Research workbench
Cryo-EM structure of apo hybrid respiratory supercomplex consisting of mycobacterium tuberculosis complexiii and mycobacterium smegmatis complexiv
Analyse Cryo-EM structure of apo hybrid respiratory supercomplex consisting of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7E1V
- Type
- protein
- Length
- 5,122 residues
- Chains
- 20
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C oxidase subunit 2; Cytochrome C oxidase subunit 1; Cytochrome C oxidase…
- EC
- 7.1.1.9, 7.1.1.8
- UniProt
- A0R057, A0R049, A0R056, A0R1B6, A0R1B5, P9WP37, P9WH23, P9WP35
- Ligands
- CDL, MQ9, PLM, HEA, HEM, 9YF, HEC, 9Y0, FES, CU
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 14 distinct chains · 51% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Cytochrome C oxidase subunit 2 (EC 7.1.1.9) | protein | 276 | 31% helix, 22% strand | A0R057 |
| F, R | Cytochrome C oxidase subunit 1 | protein | 552 | 66% helix, 1% strand | — |
| G | Cytochrome C oxidase subunit 3 | protein | 186 | 78% helix, 0% strand | A0R049 |
| H, T | Cytochrome C oxidase polypeptide 4 (EC 7.1.1.9) | protein | 139 | 64% helix, 3% strand | A0R056 |
| I, U | Cytochrome C oxidase subunit ctaj | protein | 67 | 34% helix, 9% strand | A0R1B6 |
| J, V | Uncharacterized protein MSMEG_4692/MSMEI_4575 | protein | 145 | 39% helix, 13% strand | A0R1B5 |
| D | Prokaryotic respiratory supercomplex associate factor 1 PRSAF1 | protein | 76 | 57% helix, 0% strand | — |
| Q | Cytochrome C oxidase subunit 2 (EC 7.1.1.9) | protein | 283 | 29% helix, 20% strand | A0R057 |
| S | Cytochrome C oxidase subunit 3 | protein | 185 | 78% helix, 0% strand | A0R049 |
| P | Prokaryotic respiratory supercomplex associate factor 1 PRSAF1 | protein | 75 | 56% helix, 0% strand | — |
| N, B | Cytochrome BC1 complex cytochrome B subunit (EC 7.1.1.8) | protein | 524 | 61% helix, 6% strand | P9WP37 |
| M, A | Cytochrome BC1 complex rieske iron-sulfur subunit | protein | 378 | 35% helix, 16% strand | P9WH23 |
| O | Cytochrome BC1 complex cytochrome C subunit (EC 7.1.1.8) | protein | 213 | 43% helix, 3% strand | P9WP35 |
| C | Cytochrome BC1 complex cytochrome C subunit (EC 7.1.1.8) | protein | 218 | 42% helix, 3% strand | P9WP35 |
Ligands and binding sites
- CDL · Cardiolipin · ligand · 17 copies · chains F, G, H, D, N, R, S, T, B, P, O, M, C, A
- MQ9 · Menaquinone-9 · ligand · 10 copies · chains N, B, A, M, F, H, O, R, T, C
- PLM · Palmitic acid · ligand · 4 copies · chains F, D, R, N, P, B
- HEA · Heme-A · ligand · 4 copies · chains E, F, Q, R
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains N, B
- 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 M, N, B, A
- HEC · Heme C · ligand · 4 copies · chains O, M, A, C
- 9Y0 · (2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (E)-octadec-9-enoate · ligand · 2 copies · chains F, G, H, R, S, T
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains M, A
- CU · Copper (II) ion · metal · 8 copies · chains E, F, Q, 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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1054 | 0.89 | 0.91 | 106 | CU, HEA |
| 2 | 1159 | 0.89 | 0.90 | 100 | CU, HEA |
| 3 | 884 | 0.88 | 0.90 | 92 | HEM |
| 4 | 1020 | 0.83 | 0.84 | 66 | CDL |
| 5 | 1051 | 0.83 | 0.83 | 78 | CDL |
Interfaces
57 interfaces between chains.
- B–A · 4492 Ų buried · 48 hydrogen bonds · protein-protein
- N–M · 4442 Ų buried · 42 hydrogen bonds · protein-protein
- Q–R · 4385 Ų buried · 45 hydrogen bonds · protein-protein
- E–F · 4290 Ų buried · 42 hydrogen bonds · protein-protein
- M–A · 2773 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 covalent, 5 cofactor, 2 disulfide (covalent ligand, heme c attachment, disulfide).
Compared structures
- 7E1V · Cryo-EM structure of apo hybrid respiratory supercomplex consisting of Mycobacterium… · the same entry in another collection · chain G against G, 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 A0R057
- Every structure of UniProt A0R049
- Every structure of UniProt A0R056
- Every structure of UniProt A0R1B6
- Every structure of UniProt A0R1B5
- Every structure of UniProt P9WP37
- Every structure of UniProt P9WH23
- Every structure of UniProt P9WP35
- Elsewhere: RCSB PDB 7E1V · PDBe 7E1V · UniProt A0R057 · UniProt A0R049 · UniProt A0R056 · UniProt A0R1B6 · UniProt A0R1B5 · UniProt P9WP37 · UniProt P9WH23 · UniProt P9WP35
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