Research workbench
Geranyl pyrophosphate C6-methyltransferase beza binding with S- adenosylhomocysteine
Analyse Geranyl pyrophosphate C6-methyltransferase beza binding with S… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7FBO
- Type
- protein
- Length
- 845 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beza
- Ligands
- SAH
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Beza | protein | 282 | 50% helix, 20% strand | — |
| B | Beza | protein | 281 | 49% helix, 19% strand | — |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 3 copies · chains A, B, C
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 358 | 0.82 | 0.91 | 63 | EPE, SAH |
| 2 | 408 | 0.81 | 0.89 | 65 | SAH, EPE |
| 3 | 409 | 0.81 | 0.89 | 63 | SAH, EPE |
| 4 | 361 | 0.60 | 0.77 | 44 | empty |
| 5 | 309 | 0.59 | 0.78 | 40 | empty |
Interfaces
3 interfaces between chains.
- A–C · 594 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 312 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 232 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7FBO · geranyl pyrophosphate C6-methyltransferase BezA binding with S-adenosylhomocysteine · 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
- Elsewhere: RCSB PDB 7FBO · PDBe 7FBO
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.