Research workbench
Geranyl pyrophosphate C6-methyltransferase beza
Analyse Geranyl pyrophosphate C6-methyltransferase beza in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7FBH
- Type
- protein
- Length
- 823 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beza
- Ligands
- LYS
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beza | protein | 276 | 49% helix, 20% strand | — |
| B | Beza | protein | 272 | 49% helix, 19% strand | — |
| C | Beza | protein | 275 | 49% helix, 19% strand | — |
Ligands and binding sites
- LYS · Lysine · ligand · 2 copies · chains B, C
- GOL · Glycerol · additive · 5 copies · chains A, B, C
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 3 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 3 copies · chains 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 628 | 0.77 | 0.83 | 60 | EPE, GOL |
| 2 | 570 | 0.76 | 0.83 | 60 | EPE |
| 3 | 529 | 0.75 | 0.83 | 57 | EPE |
| 4 | 528 | 0.69 | 0.79 | 68 | GOL |
| 5 | 351 | 0.64 | 0.79 | 39 | GOL |
Interfaces
3 interfaces between chains.
- A–C · 531 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 339 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 133 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7FBH · geranyl pyrophosphate C6-methyltransferase BezA · 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 7FBH · PDBe 7FBH
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