Research workbench
Structure of MA1831 from methanosarcina acetivorans in complex with dimethylallyl diphosphate.
Analyse Structure of MA1831 from methanosarcina acetivorans in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VQA
- Type
- protein
- Length
- 406 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Di-trans-poly-cis-decaprenylcistransferase
- UniProt
- Q8TPS4
- Ligands
- DMA, MG, SO4
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Di-trans-poly-cis-decaprenylcistransferase | protein | 201 | 40% helix, 19% strand | Q8TPS4 |
| B | Di-trans-poly-cis-decaprenylcistransferase | protein | 205 | 40% helix, 20% strand | Q8TPS4 |
Ligands and binding sites
- DMA · Dimethylallyl diphosphate · ligand · 4 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 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 | 329 | 0.75 | 0.86 | 44 | DMA, MG |
| 2 | 335 | 0.74 | 0.85 | 39 | DMA, MG |
| 3 | 71 | 0.43 | 0.80 | 11 | SO4 |
| 4 | 51 | 0.30 | 0.76 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1190 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 7VQA · Structure of MA1831 from Methanosarcina acetivorans in complex with dimethylallyl… · 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 7VQA · PDBe 7VQA · UniProt Q8TPS4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.