MolNFT v1 · #181205 · protein
Apo structure of isopentenyl phosphate kinase from candidatus methanomethylophilus alvus
7LNV: “Apo structure of isopentenyl phosphate kinase from candidatus methanomethylophilus alvus”. X-ray diffraction, 10 pockets (best druggability 0.56). MolNFT v1 #181205 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7LNV
- Type
- protein
- Length
- 735 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isopentenyl phosphate kinase
- EC
- 2.7.4.26
- UniProt
- A0A3G3II74
- Pockets
- 10 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isopentenyl phosphate kinase (EC 2.7.4.26) | protein | 232 | 37% helix, 25% strand | A0A3G3II74 |
| B | Isopentenyl phosphate kinase (EC 2.7.4.26) | protein | 256 | 40% helix, 21% strand | A0A3G3II74 |
| C | Isopentenyl phosphate kinase (EC 2.7.4.26) | protein | 247 | 40% helix, 21% strand | A0A3G3II74 |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains A, B
- MLI · Malonate ion · additive · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 292 | 0.56 | 0.76 | 40 | MLI |
| 2 | 291 | 0.55 | 0.76 | 40 | MLI, GOL |
| 3 | 209 | 0.50 | 0.76 | 42 | GOL |
| 4 | 118 | 0.49 | 0.80 | 20 | empty |
| 5 | 199 | 0.48 | 0.75 | 23 | empty |
Interfaces
2 interfaces between chains.
- B–C · 1609 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 317 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7LNV · Apo Structure of 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 7LNV · PDBe 7LNV · UniProt A0A3G3II74
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