Bovine complex I in lipid nanodisc, deactive-ligand (composite)

Structure

electron microscopy · 45 distinct chains · 53% helix, 8% strand (DSSP).

Ligands and binding sites

• 3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · 29 copies · chains A, J, b, H, I, D, Z, r, N, e, K, L, M, l, i, Y, O, d, m, c, f, g, h, p, j, k, o
• PC1 · 1,2-diacyl-sn-glycero-3-phosphocholine · ligand · 7 copies · chains A, B, H, P, I, q, J, Z, a, L, M, g, Y, N, O, 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
• 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
• GTP · Guanosine-5'-triphosphate · ligand · chains O
• NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · chains B, P
• CHD · Cholic acid · ligand · chains L, i
• MYR · Myristic acid · ligand · chains L, l, o
• K · Potassium ion · metal · chains G
• MG · Magnesium ion · metal · chains O
• ZN · Zinc ion · metal · chains R
• GOL · Glycerol · additive · chains B, D, H
• LMT · Dodecyl-beta-D-maltoside · additive · chains B, D, H

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

200 interfaces between chains.

• E–F · 3136 Ų buried · 43 hydrogen bonds · protein-protein
• J–K · 2934 Ų buried · 16 hydrogen bonds · protein-protein
• A–H · 2713 Ų buried · 5 hydrogen bonds · protein-protein
• C–D · 2702 Ų buried · 42 hydrogen bonds · protein-protein
• L–M · 2386 Ų buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 modified, 7 disulfide, 2 covalent, 1 lipid (disulfide, formylation, nonstandard, covalent ligand, myristoylation, acetylation).

Compared structures

• 7QSM · Bovine complex I in lipid nanodisc, Deactive-ligand (composite) · the same entry in another collection · chain L against L, 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
• Every structure of UniProt P03887
• Every structure of UniProt P42028
• Every structure of UniProt P03924
• Every structure of UniProt P03902
• Every structure of UniProt P03920
• Every structure of UniProt P03910
• Every structure of UniProt P03892
• Every structure of UniProt P34942
• Every structure of UniProt P34943
• Every structure of UniProt Q02375
• Every structure of UniProt P23934
• Every structure of UniProt Q02370
• Every structure of UniProt P52505
• Every structure of UniProt P23935
• Every structure of UniProt Q02366
• Every structure of UniProt P42029
• Every structure of UniProt Q8HXG6
• Every structure of UniProt Q95KV7
• Every structure of UniProt Q02377
• Every structure of UniProt Q02371
• Every structure of UniProt Q02376
• Every structure of UniProt Q02827
• Every structure of UniProt Q02379
• Every structure of UniProt Q02378
• Every structure of UniProt Q8HXG5
• Every structure of UniProt Q02380
• Every structure of UniProt Q02367
• Every structure of UniProt Q02374
• Every structure of UniProt Q02365
• Every structure of UniProt Q02372
• Every structure of UniProt P48305
• Every structure of UniProt Q02369
• Every structure of UniProt Q02368
• Every structure of UniProt Q02373
• Every structure of UniProt O97725
• Every structure of UniProt Q05752
• Every structure of UniProt P25712
• Elsewhere: RCSB PDB 7QSM · PDBe 7QSM · 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