MolNFT v1 · #189678 · protein
Structure of MA1831 from methanosarcina acetivorans in complex with farnesyl pyrophosphate and geranylgeranyl pyrophosphate.
7VQD · Di-trans-poly-cis-decaprenylcistransferase: “Structure of MA1831 from methanosarcina acetivorans in complex with farnesyl pyrophosphate and geranylgeranyl…”. X-ray diffraction, 3 ligands (FPP, BUE, SO4), 3 pockets (best druggability…
- PDB
- 7VQD
- Type
- protein
- Length
- 408 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Di-trans-poly-cis-decaprenylcistransferase
- UniProt
- Q8TPS4
- Ligands
- FPP, BUE, SO4
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Di-trans-poly-cis-decaprenylcistransferase | protein | 204 | 40% helix, 16% strand | Q8TPS4 |
| B | Di-trans-poly-cis-decaprenylcistransferase | protein | 204 | 39% helix, 18% strand | Q8TPS4 |
Ligands and binding sites
- FPP · Farnesyl diphosphate · ligand · chains A
- BUE · NerylNeryl pyrophosphate · ligand · chains B
- SO4 · Sulfate ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 342 | 0.75 | 0.86 | 40 | BUE |
| 2 | 294 | 0.74 | 0.87 | 32 | FPP, SO4 |
| 3 | 61 | 0.26 | 0.72 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1383 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 7VQD · 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 7VQD · PDBe 7VQD · UniProt Q8TPS4
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