Research workbench
Crystal structure of YPT31 in complex with yeast rab-gdi
Analyse Crystal structure of YPT31 in complex with yeast rab-gdi in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CPJ
- Type
- protein
- Length
- 602 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rab GDP-dissociation inhibitor; GTP-binding protein YPT31/YPT8
- UniProt
- P39958, P38555
- Ligands
- GDP, MG, CL
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Rab GDP-dissociation inhibitor | protein | 438 | 36% helix, 24% strand | P39958 |
| B | GTP-binding protein YPT31/YPT8 | protein | 164 | 35% helix, 25% strand | P38555 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · chains B
- MG · Magnesium ion · metal · chains B
- CL · Chloride ion · ion · 2 copies · chains G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 300 | 0.62 | 0.80 | 38 | empty |
| 2 | 244 | 0.62 | 0.80 | 31 | empty |
| 3 | 256 | 0.56 | 0.77 | 45 | empty |
| 4 | 166 | 0.54 | 0.80 | 31 | empty |
| 5 | 107 | 0.49 | 0.80 | 18 | empty |
Interfaces
1 interface between chains.
- G–B · 1205 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 3CPJ · Crystal structure of Ypt31 in complex with yeast Rab-GDI · 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
- P38555 · AlphaFold monomer V2.0 prediction for GTP-binding protein YPT31/YPT8 (P38555) · a predicted model of the same protein · chain B against A, TM-score 0.93
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 P38555
- Elsewhere: RCSB PDB 3CPJ · PDBe 3CPJ · UniProt P39958 · UniProt P38555
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