MolNFT v1 · #158832 · protein
Crystal structure of GGTASE3-FBXL2-SKP1 complex
6O60 · Protein prenyltransferase alpha subunit repeat-containing…: “Crystal structure of GGTASE3-FBXL2-SKP1 complex”. X-ray diffraction, 1 ligand (ZN), 15 pockets (best druggability 0.82). MolNFT v1 #158832 on GenesisL1: 3D structure…
- PDB
- 6O60
- Type
- protein
- Length
- 1,157 residues
- Chains
- 4
- 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, Q9UKC9, P63208
- Ligands
- ZN
- Pockets
- 15 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 53% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein prenyltransferase alpha subunit repeat-containing protein 1 | protein | 300 | 71% helix, 5% strand | Q7Z6K3 |
| B | Geranylgeranyl transferase type-2 subunit beta (EC 2.5.1.60) | protein | 320 | 53% helix, 5% strand | P53611 |
| C | F-BOX/LRR-repeat protein 2 | protein | 389 | 41% helix, 11% strand | Q9UKC9 |
| D | S-phase kinase-associated protein 1 | protein | 148 | 52% helix, 8% strand | P63208 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 825 | 0.82 | 0.84 | 78 | empty |
| 2 | 716 | 0.73 | 0.79 | 75 | empty |
| 3 | 796 | 0.72 | 0.77 | 62 | empty |
| 4 | 103 | 0.64 | 0.88 | 18 | empty |
| 5 | 53 | 0.59 | 0.91 | 17 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1992 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1900 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 1359 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 102 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 83 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6O60 · Crystal structure of GGTase3-FBXL2-SKP1 complex · the same entry in another collection · chain D against D, TM-score 1.00
- Q7Z6K3 · AlphaFold monomer V2.0 prediction for protein prenyltransferase alpha subunit… · a predicted model of the same protein · chain A against A, TM-score 0.99
- 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 0.98
- Q9UKC9 · AlphaFold monomer V2.0 prediction for F-BOX/LRR-repeat protein 2 (Q9UKC9) · a predicted model of the same protein · chain C against A, TM-score 0.95
- P63208 · AlphaFold monomer V2.0 prediction for S-phase kinase-associated protein 1 (P63208) · a predicted model of the same protein · chain D against A, TM-score 0.92
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 Q9UKC9
- Every structure of UniProt P63208
- Elsewhere: RCSB PDB 6O60 · PDBe 6O60 · UniProt Q7Z6K3 · UniProt P53611 · UniProt Q9UKC9 · UniProt P63208
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