MolNFT v1 · #38742 · protein
Co-crystal structure of ypka-RAC1
2H7V · Migration-inducing protein 5: “Co-crystal structure of ypka-RAC1”. X-ray diffraction, 2 ligands (GDP, MG), 11 pockets (best druggability 0.61). MolNFT v1 #38742 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2H7V
- Type
- protein
- Length
- 893 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Migration-inducing protein 5; Protein kinase ypka
- UniProt
- P63000, Q05608
- Ligands
- GDP, MG
- Pockets
- 11 · best druggability 0.61
Structure
x-ray diffraction · 4 distinct chains · 64% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Migration-inducing protein 5 | protein | 182 | 40% helix, 22% strand | P63000 |
| B | Migration-inducing protein 5 | protein | 183 | 40% helix, 20% strand | P63000 |
| C | Protein kinase ypka | protein | 269 | 79% helix, 0% strand | Q05608 |
| D | Protein kinase ypka | protein | 259 | 84% helix, 0% strand | Q05608 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 245 | 0.61 | 0.80 | 28 | empty |
| 2 | 89 | 0.51 | 0.83 | 19 | empty |
| 3 | 180 | 0.50 | 0.77 | 31 | empty |
| 4 | 107 | 0.42 | 0.77 | 25 | MG, GDP |
| 5 | 109 | 0.41 | 0.77 | 27 | MG, GDP |
Interfaces
4 interfaces between chains.
- A–C · 846 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 761 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 443 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 303 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2H7V · Co-crystal structure of YpkA-Rac1 · the same entry in another collection · chain D against D, TM-score 1.00
- P63000 · AlphaFold monomer V2.0 prediction for RAS-related C3 botulinum toxin substrate 1 (P63000) · a predicted model of the same protein · chain A against A, TM-score 0.94
- Q05608 · AlphaFold monomer V2.0 prediction for protein kinase ypka (Q05608) · a predicted model of the same protein · chain D against A, TM-score 0.86
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 P63000
- Every structure of UniProt Q05608
- Elsewhere: RCSB PDB 2H7V · PDBe 2H7V · UniProt P63000 · UniProt Q05608
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