Research workbench
Mycobacterial CIII2CIV2 supercomplex, telacebec (Q203) bound
Analyse Mycobacterial CIII2CIV2 supercomplex, telacebec (Q203) bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RH7
- Type
- protein
- Length
- 6,072 residues
- Chains
- 24
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lpqe protein; Cytochrome AA3 subunit 2; Cytochrome C oxidase subunit 1; Cytochrome AA3…
- EC
- 7.1.1.9, 1.15.1.1, 7.1.1.8
- UniProt
- I7GFE1, I7GD63, A0R049, I7FPH7, I7FQK8, A0R1B5, A0QVH4, I7G2H6, I7FPH1, I7FGS8, I7GD61
- Ligands
- CDL, 9YF, MQ9, 9XX, PLM, HEA, 9Y0, HEC, HEM, HUU, FES, CU
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 12 distinct chains · 46% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| W, c | Lpqe protein | protein | 158 | 0% helix, 28% strand | I7GFE1 |
| Q, K | Cytochrome AA3 subunit 2 (EC 7.1.1.9) | protein | 312 | 26% helix, 20% strand | I7GD63 |
| R, L | Cytochrome C oxidase subunit 1 (EC 7.1.1.9) | protein | 552 | 67% helix, 1% strand | — |
| 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 | 68% helix, 1% strand | I7FPH7 |
| U, a | Cytochrome C oxidase subunit ctaj | protein | 79 | 30% helix, 11% strand | I7FQK8 |
| V, b | Uncharacterized protein MSMEG_4692/MSMEI_4575 | protein | 145 | 37% helix, 16% strand | A0R1B5 |
| P, J | Conserved transmembrane protein | protein | 92 | 50% helix, 0% strand | A0QVH4 |
| G, D | Superoxide dismutase [cu-zn] (EC 1.15.1.1) | protein | 216 | 4% helix, 21% strand | I7G2H6 |
| O, I | Cytochrome BC1 complex cytochrome C subunit (EC 7.1.1.8) | protein | 223 | 44% helix, 4% strand | I7FPH1 |
| E, F | Cytochrome BC1 complex cytochrome B subunit (EC 7.1.1.8) | protein | 535 | 62% helix, 5% strand | I7FGS8 |
| Y, M | Cytochrome BC1 complex rieske iron-sulfur subunit | protein | 382 | 36% helix, 17% strand | I7GD61 |
Ligands and binding sites
- CDL · Cardiolipin · ligand · 16 copies · chains R, E, S, T, O, M, P, F, L, X, Z, I, Y, J
- 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 T, O, E, W, R, P, Z, I, F, L, J, c, Y, M
- MQ9 · Menaquinone-9 · ligand · 6 copies · chains R, T, O, E, Y, M, L, Z, I, F
- 9XX · (2S)-1-(hexadecanoyloxy)propan-2-yl (10S)-10-methyloctadecanoate · ligand · 4 copies · chains W, R, P, E, G, D, F, L, J, c
- PLM · Palmitic acid · ligand · 4 copies · chains W, R, P, G, E, J, D, F, L, c
- HEA · Heme-A · ligand · 4 copies · chains Q, R, K, L
- 9Y0 · (2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (E)-octadec-9-enoate · ligand · 4 copies · chains R, S, T, W, Q, P, K, L, J, c, X, Z
- HEC · Heme C · ligand · 4 copies · chains W, Q, O, M, K, c, I, Y
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains E, F
- HUU · 6-chloranyl-2-ethyl-N-[[4-[4-[4-(trifluoromethyloxy) phenyl]piperidin-1-yl]phenyl]methyl]imidazo[1,2-a]pyridine-3-carboxamide · ligand · 2 copies · chains E, M, F, Y
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains Y, M
- CU · Copper (II) ion · metal · 6 copies · chains Q, R, K, L
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 | 911 | 0.89 | 0.91 | 92 | HEA |
| 2 | 1021 | 0.89 | 0.90 | 111 | HEA |
| 3 | 1196 | 0.86 | 0.87 | 75 | CDL |
| 4 | 1118 | 0.86 | 0.86 | 69 | CDL |
| 5 | 636 | 0.85 | 0.89 | 78 | HEM |
Interfaces
82 interfaces between chains.
- F–Y · 4729 Ų buried · 54 hydrogen bonds · protein-protein
- E–M · 4681 Ų buried · 49 hydrogen bonds · protein-protein
- K–L · 4503 Ų buried · 48 hydrogen bonds · protein-protein
- Q–R · 4429 Ų buried · 54 hydrogen bonds · protein-protein
- Y–M · 2898 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 covalent, 4 disulfide, 4 lipid, 1 cofactor (covalent ligand, disulfide, palmitoylation, heme c attachment).
Compared structures
- 7RH7 · Mycobacterial CIII2CIV2 supercomplex, Telacebec (Q203) bound · the same entry in another collection · chain W against W, 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 I7GFE1
- 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 A0QVH4
- Every structure of UniProt I7G2H6
- Every structure of UniProt I7FPH1
- Every structure of UniProt I7FGS8
- Every structure of UniProt I7GD61
- Elsewhere: RCSB PDB 7RH7 · PDBe 7RH7 · UniProt I7GFE1 · UniProt I7GD63 · UniProt A0R049 · UniProt I7FPH7 · UniProt I7FQK8 · UniProt A0R1B5 · UniProt A0QVH4 · UniProt I7G2H6 · UniProt I7FPH1 · UniProt I7FGS8 · UniProt I7GD61
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