Research workbench
Se-crte C-term his-tag with ipp added
Analyse Se-crte C-term his-tag with ipp added in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MY6
- Type
- protein
- Length
- 573 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Farnesyl-diphosphate synthase
- EC
- 2.5.1.10
- UniProt
- Q31Q61
- Ligands
- IPE, MG, SO4, CL
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 75% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Farnesyl-diphosphate synthase (EC 2.5.1.10) | protein | 287 | 75% helix, 1% strand | Q31Q61 |
| B | Farnesyl-diphosphate synthase (EC 2.5.1.10) | protein | 286 | 75% helix, 1% strand | Q31Q61 |
Ligands and binding sites
- IPE · 3-methylbut-3-enyl trihydrogen diphosphate · ligand · chains A
- MG · Magnesium ion · metal · 6 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 552 | 0.69 | 0.79 | 50 | IPE, EDO, SO4, MG, CL |
| 2 | 429 | 0.65 | 0.78 | 44 | EDO, SO4, MG |
| 3 | 127 | 0.43 | 0.77 | 17 | empty |
| 4 | 145 | 0.41 | 0.74 | 28 | empty |
| 5 | 83 | 0.35 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1942 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 7MY6 · Se-CrtE C-term His-tag with IPP added · 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 Q31Q61
- Elsewhere: RCSB PDB 7MY6 · PDBe 7MY6 · UniProt Q31Q61
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