Research workbench
Crystal structure of a putative farnesyl-diphosphate synthase from Marinomonas sp. MED121 (Target EFI-501980)
Analyse Crystal structure of a putative farnesyl-diphosphate synthase from Marinomonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4F62
- Type
- protein
- Length
- 522 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.101
- Source
- Marinomonas sp. MED121
- Molecule
- Geranyltranstransferase
- EC
- 2.5.1.-
- UniProt
- A3YCB7
- Ligands
- SO4, CL
- Pockets
- 4 · best druggability 0.61
Structure
x-ray diffraction · resolution 2.101 · 2 distinct chains · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Geranyltranstransferase (EC 2.5.1.-) | protein | 267 | 79% helix, 0% strand | A3YCB7 |
| B | Geranyltranstransferase (EC 2.5.1.-) | protein | 255 | 79% helix, 0% strand | A3YCB7 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains A
- CL · Chloride ion · ion · chains A, B
- GOL · Glycerol · additive · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 318 | 0.61 | 0.78 | 50 | GOL |
| 2 | 278 | 0.54 | 0.75 | 39 | GOL |
| 3 | 76 | 0.39 | 0.78 | 19 | empty |
| 4 | 73 | 0.34 | 0.75 | 22 | GOL |
Interfaces
1 interface between chains.
- A–B · 2179 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 4F62 · Crystal structure of a putative farnesyl-diphosphate synthase from marinomonas sp. MED121… · 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 A3YCB7
- Elsewhere: RCSB PDB 4F62 · PDBe 4F62 · UniProt A3YCB7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.