Research workbench
RV1086 native
Analyse RV1086 native in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VFW
- Type
- protein
- Length
- 454 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Short-chain Z-isoprenyl diphosphate synthetase
- EC
- 2.5.1.68
- UniProt
- O53434
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Short-chain Z-isoprenyl diphosphate synthetase (EC 2.5.1.68) | protein | 227 | 48% helix, 15% strand | O53434 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 87 | 0.77 | 0.98 | 31 | empty |
| 2 | 207 | 0.64 | 0.83 | 29 | SO4 |
| 3 | 205 | 0.64 | 0.83 | 29 | SO4 |
| 4 | 60 | 0.30 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1902 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 2VFW · Rv1086 native · 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 O53434
- Elsewhere: RCSB PDB 2VFW · PDBe 2VFW · UniProt O53434
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