Research workbench
I146A mutant of the isopentenyl phosphate kinase from candidatus methanomethylophilus alvus
Analyse I146A mutant of the isopentenyl phosphate kinase from candidatus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LNX
- Type
- protein
- Length
- 481 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
- ADP, Y7D, WOG
- Pockets
- 4 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isopentenyl phosphate kinase (EC 2.7.4.26) | protein | 234 | 36% helix, 23% strand | A0A3G3II74 |
| B | Isopentenyl phosphate kinase (EC 2.7.4.26) | protein | 247 | 39% helix, 22% strand | A0A3G3II74 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- Y7D · (2Z)-3-methylhept-2-en-1-yl trihydrogen diphosphate · ligand · chains A
- WOG · (2E)-3-methylhept-2-en-1-yl dihydrogen phosphate · ligand · chains B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 366 | 0.64 | 0.79 | 47 | ADP, WOG |
| 2 | 258 | 0.57 | 0.78 | 43 | ADP, Y7D |
| 3 | 95 | 0.39 | 0.76 | 22 | GOL |
| 4 | 65 | 0.31 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1628 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 7LNX · I146A mutant 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 7LNX · PDBe 7LNX · UniProt A0A3G3II74
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