Crystal structure of the rab GTPase SEC4P mutant - S29V in complex with SEC2P and GDP

Structure

x-ray diffraction · 2 distinct chains · 57% helix, 13% strand (DSSP).

Ligands and binding sites

• GDP · Guanosine-5'-diphosphate · ligand · chains A

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 · 2380 Ų buried · 13 hydrogen bonds · protein-protein
• A–B · 799 Ų buried · 7 hydrogen bonds · protein-protein
• A–C · 481 Ų buried · 5 hydrogen bonds · protein-protein

Compared structures

• 4ZDW · Crystal structure of the Rab GTPase Sec4p mutant - S29V in complex with Sec2p and GDP · 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 0.83

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 4ZDW · PDBe 4ZDW · UniProt P07560 · UniProt P17065