Structure of yarrowia lipolytica complex I at 2.7 a

Structure

electron microscopy · 42 distinct chains · 51% helix, 8% strand (DSSP).

Ligands and binding sites

• 3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · 18 copies · chains A, H, J, B, P, Z, D, I, b, L, M, l, N, Y, m, K, X, d, g
• PLC · Diundecyl phosphatidyl choline · ligand · 8 copies · chains D, L, M, N, B, H, f, n, l, i, d, P, O
• SF4 · Iron/sulfur cluster · ligand · 6 copies · chains B, D, F, G, I
• CDL · Cardiolipin · ligand · 6 copies · chains L, M, g, h, i, A, H, J, N, O, b, P, I, Z, c, a, f
• FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains E, 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
• NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · chains B, P
• ZN · Zinc ion · metal · chains R
• LMT · Dodecyl-beta-D-maltoside · additive · 5 copies · chains B, D, H, M, h, N, Y, 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

201 interfaces between chains.

• E–F · 3469 Ų buried · 50 hydrogen bonds · protein-protein
• A–H · 3160 Ų buried · 8 hydrogen bonds · protein-protein
• J–K · 3004 Ų buried · 12 hydrogen bonds · protein-protein
• C–c · 2908 Ų buried · 28 hydrogen bonds · protein-protein
• C–D · 2787 Ų buried · 43 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 modified, 5 disulfide, 3 covalent, 1 cofactor (formylation, disulfide, covalent ligand, flavinylation, methylation).

Compared structures

• 6YJ4 · Structure of Yarrowia lipolytica complex I at 2.7 A · the same entry in another collection · chain A against A, 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 S5TMS4
• Every structure of UniProt Q9UUT7
• Every structure of UniProt Q9UUU0
• Every structure of UniProt Q9UUU1
• Every structure of UniProt Q9UUT9
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• Every structure of UniProt S5TF58
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• Every structure of UniProt A0A1H6Q8Z5
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• Every structure of UniProt A0A1D8N3C8
• Every structure of UniProt A0A371C2D0
• Every structure of UniProt A0A371CB65
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• Every structure of UniProt A0A1D8NJR0
• Every structure of UniProt A0A1D8N3H5
• Every structure of UniProt A0A1D8NGI5
• Every structure of UniProt A0A1D8NNZ0
• Every structure of UniProt A0A1D8N5V2
• Every structure of UniProt Q6ZY23
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• Every structure of UniProt A0A1H6Q311
• Every structure of UniProt A0A1D8NFX6
• Every structure of UniProt A0A371C0F2
• Every structure of UniProt A0A1D8ND94
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• Elsewhere: RCSB PDB 6YJ4 · PDBe 6YJ4 · UniProt S5TMS4 · UniProt Q9UUT7 · UniProt Q9UUU0 · UniProt Q9UUU1 · UniProt Q9UUT9 · UniProt Q9UUU2 · UniProt Q9UUU3 · UniProt S5U3V2 · UniProt Q9UUT8 · UniProt Q9B6E9 · UniProt S5U4U1 · UniProt S5TF58 · UniProt S5TMP9 · UniProt S5U4R9 · UniProt A0A1D8NKB4 · UniProt A0A371BY45 · UniProt A0A1D8N7X0 · UniProt A0A1H6Q8Z5 · UniProt A0A1H6PJS3 · UniProt A0A1H6PXT9 · UniProt A0A1D8NG21 · UniProt A0A371C5F3 · UniProt A0A1D8N3C8 · UniProt A0A371C2D0 · UniProt A0A371CB65 · UniProt A0A1H6PPE5 · UniProt A0A1D8NC63 · UniProt A0A1D8NJR0 · UniProt A0A1D8N3H5 · UniProt A0A1D8NGI5 · UniProt A0A1D8NNZ0 · UniProt A0A1D8N5V2 · UniProt Q6ZY23 · UniProt A0A371CFV9 · UniProt A0A1H6Q311 · UniProt A0A1D8NFX6 · UniProt A0A371C0F2 · UniProt A0A1D8ND94 · UniProt Q6ZY24 · UniProt A0A1D8NDL1 · UniProt A0A1H6PKH9 · UniProt A0A1D8N596