Research workbench
I74A mutant of the isopentenyl phosphate kinase from candidatus methanomethylophilus alvus
Analyse I74A 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
- 7N9D
- Type
- protein
- Length
- 509 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, 0XI
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isopentenyl phosphate kinase (EC 2.7.4.26) | protein | 253 | 41% helix, 22% strand | A0A3G3II74 |
| B | Isopentenyl phosphate kinase (EC 2.7.4.26) | protein | 256 | 40% helix, 21% strand | A0A3G3II74 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- 0XI · (2E)-3-phenylbut-2-en-1-yl dihydrogen phosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 296 | 0.77 | 0.89 | 49 | ADP, 0XI |
| 2 | 254 | 0.70 | 0.85 | 44 | ADP, 0XI |
| 3 | 103 | 0.69 | 0.92 | 32 | empty |
| 4 | 143 | 0.43 | 0.75 | 20 | empty |
| 5 | 96 | 0.35 | 0.74 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 1576 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 7N9D · I74A mutant of the isopentenyl phosphate kinase from Candidatus methanomethylophilus alvus · 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 7N9D · PDBe 7N9D · UniProt A0A3G3II74
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.