MolNFT v1 · #189674 · protein
Structure of MA1831 from methanosarcina acetivorans in complex with farnesyl thiopyrophosphate and isopentyl S-thiolodiphosphate
7VQ9 · Di-trans-poly-cis-decaprenylcistransferase: “Structure of MA1831 from methanosarcina acetivorans in complex with farnesyl thiopyrophosphate and isopentyl…”. X-ray diffraction, 4 ligands (ISY, FPS, MG), 4 pockets (best druggability…
- PDB
- 7VQ9
- Type
- protein
- Length
- 409 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Di-trans-poly-cis-decaprenylcistransferase
- UniProt
- Q8TPS4
- Ligands
- ISY, FPS, MG, SO4
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Di-trans-poly-cis-decaprenylcistransferase | protein | 206 | 42% helix, 19% strand | Q8TPS4 |
| B | Di-trans-poly-cis-decaprenylcistransferase | protein | 203 | 41% helix, 20% strand | Q8TPS4 |
Ligands and binding sites
- ISY · 3-methylbut-3-enylsulfanyl(phosphonooxy)phosphinic acid · ligand · 2 copies · chains A, B
- FPS · S-[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trienyl] trihydrogen thiodiphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, 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 | 330 | 0.75 | 0.86 | 42 | ISY, FPS, MG |
| 2 | 333 | 0.74 | 0.85 | 39 | ISY, FPS, MG |
| 3 | 63 | 0.42 | 0.81 | 11 | empty |
| 4 | 52 | 0.26 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1321 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 7VQ9 · Structure of MA1831 from Methanosarcina acetivorans in complex with farnesyl… · 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 Q8TPS4
- Elsewhere: RCSB PDB 7VQ9 · PDBe 7VQ9 · UniProt Q8TPS4
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