Research workbench
Ternary complex of the isopentenyl phosphate kinase from candidatus methanomethylophilus alvus bound to benzyl monophosphate and ATP
Analyse Ternary complex 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
- 7LNT
- Type
- protein
- Length
- 498 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
- WZT, ADP
- Pockets
- 5 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isopentenyl phosphate kinase (EC 2.7.4.26) | protein | 238 | 39% helix, 24% strand | A0A3G3II74 |
| B | Isopentenyl phosphate kinase (EC 2.7.4.26) | protein | 260 | 40% helix, 21% strand | A0A3G3II74 |
Ligands and binding sites
- WZT · (phenylmethyl) dihydrogen phosphate · ligand · 2 copies · chains A, B
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 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 | 399 | 0.63 | 0.78 | 51 | WZT, ADP |
| 2 | 254 | 0.59 | 0.79 | 41 | WZT, ADP |
| 3 | 76 | 0.34 | 0.75 | 17 | empty |
| 4 | 83 | 0.32 | 0.73 | 18 | empty |
| 5 | 64 | 0.28 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1624 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 7LNT · 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 7LNT · PDBe 7LNT · UniProt A0A3G3II74
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