Research workbench
Complex of ggtaseiii, farnesyl-YKT6 (C-terminal methylated), and ggpp
Analyse Complex of ggtaseiii, farnesyl-YKT6 (C-terminal methylated), and ggpp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6J7F
- Type
- protein
- Length
- 806 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
- FAR, GER, DPO
- Pockets
- 10 · best druggability 0.87
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 | 282 | 67% helix, 5% strand | Q7Z6K3 |
| B | Geranylgeranyl transferase type-2 subunit beta (EC 2.5.1.60) | protein | 329 | 51% helix, 5% strand | P53611 |
| C | Synaptobrevin homolog YKT6 (EC 2.3.1.-) | protein | 195 | 31% helix, 21% strand | O15498 |
Ligands and binding sites
- FAR · Farnesyl · ligand · chains B, C
- GER · Geran-8-yl geran · ligand · chains B, C
- DPO · Diphosphate · ligand · chains A, B, C
- TLA · L(+)-tartaric acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 622 | 0.87 | 0.91 | 69 | GER, DPO |
| 2 | 132 | 0.69 | 0.90 | 23 | FAR |
| 3 | 108 | 0.67 | 0.89 | 20 | empty |
| 4 | 87 | 0.66 | 0.92 | 26 | empty |
| 5 | 85 | 0.61 | 0.89 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1846 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 975 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 710 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 lipid, 1 modified (farnesylation, geranylgeranylation, nonstandard).
Compared structures
- 6J7F · Complex of GGTaseIII, farnesyl-Ykt6 (C-terminal methylated), 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 0.97
- O15498 · AlphaFold monomer V2.0 prediction for synaptobrevin homolog YKT6 (O15498) · a predicted model of the same protein · chain C against A, TM-score 0.96
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 6J7F · PDBe 6J7F · UniProt Q7Z6K3 · UniProt P53611 · UniProt O15498
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