Bovine complex I in lipid nanodisc, State 3 (Slack)

Structure

electron microscopy · resolution 3.02 · 45 distinct chains · 52% helix, 8% strand (DSSP).

Ligands and binding sites

• 3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · 14 copies · chains A, b, H, J, N, e, D, I, Z, r, L, M, l, i, O, d, c, Y, h, p
• PC1 · 1,2-diacyl-sn-glycero-3-phosphocholine · ligand · 6 copies · chains A, B, H, P, I, q, J, Z, a, L, M, g, N, d, e
• SF4 · Iron/sulfur cluster · ligand · 6 copies · chains B, D, F, G, I
• CDL · Cardiolipin · ligand · 6 copies · chains L, M, g, h, N, O, X, d, f, c, i, p, H, a, q, r
• FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains E, F, G
• CHD · Cholic acid · ligand · 2 copies · chains B, H, L, i
• 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, L, U, n
• FMN · Flavin mononucleotide · ligand · chains F
• U10 · Ubiquinone-10 · ligand · chains M, N
• GTP · Guanosine-5'-triphosphate · ligand · chains O
• NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · chains B, P
• MYR · Myristic acid · ligand · chains L, o
• K · Potassium ion · metal · chains G
• MG · Magnesium ion · metal · chains O
• 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

187 interfaces between chains.

• E–F · 3080 Ų buried · 36 hydrogen bonds · protein-protein
• J–K · 2808 Ų buried · 7 hydrogen bonds · protein-protein
• A–H · 2806 Ų buried · 7 hydrogen bonds · protein-protein
• C–D · 2712 Ų buried · 36 hydrogen bonds · protein-protein
• D–I · 2274 Ų buried · 47 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 11 modified, 7 disulfide, 2 covalent, 1 lipid (disulfide, formylation, covalent ligand, nonstandard, myristoylation, acetylation).

Compared structures

• 7QSO · Bovine complex I in lipid nanodisc, state 3 (slack) · 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
• Every structure of UniProt Q7JAS9
• Every structure of UniProt P42026
• Every structure of UniProt P23709
• Every structure of UniProt P17694
• Every structure of UniProt P04394
• Every structure of UniProt P25708
• Every structure of UniProt P15690
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• Every structure of UniProt P34942
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• Every structure of UniProt Q02375
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• Every structure of UniProt Q02366
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• Every structure of UniProt Q8HXG5
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• Every structure of UniProt P48305
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• Every structure of UniProt O97725
• Every structure of UniProt Q05752
• Every structure of UniProt P25712
• Elsewhere: RCSB PDB 7QSO · PDBe 7QSO · UniProt Q7JAS9 · UniProt P42026 · UniProt P23709 · UniProt P17694 · UniProt P04394 · UniProt P25708 · UniProt P15690 · UniProt P03887 · UniProt P42028 · UniProt P03924 · UniProt P03902 · UniProt P03920 · UniProt P03910 · UniProt P03892 · UniProt P34942 · UniProt P34943 · UniProt Q02375 · UniProt P23934 · UniProt Q02370 · UniProt P52505 · UniProt P23935 · UniProt Q02366 · UniProt P42029 · UniProt Q8HXG6 · UniProt Q95KV7 · UniProt Q02377 · UniProt Q02371 · UniProt Q02376 · UniProt Q02827 · UniProt Q02379 · UniProt Q02378 · UniProt Q8HXG5 · UniProt Q02380 · UniProt Q02367 · UniProt Q02374 · UniProt Q02365 · UniProt Q02372 · UniProt P48305 · UniProt Q02369 · UniProt Q02368 · UniProt Q02373 · UniProt O97725 · UniProt Q05752 · UniProt P25712