Research workbench
Structure of doubly prenylated YPT1:GDI complex
Analyse Structure of doubly prenylated YPT1:GDI complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2BCG
- Type
- protein
- Length
- 636 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Secretory pathway GDP dissociation inhibitor; GTP-binding protein YPT1
- UniProt
- P39958, P01123
- Ligands
- GER, GDP, MG
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Secretory pathway GDP dissociation inhibitor | protein | 442 | 36% helix, 25% strand | P39958 |
| Y | GTP-binding protein YPT1 | protein | 194 | 33% helix, 22% strand | P01123 |
Ligands and binding sites
- GER · Geran-8-yl geran · ligand · 2 copies · chains G
- GDP · Guanosine-5'-diphosphate · ligand · chains Y
- MG · Magnesium ion · metal · chains Y
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains Y
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 432 | 0.70 | 0.81 | 64 | empty |
| 2 | 720 | 0.70 | 0.77 | 64 | empty |
| 3 | 307 | 0.65 | 0.81 | 35 | GER |
| 4 | 363 | 0.62 | 0.78 | 44 | MG, GDP |
| 5 | 252 | 0.56 | 0.78 | 41 | empty |
Interfaces
1 interface between chains.
- G–Y · 1448 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 2BCG · Structure of doubly prenylated Ypt1:GDI complex · the same entry in another collection · chain G against G, TM-score 1.00
- P39958 · AlphaFold monomer V2.0 prediction for rab GDP-dissociation inhibitor (P39958) · a predicted model of the same protein · chain G against A, TM-score 0.97
- P01123 · AlphaFold monomer V2.0 prediction for GTP-binding protein YPT1 (P01123) · a predicted model of the same protein · chain Y against A, TM-score 0.84
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 P39958
- Every structure of UniProt P01123
- Elsewhere: RCSB PDB 2BCG · PDBe 2BCG · UniProt P39958 · UniProt P01123
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