Zebrafish SIRT5 in complex with stalled peptidylimidate and bicyclic intermediate of inhibitory compound 29

Structure

x-ray diffraction · 2 distinct chains · 37% helix, 19% strand (DSSP).

Ligands and binding sites

• BVT · 3-[[(2~{S},3~{A}~{R},5~{R},6~{R},6~{A}~{R})-5-[[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3, 4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-2-[[(5~{S})-6-[[(2~{S})-3-(1~{H}-indol-3-yl)-1-oxidanylidene-1-(propan-2-ylamino)propan-2-yl]amino]-6-oxidanylidene-5-(phenylmethoxycarbonylamino) hexyl]amino]-6-oxidanyl-3~{A},5,6,6~{A}-tetrahydrofuro[2,3-d][1,3]oxathiol-2-yl]amino]propanoic acid · ligand · 4 copies · chains A, C, B, D
• BV8 · 3-[[(~{Z})-~{C}-[(2~{R},3~{R},4~{S},5~{R})-5-[[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3, 4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-3,4-bis(oxidanyl)oxolan-2-yl]sulfanyl-~{N}-[(5~{S})-6-[[(2~{S})-3-(1~{H}-indol-3-yl)-1-oxidanylidene-1-(propan-2-ylamino)propan-2-yl]amino]-6-oxidanylidene-5-(phenylmethoxycarbonylamino) hexyl]carbonimidoyl]amino]propanoic acid · ligand · chains A, C
• ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
• EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, D, C

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

Pockets

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

Interfaces

5 interfaces between chains.

• C–D · 1629 Ų buried · 14 hydrogen bonds · protein-protein
• A–B · 1538 Ų buried · 11 hydrogen bonds · protein-protein
• B–D · 798 Ų buried · 12 hydrogen bonds · protein-protein
• A–C · 756 Ų buried · 10 hydrogen bonds · protein-protein
• B–C · 22 Ų buried · 0 hydrogen bonds · protein-protein

Compared structures

• 6EO0 · Zebrafish Sirt5 in complex with stalled peptidylimidate and bicyclic intermediate of… · the same entry in another collection · chain A against A, TM-score 1.00
• Q6DHI5 · AlphaFold monomer V2.0 prediction for NAD-dependent protein deacylase sirtuin-5… · a predicted model of the same protein · chain A 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 Q6DHI5
• Elsewhere: RCSB PDB 6EO0 · PDBe 6EO0 · UniProt Q6DHI5