Research workbench
Complex of GGTaseIII and full-length Ykt6
Analyse Complex of GGTaseIII and full-length Ykt6 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6J74
- Type
- protein
- Length
- 796 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.212
- Source
- Homo sapiens
- Molecule
- Protein prenyltransferase alpha subunit repeat-containing protein 1; Geranylgeranyl…
- EC
- 2.5.1.60, 2.3.1.-
- UniProt
- Q7Z6K3, P53611, O15498
- Ligands
- ZN, PO4
- Pockets
- 12 · best druggability 0.84
Structure
x-ray diffraction · resolution 3.212 · 3 distinct chains · 53% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein prenyltransferase alpha subunit repeat-containing protein 1 | protein | 276 | 67% helix, 5% strand | Q7Z6K3 |
| B | Geranylgeranyl transferase type-2 subunit beta (EC 2.5.1.60) | protein | 328 | 50% helix, 5% strand | P53611 |
| C | Synaptobrevin homolog YKT6 (EC 2.3.1.-) | protein | 192 | 36% helix, 21% strand | O15498 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 706 | 0.84 | 0.88 | 83 | PO4 |
| 2 | 290 | 0.75 | 0.87 | 39 | empty |
| 3 | 171 | 0.61 | 0.83 | 25 | empty |
| 4 | 126 | 0.47 | 0.78 | 13 | empty |
| 5 | 78 | 0.44 | 0.80 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1797 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 733 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 398 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6J74 · Complex of ggtaseiii and full-length YKT6 · 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
- 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
- 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
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 6J74 · PDBe 6J74 · UniProt Q7Z6K3 · UniProt P53611 · UniProt O15498
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