
| B | Pantothenate kinase (EC 2.7.1.33) | protein | 301 | 50% helix, 17% strand | B5XYG3 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- SH2 · (R)-N-(3-((2-(benzo[d][1,3]dioxol-5-yl)ethyl)amino)-3-oxopropyl)-2,4-dihydroxy-3,3-dimethylbutanamide · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 691 | 0.80 | 0.84 | 69 | ADP, SH2, MG |
| 2 | 488 | 0.77 | 0.84 | 52 | ADP, SH2, MG |
| 3 | 101 | 0.39 | 0.76 | 22 | empty |
| 4 | 62 | 0.37 | 0.79 | 15 | empty |
| 5 | 52 | 0.29 | 0.75 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 414 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
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 B5XYG3
- Elsewhere: RCSB PDB 4NE2 · PDBe 4NE2 · UniProt B5XYG3
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