Research workbench

Co-crystal structure of ypka-RAC1

Analyse Co-crystal structure of ypka-RAC1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

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.

Pocket	Volume (Å³)	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 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 761 Å² buried · 5 hydrogen bonds · protein-protein
A–D · 443 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 303 Å² 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

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.