Research workbench
Cytochrome bcc-AA3 supercomplex (respiratory supercomplex III2/IV2) from corynebacterium glutamicum (as isolated)
Analyse Cytochrome bcc-AA3 supercomplex (respiratory supercomplex III2/IV2) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7QHO
- Type
- protein
- Length
- 5,870 residues
- Chains
- 26
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome BC1 complex rieske iron-sulfur subunit; Cytochrome BC1 complex cytochrome B…
- EC
- 7.1.1.8, 7.1.1.9
- UniProt
- Q79VE8, Q79VE9, Q8NNK5, Q79VD7, Q8NNK2, Q9AEL8, Q8NNK3, Q8NMB4, Q8NP09, Q8NTD4, Q8NS61, Q8NSJ8, P42461
- Ligands
- CDL, 3PE, MQ9, DGA, 9YF, HEM, HEC, HAS, PLM, FES, IZL, LYC, 3PH, IX7, CUA, CU…
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 13 distinct chains · 52% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, N | Cytochrome BC1 complex rieske iron-sulfur subunit | protein | 402 | 36% helix, 18% strand | Q79VE8 |
| B, O | Cytochrome BC1 complex cytochrome B subunit (EC 7.1.1.8) | protein | 534 | 63% helix, 9% strand | Q79VE9 |
| C, P | Cytochrome BC1 complex cytochrome C subunit (EC 7.1.1.8) | protein | 233 | 46% helix, 5% strand | Q8NNK5 |
| D, Q | Cytochrome C oxidase subunit 1 (EC 7.1.1.9) | protein | 574 | 66% helix, 1% strand | Q79VD7 |
| E, R | Cytochrome C oxidase subunit 2 (EC 7.1.1.9) | protein | 331 | 34% helix, 21% strand | Q8NNK2 |
| F, S | Cytochrome C oxidase subunit 3 (EC 7.1.1.9) | protein | 190 | 85% helix, 1% strand | Q9AEL8 |
| G, T | Cytochrome C oxidase polypeptide 4 (EC 7.1.1.9) | protein | 143 | 64% helix, 3% strand | Q8NNK3 |
| H, U | Uncharacterized protein CGL2664/CG2949 | protein | 154 | 3% helix, 44% strand | Q8NMB4 |
| I, V | Uncharacterized membrane protein CGL2017/CG2211 | protein | 129 | 50% helix, 4% strand | Q8NP09 |
| J, W | Hypothetical membrane protein | protein | 100 | 65% helix, 0% strand | Q8NTD4 |
| K, X | Actinobacterial supercomplex, subunit C (ascc) | protein | 57 | 12% helix, 7% strand | Q8NS61 |
| L, Y | Hypothetical membrane protein | protein | 63 | 78% helix, 2% strand | Q8NSJ8 |
| M, Z | Thiamine biosynthesis protein X | protein | 25 | 0% helix, 8% strand | P42461 |
Ligands and binding sites
- CDL · Cardiolipin · ligand · 14 copies · chains B, C, D, G, F, A, I, O, P, Q, T, S, N, V
- 3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · 10 copies · chains A, N, O, D, E, L, F, G, J, B, Q, R, Y, S, T, W
- MQ9 · Menaquinone-9 · ligand · 6 copies · chains A, B, N, O
- DGA · Diacyl glycerol · ligand · 6 copies · chains E, D, H, I, B, M, R, Q, U, V, O, Z
- 9YF · (2R)-2-(hexadecanoyloxy)-3-{[(S)-hydroxy{[(1r,2r,3r,4r, 5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl (9S)-9-methyloctadecanoate · ligand · 4 copies · chains A, N, O, B, C, H, I, P, U, V
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains B, O
- HEC · Heme C · ligand · 4 copies · chains C, E, H, A, P, R, U, N
- HAS · Heme-as · ligand · 4 copies · chains D, E, Q, R
- PLM · Palmitic acid · ligand · 4 copies · chains D, H, B, M, Q, U, O, Z
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains A, N
- IZL · [(2~{R})-3-[[(1~{S},2~{R},3~{S},4~{S},5~{R},6~{R})-2-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-[[(2~{S},3~{S}, 4~{S},5~{S},6~{R})-6-[[(2~{S},3~{S},4~{S},5~{S}, 6~{R})-6-(hydroxymethyl)-3-[(2~{R},3~{S},4~{S},5~{S}, 6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-4,5-bis(oxidanyl)oxan-2-yl]oxymethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxymethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4,5-tris(oxidanyl)-6-[(2~{R},3~{S},4~{S},5~{S},6~{R})-3,4,5-tris(oxidanyl)-6-(undecanoyloxymethyl)oxan-2-yl]oxy-cyclohe · ligand · 2 copies · chains A, B, N, O
- LYC · Lycopene · ligand · 2 copies · chains B, I, O, V
- 3PH · 1,2-diacyl-glycerol-3-sn-phosphate · ligand · 2 copies · chains B, C, G, O, P, T
- IX7 · [(2~{R})-3-[[(1~{S},2~{R},3~{R},4~{S},5~{S},6~{R})-2-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-(hexadecanoyloxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-6-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4, 5-tris(oxidanyl)cyclohexyl]oxy-oxidanyl-phosphoryl]oxy-2-undecanoyloxy-propyl] (10~{S})-10-methylhenicosanoate · ligand · 2 copies · chains D, E, H, I, Q, R, U, V
- CUA · Dinuclear copper ion · metal · 4 copies · chains E, R
- CU · Copper (II) ion · metal · 2 copies · chains D, Q
- CA · Calcium ion · metal · 2 copies · chains D, Q
- MN · Manganese (II) ion · metal · 2 copies · chains D, E, Q, R
- LMT · Dodecyl-beta-D-maltoside · additive · 2 copies · chains B, N, A, O
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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1194 | 0.89 | 0.90 | 113 | HAS |
| 2 | 1157 | 0.89 | 0.90 | 110 | HAS, DGA |
| 3 | 1003 | 0.87 | 0.87 | 73 | CDL |
| 4 | 961 | 0.87 | 0.87 | 77 | CDL |
| 5 | 697 | 0.86 | 0.90 | 75 | HEM |
Interfaces
86 interfaces between chains.
- A–B · 4799 Ų buried · 46 hydrogen bonds · protein-protein
- N–O · 4762 Ų buried · 42 hydrogen bonds · protein-protein
- D–E · 4675 Ų buried · 42 hydrogen bonds · protein-protein
- Q–R · 4663 Ų buried · 42 hydrogen bonds · protein-protein
- A–N · 3286 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor, 6 covalent, 4 disulfide, 4 lipid (heme c attachment, covalent ligand, disulfide, palmitoylation).
Compared structures
- 7QHO · Cytochrome bcc-aa3 supercomplex (respiratory supercomplex III2/IV2) from Corynebacterium… · 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 Q79VE8
- Every structure of UniProt Q79VE9
- Every structure of UniProt Q8NNK5
- Every structure of UniProt Q79VD7
- Every structure of UniProt Q8NNK2
- Every structure of UniProt Q9AEL8
- Every structure of UniProt Q8NNK3
- Every structure of UniProt Q8NMB4
- Every structure of UniProt Q8NP09
- Every structure of UniProt Q8NTD4
- Every structure of UniProt Q8NS61
- Every structure of UniProt Q8NSJ8
- Every structure of UniProt P42461
- Elsewhere: RCSB PDB 7QHO · PDBe 7QHO · UniProt Q79VE8 · UniProt Q79VE9 · UniProt Q8NNK5 · UniProt Q79VD7 · UniProt Q8NNK2 · UniProt Q9AEL8 · UniProt Q8NNK3 · UniProt Q8NMB4 · UniProt Q8NP09 · UniProt Q8NTD4 · UniProt Q8NS61 · UniProt Q8NSJ8 · UniProt P42461
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