MolNFT v1 · #181204 · protein
Ternary complex of the isopentenyl phosphate kinase from candidatus methanomethylophilus alvus bound to isopentenyl monophosphate and ATP
7LNU: “Ternary complex of the isopentenyl phosphate kinase from candidatus methanomethylophilus alvus bound to…”. X-ray diffraction, 4 ligands (IP8, ADP, ATP), 5 pockets (best druggability 0.61). MolNFT v1 #181204 on GenesisL1: 3D…
- PDB
- 7LNU
- Type
- protein
- Length
- 500 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isopentenyl phosphate kinase
- EC
- 2.7.4.26
- UniProt
- A0A3G3II74
- Ligands
- IP8, ADP, ATP, IPE
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isopentenyl phosphate kinase (EC 2.7.4.26) | protein | 239 | 39% helix, 24% strand | A0A3G3II74 |
| B | Isopentenyl phosphate kinase (EC 2.7.4.26) | protein | 261 | 39% helix, 21% strand | A0A3G3II74 |
Ligands and binding sites
- IP8 · Isopentenyl phosphate · ligand · 2 copies · chains A, B
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- IPE · 3-methylbut-3-enyl trihydrogen diphosphate · ligand · chains A
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 | 357 | 0.61 | 0.78 | 43 | IP8, ADP |
| 2 | 254 | 0.59 | 0.79 | 38 | IP8, ADP, ATP, IPE |
| 3 | 87 | 0.33 | 0.74 | 19 | empty |
| 4 | 70 | 0.32 | 0.75 | 18 | empty |
| 5 | 52 | 0.25 | 0.73 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1630 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 7LNU · Ternary complex of the Isopentenyl Phosphate Kinase from Candidatus methanomethylophilus… · 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 A0A3G3II74
- Elsewhere: RCSB PDB 7LNU · PDBe 7LNU · UniProt A0A3G3II74
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.