Homo sapiens FKBP12 protein bound with APX879 in P32 space group

Structure

x-ray diffraction · 2 distinct chains · 9% helix, 40% strand (DSSP).

Ligands and binding sites

• R27 · N'-[(3s,4r,5s,8r,9e,12s,14s,15r,16s,18r,19r,26as)-5,19-dihydroxy-3-{(1E)-1-[(1R,3R,4R)-4-hydroxy-3-methoxycyclohexyl]prop-1-en-2-yl}-14,16-dimethoxy-4, 10,12,18-tetramethyl-1,20,21-trioxo-8-(prop-2-en-1-yl)-1,3,4,5,6,8,11,12,13,14,15,16,17,18,19,20,21,23, 24,25,26,26A-docosahydro-7H-15,19-epoxypyrido[2,1-c][1,4]oxazacyclotricosin-7-ylidene]acetohydrazide · ligand · 4 copies · chains A, C, D, B
• ACT · Acetate ion · additive · 5 copies · chains A, B, D

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

Pockets

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

Interfaces

6 interfaces between chains.

• B–D · 671 Ų buried · 14 hydrogen bonds · protein-protein
• A–C · 666 Ų buried · 16 hydrogen bonds · protein-protein
• A–D · 383 Ų buried · 1 hydrogen bond · protein-protein
• B–C · 377 Ų buried · 1 hydrogen bond · protein-protein
• C–D · 99 Ų buried · 0 hydrogen bonds · protein-protein

Compared structures

• 6VCU · Homo sapiens FKBP12 protein bound with APX879 in P32 space group · the same entry in another collection · chain D against D, TM-score 1.00
• P62942 · AlphaFold monomer V2.0 prediction for peptidyl-prolyl cis-trans isomerase FKBP1A (P62942) · a predicted model of the same protein · chain B against A, TM-score 0.97

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 P62942
• Elsewhere: RCSB PDB 6VCU · PDBe 6VCU · UniProt P62942