MolNFT v1 · #186537 · protein
Mycobacterial CIII2CIV2 supercomplex, inhibitor free
7RH5 · Cytochrome C oxidase subunit 1: “Mycobacterial CIII2CIV2 supercomplex, inhibitor free”. Electron microscopy, 11 ligands (CDL, MQ9, 9YF), 20 pockets (best druggability 0.90). MolNFT v1 #186537 on GenesisL1: 3D structure, binding…
- PDB
- 7RH5
- Type
- protein
- Length
- 6,072 residues
- Chains
- 24
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C oxidase subunit 1; Cytochrome BC1 complex cytochrome B subunit; Superoxide…
- EC
- 7.1.1.9, 7.1.1.8, 1.15.1.1
- UniProt
- I7FGS8, I7G2H6, I7GD63, A0R049, I7FPH7, I7FQK8, A0R1B5, I7FPH1, I7GFE1, I7GD61
- Ligands
- CDL, MQ9, 9YF, 9Y0, HEA, HEM, PLM, 9XX, HEC, FES, CU
- Pockets
- 20 · best druggability 0.90
Structure
electron microscopy · 12 distinct chains · 47% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R, L | Cytochrome C oxidase subunit 1 (EC 7.1.1.9) | protein | 552 | 68% helix, 1% strand | — |
| E, F | Cytochrome BC1 complex cytochrome B subunit (EC 7.1.1.8) | protein | 535 | 63% helix, 5% strand | I7FGS8 |
| D, G | Superoxide dismutase [cu-zn] (EC 1.15.1.1) | protein | 216 | 4% helix, 23% strand | I7G2H6 |
| Q, K | Cytochrome AA3 subunit 2 (EC 7.1.1.9) | protein | 312 | 28% helix, 20% strand | I7GD63 |
| S, X | Cytochrome AA3 subunit 3 | protein | 203 | 74% helix, 0% strand | A0R049 |
| T, Z | Cytochrome C oxidase polypeptide 4 (EC 7.1.1.9) | protein | 139 | 66% helix, 1% strand | I7FPH7 |
| U, a | Cytochrome C oxidase subunit ctaj | protein | 79 | 29% helix, 6% strand | I7FQK8 |
| V, b | Uncharacterized protein MSMEG_4692/MSMEI_4575 | protein | 145 | 41% helix, 16% strand | A0R1B5 |
| P, J | Putative conserved transmembrane protein | protein | 92 | 50% helix, 0% strand | — |
| O, I | Cytochrome BC1 complex cytochrome C subunit (EC 7.1.1.8) | protein | 223 | 44% helix, 4% strand | I7FPH1 |
| c, W | Lpqe protein | protein | 158 | 0% helix, 30% strand | I7GFE1 |
| Y, M | Cytochrome BC1 complex rieske iron-sulfur subunit | protein | 382 | 35% helix, 17% strand | I7GD61 |
Ligands and binding sites
- CDL · Cardiolipin · ligand · 16 copies · chains R, F, E, I, O, L, S, T, M, P, X, Z, Y, J
- MQ9 · Menaquinone-9 · ligand · 8 copies · chains E, Y, M, F, R, T, O, L, Z, I
- 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 · 8 copies · chains F, T, O, E, L, J, c, I, Z, Y, M, R, P, W
- 9Y0 · (2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (E)-octadec-9-enoate · ligand · 6 copies · chains F, P, R, S, T, Q, W, L, X, Z, E, J, K, c
- HEA · Heme-A · ligand · 4 copies · chains R, Q, L, K
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains E, F
- PLM · Palmitic acid · ligand · 4 copies · chains E, D, J, F, G, P, L, c, R, W
- 9XX · (2S)-1-(hexadecanoyloxy)propan-2-yl (10S)-10-methyloctadecanoate · ligand · 4 copies · chains E, D, F, G, L, J, c, R, P, W
- HEC · Heme C · ligand · 4 copies · chains Q, O, W, M, K, c, I, Y
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains Y, M
- CU · Copper (II) ion · metal · 6 copies · chains R, L, Q, K
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 | 912 | 0.90 | 0.92 | 91 | CU, HEA |
| 2 | 974 | 0.90 | 0.91 | 104 | HEA |
| 3 | 912 | 0.87 | 0.88 | 59 | CDL |
| 4 | 1112 | 0.86 | 0.86 | 78 | CDL |
| 5 | 650 | 0.85 | 0.89 | 76 | HEM |
Interfaces
83 interfaces between chains.
- F–M · 4748 Ų buried · 56 hydrogen bonds · protein-protein
- E–Y · 4717 Ų buried · 57 hydrogen bonds · protein-protein
- R–Q · 4532 Ų buried · 49 hydrogen bonds · protein-protein
- L–K · 4521 Ų buried · 51 hydrogen bonds · protein-protein
- Y–M · 2909 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent, 4 lipid, 2 disulfide (covalent ligand, palmitoylation, disulfide).
Compared structures
- 7RH5 · Mycobacterial CIII2CIV2 supercomplex, Inhibitor free · the same entry in another collection · chain R against R, 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 I7FGS8
- Every structure of UniProt I7G2H6
- Every structure of UniProt I7GD63
- Every structure of UniProt A0R049
- Every structure of UniProt I7FPH7
- Every structure of UniProt I7FQK8
- Every structure of UniProt A0R1B5
- Every structure of UniProt I7FPH1
- Every structure of UniProt I7GFE1
- Every structure of UniProt I7GD61
- Elsewhere: RCSB PDB 7RH5 · PDBe 7RH5 · UniProt I7FGS8 · UniProt I7G2H6 · UniProt I7GD63 · UniProt A0R049 · UniProt I7FPH7 · UniProt I7FQK8 · UniProt A0R1B5 · UniProt I7FPH1 · UniProt I7GFE1 · UniProt I7GD61
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