Cryo-EM structure of respiratory complex I from yarrowia lipolytica

Structure

electron microscopy · 42 distinct chains · 45% helix, 6% strand (DSSP).

Ligands and binding sites

• SF4 · Iron/sulfur cluster · ligand · 6 copies · chains A, C, B, I, K
• 3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · 3 copies · chains g, 1, 2, 3, C, I, W, b, 4
• FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains A, H
• FMN · Flavin mononucleotide · ligand · chains B
• NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · chains E, K
• ZMP · S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy) butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate · ligand · chains O, P
• CDL · Cardiolipin · ligand · chains X, g, 2, 3, 6
• ZN · Zinc ion · metal · chains M

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

174 interfaces between chains.

• 1–3 · 2735 Ų buried · 6 hydrogen bonds · protein-protein
• C–G · 2681 Ų buried · 19 hydrogen bonds · protein-protein
• A–Y · 2484 Ų buried · 26 hydrogen bonds · protein-protein
• L–6 · 2428 Ų buried · 4 hydrogen bonds · protein-protein
• B–H · 2377 Ų buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 1 covalent (disulfide, covalent ligand).

Compared structures

• 6GCS · Cryo-EM structure of respiratory complex I from Yarrowia lipolytica · the same entry in another collection · chain K against K, 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
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• Elsewhere: RCSB PDB 6GCS · PDBe 6GCS · UniProt Q9UUU3 · UniProt Q9UUU2 · UniProt Q9UUU1 · UniProt A0A1D8NC63 · UniProt Q6C7X4 · UniProt Q6C4W9 · UniProt Q9UUU0 · UniProt Q9UUT9 · UniProt Q9UUT8 · UniProt Q6C674 · UniProt Q9UUT7 · UniProt Q9B6D4 · UniProt A0A1H6Q8Z5 · UniProt A0A1H6PXT9 · UniProt A0A1D8N3C8 · UniProt A0A1D8NG21 · UniProt A0A1D8NDL1 · UniProt Q6CGB4 · UniProt A0A1H6PPE5 · UniProt A0A1D8NKB4 · UniProt A0A1D8N7X0 · UniProt B5FVE5 · UniProt A0A1D8N596 · UniProt A0A1H6PJS3 · UniProt A0A1D8NJR0 · UniProt Q6CG53 · UniProt Q6ZY24 · UniProt Q9B6E8 · UniProt Q9B6C8 · UniProt Q9B6C7 · UniProt Q9B6D6 · UniProt Q9B6D3 · UniProt Q9B6E9 · UniProt A0A1H6PKH9 · UniProt A0A1D8NNZ0