Research workbench
Crystal structure of apo ggtaseiii
Analyse Crystal structure of apo ggtaseiii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6J6X
- Type
- protein
- Length
- 576 residues
- Chains
- 2
- 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
- UniProt
- Q7Z6K3, P53611
- Ligands
- MG
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 59% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein prenyltransferase alpha subunit repeat-containing protein 1 | protein | 278 | 67% helix, 4% strand | Q7Z6K3 |
| B | Geranylgeranyl transferase type-2 subunit beta (EC 2.5.1.60) | protein | 298 | 51% helix, 5% strand | P53611 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 947 | 0.79 | 0.81 | 62 | empty |
| 2 | 423 | 0.62 | 0.76 | 33 | MPD |
| 3 | 310 | 0.62 | 0.79 | 39 | empty |
| 4 | 125 | 0.56 | 0.83 | 28 | empty |
| 5 | 154 | 0.50 | 0.78 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1523 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (artifact).
Compared structures
- 6J6X · Crystal structure of apo GGTaseIII · 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 0.97
- Q7Z6K3 · AlphaFold monomer V2.0 prediction for protein prenyltransferase alpha subunit… · a predicted model of the same protein · chain A against A, TM-score 0.96
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
- Elsewhere: RCSB PDB 6J6X · PDBe 6J6X · UniProt Q7Z6K3 · UniProt P53611
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