Ternary complex of the WH2 domain of mim with actin-DNase I

Structure

x-ray diffraction · 3 distinct chains · 37% helix, 23% strand (DSSP).

Ligands and binding sites

• ATP · Adenosine-5'-triphosphate · ligand · chains A
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B
• BMA · beta-D-mannopyranose · sugar
• CA · Calcium ion · metal · 2 copies · chains A, B
• MG · Magnesium ion · metal · chains B

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Interfaces

3 interfaces between chains.

• A–C · 1410 Ų buried · 16 hydrogen bonds · protein-protein
• A–B · 954 Ų buried · 18 hydrogen bonds · protein-protein
• B–C · 97 Ų buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide, 1 glycan, 1 modified (disulfide, N-glycosylation, methylation).

Compared structures

• 2D1K · Ternary complex of the WH2 domain of mim with actin-dnase I · the same entry in another collection · chain A against A, TM-score 1.00
• P00639 · AlphaFold monomer V2.0 prediction for deoxyribonuclease-1 (P00639) · a predicted model of the same protein · chain B against A, TM-score 0.98
• P68135 · AlphaFold monomer V2.0 prediction for actin, alpha skeletal muscle (P68135) · a predicted model of the same protein · chain A against A, TM-score 0.97
• O43312 · AlphaFold monomer V2.0 prediction for protein mtss 1 (O43312) · a predicted model of the same protein · chain C against A, TM-score 0.41

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 P68135
• Every structure of UniProt P00639
• Every structure of UniProt O43312
• Elsewhere: RCSB PDB 2D1K · PDBe 2D1K · UniProt P68135 · UniProt P00639 · UniProt O43312