MolNFT v1 · #142732 · protein
Respiratory complex CIII2CIV2SOD2 from mycobacterium smegmatis
6ADQ · Cytochrome C oxidase subunit 2: “Respiratory complex CIII2CIV2SOD2 from mycobacterium smegmatis”. Electron microscopy, 11 ligands (CDL, MQ9, 9Y0), 20 pockets (best druggability 0.90). MolNFT v1 #142732 on GenesisL1: 3D structure…
- PDB
- 6ADQ
- Type
- protein
- Length
- 6,026 residues
- Chains
- 24
- 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
- 1.9.3.1, 1.15.1.1, 1.10.2.2
- UniProt
- A0R057, A0R049, A0R056, A0R1B6, A0R1B5, A0QQQ1, A0R562, A0R052, I7FPH1, I7GD61
- Ligands
- CDL, MQ9, 9Y0, 9YF, HEA, PLM, 9XX, HEM, HEC, FES, CU
- Pockets
- 20 · best druggability 0.90
Structure
electron microscopy · 12 distinct chains · 43% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, Q | Cytochrome C oxidase subunit 2 (EC 1.9.3.1) | protein | 312 | 25% helix, 17% strand | A0R057 |
| F, R | Cytochrome C oxidase subunit 1 (EC 1.9.3.1) | protein | 552 | 63% helix, 1% strand | — |
| G, S | Cytochrome C oxidase subunit 3 (EC 1.9.3.1) | protein | 203 | 69% helix, 0% strand | A0R049 |
| H, T | Cytochrome C oxidase polypeptide 4 (EC 1.9.3.1) | protein | 139 | 62% helix, 1% strand | A0R056 |
| I, U | Cytochrome C oxidase subunit ctaj | protein | 67 | 34% helix, 6% strand | A0R1B6 |
| J, V | Uncharacterized protein MSMEG_4692/MSMEI_4575 | protein | 145 | 31% helix, 11% strand | A0R1B5 |
| D, P | Prokaryotic respiratory supercomplex associate factor 1 PRSAF1 | protein | 92 | 47% helix, 0% strand | — |
| Y, Z | Superoxide dismutase [cu-zn] (EC 1.15.1.1) | protein | 216 | 4% helix, 23% strand | A0QQQ1 |
| K, W | Lpqe protein | protein | 147 | 0% helix, 27% strand | A0R562 |
| B, N | Ubiquinol-cytochrome C reductase cytochrome B subunit | protein | 535 | 59% helix, 5% strand | A0R052 |
| C, O | Cytochrome BC1 complex cytochrome C subunit (EC 1.10.2.2) | protein | 223 | 42% helix, 4% strand | I7FPH1 |
| A, M | Rieske iron-sulfur protein qcra | protein | 382 | 31% helix, 17% strand | I7GD61 |
Ligands and binding sites
- CDL · Cardiolipin · ligand · 18 copies · chains F, G, H, D, B, C, A, N, M, R, S, T, P, O
- MQ9 · Menaquinone-9 · ligand · 10 copies · chains B, A, M, F, H, C, N, R, T, O
- 9Y0 · (2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (E)-octadec-9-enoate · ligand · 8 copies · chains F, G, H, D, B, E, K, N, R, S, T, P, Q, W
- 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, D, K, B, C, H, A, N, M, R, P, W, O, T
- HEA · Heme-A · ligand · 4 copies · chains E, F, Q, R
- PLM · Palmitic acid · ligand · 4 copies · chains D, Y, B, F, K, P, Z, N, R, W
- 9XX · (2S)-1-(hexadecanoyloxy)propan-2-yl (10S)-10-methyloctadecanoate · ligand · 4 copies · chains Y, B, F, D, K, Z, N, R, P, W
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains B, N
- HEC · Heme C · ligand · 4 copies · chains E, K, C, A, Q, W, O, M
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains A, M
- 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 | 869 | 0.90 | 0.92 | 92 | HEA, CU |
| 2 | 952 | 0.89 | 0.90 | 104 | HEA, CU |
| 3 | 1099 | 0.87 | 0.89 | 182 | empty |
| 4 | 1149 | 0.87 | 0.87 | 74 | CDL |
| 5 | 1138 | 0.86 | 0.87 | 73 | CDL |
Interfaces
83 interfaces between chains.
- N–M · 4687 Ų buried · 48 hydrogen bonds · protein-protein
- B–A · 4680 Ų buried · 46 hydrogen bonds · protein-protein
- E–F · 4613 Ų buried · 46 hydrogen bonds · protein-protein
- Q–R · 4599 Ų buried · 46 hydrogen bonds · protein-protein
- A–M · 2907 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 covalent, 4 lipid, 2 cofactor, 2 disulfide (covalent ligand, palmitoylation, heme attachment, disulfide).
Compared structures
- 6ADQ · Respiratory Complex CIII2CIV2SOD2 from Mycobacterium smegmatis · the same entry in another collection · chain E against E, 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 A0QQQ1
- Every structure of UniProt A0R562
- Every structure of UniProt A0R052
- Every structure of UniProt I7FPH1
- Every structure of UniProt I7GD61
- Elsewhere: RCSB PDB 6ADQ · PDBe 6ADQ · UniProt A0R057 · UniProt A0R049 · UniProt A0R056 · UniProt A0R1B6 · UniProt A0R1B5 · UniProt A0QQQ1 · UniProt A0R562 · UniProt A0R052 · UniProt I7FPH1 · UniProt I7GD61
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