Cryo-EM structure of mitochondrial complex I from mus musculus inhibited by iacs-2858 at 3.0 a

Structure

electron microscopy · 45 distinct chains · 51% helix, 7% strand (DSSP).

Ligands and binding sites

• 3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · 9 copies · chains D, L, M, N, A, H, J, Z, a, I, b, K, l, g, Y, f, h, i
• CDL · Cardiolipin · ligand · 7 copies · chains L, M, h, N, O, e, X, d, f, g, i, p, H, a, q, r
• SF4 · Iron/sulfur cluster · ligand · 6 copies · chains B, D, F, G, I
• PC1 · 1,2-diacyl-sn-glycero-3-phosphocholine · ligand · 4 copies · chains B, H, I, q, A, P, J, Z, r
• FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains E, F, G
• EHZ · ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] (3~{S})-3-oxidanyltetradecanethioate · ligand · 2 copies · chains T, W, U, n
• FMN · Flavin mononucleotide · ligand · chains F
• T2Q · 1-[[3-(4-methylsulfonylpiperidin-1-yl)phenyl]methyl]-5-[3-[4-(trifluoromethyloxy)phenyl]-1,2,4-oxadiazol-5-yl]pyridin-2-one · ligand · chains B, D, H
• ATP · Adenosine-5'-triphosphate · ligand · chains O
• NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · chains B, P
• ZN · Zinc ion · metal · chains R

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Interfaces

202 interfaces between chains.

• A–H · 3302 Ų buried · 14 hydrogen bonds · protein-protein
• E–F · 3091 Ų buried · 38 hydrogen bonds · protein-protein
• C–D · 2745 Ų buried · 32 hydrogen bonds · protein-protein
• J–K · 2699 Ų buried · 10 hydrogen bonds · protein-protein
• L–M · 2381 Ų buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide, 10 modified, 2 covalent (disulfide, formylation, covalent ligand, nonstandard, methylation).

Compared structures

• 7B93 · Cryo-EM structure of mitochondrial complex I from Mus musculus inhibited by IACS-2858 at… · the same entry in another collection · chain I against I, TM-score 1.00

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 P03899
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• Elsewhere: RCSB PDB 7B93 · PDBe 7B93 · UniProt P03899 · UniProt Q9DC70 · UniProt Q9DCT2 · UniProt Q91WD5 · UniProt Q9D6J6 · UniProt Q91YT0 · UniProt Q91VD9 · UniProt P03888 · UniProt Q8K3J1 · UniProt P03925 · UniProt P03903 · UniProt P03921 · UniProt P03911 · UniProt P03893 · UniProt Q99LC3 · UniProt Q9DC69 · UniProt Q9CXZ1 · UniProt P52503 · UniProt Q9CQ75 · UniProt Q9CR21 · UniProt Q9CPP6 · UniProt Q9CQZ5 · UniProt Q9DCJ5 · UniProt G5E814 · UniProt Q9ERS2 · UniProt O35683 · UniProt Q9CQ91 · UniProt Q9CQY9 · UniProt Q9CQ54 · UniProt Q99LY9 · UniProt P0DN34 · UniProt O09111 · UniProt Q9CQH3 · UniProt Q3UIU2 · UniProt Q9CPU2 · UniProt Q9CQZ6 · UniProt Q9D6J5 · UniProt Q9CQC7 · UniProt Q9CQJ8 · UniProt Q9CR61 · UniProt Q9DCS9 · UniProt Q7TMF3 · UniProt Q9Z1P6 · UniProt Q8BK30