Research workbench
Structure of MA1831 from Methanosarcina acetivorans in complex with pyrophosphate
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
- 7VQC
- Type
- protein
- Length
- 407 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.45
- Source
- Methanosarcina acetivorans (strain ATCC 35395 / DSM 2834 / JCM 12185 / C2A)
- Molecule
- Di-trans-poly-cis-decaprenylcistransferase
- UniProt
- Q8TPS4
- Ligands
- POP, SO4
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · resolution 2.45 · 2 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Di-trans-poly-cis-decaprenylcistransferase | protein | 204 | 41% helix, 19% strand | Q8TPS4 |
| B | Di-trans-poly-cis-decaprenylcistransferase | protein | 203 | 41% helix, 20% strand | Q8TPS4 |
Ligands and binding sites
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 | 336 | 0.78 | 0.88 | 47 | SO4 |
| 2 | 330 | 0.74 | 0.86 | 40 | POP |
| 3 | 57 | 0.32 | 0.76 | 18 | empty |
| 4 | 62 | 0.28 | 0.73 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1287 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 7VQC · Structure of MA1831 from methanosarcina acetivorans in complex with pyrophosphate · 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 7VQC · PDBe 7VQC · UniProt Q8TPS4
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