Crystal structure of the rab GTPase SEC4P, the SEC2P gef domain, and phosphate complex

Structure

x-ray diffraction · 2 distinct chains · 56% helix, 17% strand (DSSP).

Ligands and binding sites

• PO4 · Phosphate ion · ion · 2 copies · chains A, B, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Interfaces

3 interfaces between chains.

• B–C · 2496 Ų buried · 14 hydrogen bonds · protein-protein
• A–B · 873 Ų buried · 9 hydrogen bonds · protein-protein
• A–C · 471 Ų buried · 7 hydrogen bonds · protein-protein

Compared structures

• 2EQB · Crystal structure of the Rab GTPase Sec4p, the Sec2p GEF domain, and phosphate complex · the same entry in another collection · chain A against A, TM-score 1.00
• P07560 · AlphaFold monomer V2.0 prediction for RAS-related protein SEC4 (P07560) · a predicted model of the same protein · chain A against A, TM-score 0.89
• P17065 · AlphaFold monomer V2.0 prediction for rab guanine nucleotide exchange factor SEC2 (P17065) · a predicted model of the same protein · chain B against A, TM-score 0.85

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 P07560
• Every structure of UniProt P17065
• Elsewhere: RCSB PDB 2EQB · PDBe 2EQB · UniProt P07560 · UniProt P17065