Research workbench
Complex of ggtaseiii, farnesyl-YKT6, and ggpp
Analyse Complex of ggtaseiii, farnesyl-YKT6, and ggpp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6J7X
- Type
- protein
- Length
- 795 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein prenyltransferase alpha subunit repeat-containing protein 1; Geranylgeranyl…
- EC
- 2.5.1.60, 2.3.1.-
- UniProt
- Q7Z6K3, P53611, O15498
- Ligands
- GRG
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein prenyltransferase alpha subunit repeat-containing protein 1 | protein | 276 | 66% helix, 5% strand | Q7Z6K3 |
| B | Geranylgeranyl transferase type-2 subunit beta (EC 2.5.1.60) | protein | 327 | 51% helix, 6% strand | P53611 |
| C | Synaptobrevin homolog YKT6 (EC 2.3.1.-) | protein | 192 | 33% helix, 20% strand | O15498 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 707 | 0.81 | 0.84 | 59 | GRG, FMT |
| 2 | 813 | 0.79 | 0.82 | 85 | empty |
| 3 | 196 | 0.64 | 0.83 | 24 | empty |
| 4 | 234 | 0.51 | 0.75 | 28 | empty |
| 5 | 128 | 0.49 | 0.79 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1856 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 823 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 388 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6J7X · Complex of GGTaseIII, farnesyl-Ykt6, and GGPP · the same entry in another collection · chain A against A, TM-score 1.00
- P53611 · AlphaFold monomer V2.0 prediction for geranylgeranyl transferase type-2 subunit beta… · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q7Z6K3 · AlphaFold monomer V2.0 prediction for protein prenyltransferase alpha subunit… · a predicted model of the same protein · chain A against A, TM-score 0.98
- O15498 · AlphaFold monomer V2.0 prediction for synaptobrevin homolog YKT6 (O15498) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 Q7Z6K3
- Every structure of UniProt P53611
- Every structure of UniProt O15498
- Elsewhere: RCSB PDB 6J7X · PDBe 6J7X · UniProt Q7Z6K3 · UniProt P53611 · UniProt O15498
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