Research workbench
Structure of MA1831 from methanosarcina acetivorans in complex with farnesyl pyrophosphate and geranylgeranyl pyrophosphate.
Analyse Structure of MA1831 from methanosarcina acetivorans in complex with farnesyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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