Research workbench
Structure of a functional obligate respiratory supercomplex from mycobacterium smegmatis
Analyse Structure of a functional obligate respiratory supercomplex from mycobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HWH
- Type
- protein
- Length
- 5,304 residues
- Chains
- 28
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquinol-cytochrome C reductase iron-sulfur subunit; Co-purified unknown transmembrane…
- EC
- 1.10.2.2, 1.9.3.1
- UniProt
- A0R051, A0R050, A0R057, A0R1B6, A0R1B5, A0R0M4, A0R056, A0R049, I7FGS8
- Ligands
- CDL, MQ9, HAS, HEC, HEM, FES, CU
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 14 distinct chains · 46% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ubiquinol-cytochrome C reductase iron-sulfur subunit | protein | 380 | 27% helix, 13% strand | A0R051 |
| G, C | Co-purified unknown transmembrane helices built as polyala | protein | 74 | 39% helix, 0% strand | — |
| H, D | Co-purified unknown transmembrane helices built as polyala | protein | 65 | 72% helix, 0% strand | — |
| I, E | Co-purified unknown peptide built as polyala | protein | 20 | 20% helix, 0% strand | — |
| J, F | Co-purified unknown peptide built as polyala | protein | 35 | 0% helix, 6% strand | — |
| M, K | Cytochrome BC1 complex cytochrome C subunit (EC 1.10.2.2) | protein | 30 | 70% helix, 0% strand | A0R050 |
| P, L | Cytochrome C oxidase subunit 2 (EC 1.9.3.1) | protein | 281 | 29% helix, 12% strand | A0R057 |
| R, N | MSMEG_4693 | protein | 54 | 24% helix, 6% strand | A0R1B6 |
| T, O | Uncharacterized protein MSMEG_4692/MSMEI_4575 | protein | 142 | 38% helix, 13% strand | A0R1B5 |
| V, Q | Cytochrome C oxidase subunit 1 (EC 1.9.3.1) | protein | 550 | 59% helix, 2% strand | A0R0M4 |
| X, S | Cytochrome C oxidase polypeptide 4 (EC 1.9.3.1) | protein | 139 | 60% helix, 1% strand | A0R056 |
| Z, W | Cytochrome C oxidase subunit 3 (EC 1.9.3.1) | protein | 184 | 70% helix, 1% strand | A0R049 |
| b, Y | Ubiquinol-cytochrome C reductase qcrb (EC 1.10.2.2) | protein | 536 | 49% helix, 4% strand | I7FGS8 |
| i, j | Cytochrome BC1 complex cytochrome C subunit (EC 1.10.2.2) | protein | 162 | 43% helix, 2% strand | A0R050 |
Ligands and binding sites
- CDL · Cardiolipin · ligand · 8 copies · chains A, M, X, Z, b, J, V, K, S, Y, F, Q, W
- MQ9 · Menaquinone-9 · ligand · 4 copies · chains M, b, Y, K
- HAS · Heme-as · ligand · 4 copies · chains P, V, L, Q
- HEC · Heme C · ligand · 4 copies · chains V, i, A, j, L
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains b, Y
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains A, B
- CU · Copper (II) ion · metal · 6 copies · chains P, V, L, Q
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 | 1128 | 0.88 | 0.89 | 107 | HAS |
| 2 | 1196 | 0.88 | 0.88 | 109 | HAS |
| 3 | 716 | 0.87 | 0.90 | 78 | HEM |
| 4 | 880 | 0.87 | 0.88 | 60 | CDL |
| 5 | 1118 | 0.86 | 0.86 | 65 | CDL |
Interfaces
87 interfaces between chains.
- B–Y · 4936 Ų buried · 44 hydrogen bonds · protein-protein
- A–b · 4930 Ų buried · 48 hydrogen bonds · protein-protein
- L–Q · 4210 Ų buried · 38 hydrogen bonds · protein-protein
- P–V · 4160 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 2860 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor, 2 disulfide (heme c attachment, disulfide).
Compared structures
- 6HWH · Structure of a functional obligate respiratory supercomplex from Mycobacterium smegmatis · the same entry in another collection · chain I against I, 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 A0R051
- Every structure of UniProt A0R050
- Every structure of UniProt A0R057
- Every structure of UniProt A0R1B6
- Every structure of UniProt A0R1B5
- Every structure of UniProt A0R0M4
- Every structure of UniProt A0R056
- Every structure of UniProt A0R049
- Every structure of UniProt I7FGS8
- Elsewhere: RCSB PDB 6HWH · PDBe 6HWH · UniProt A0R051 · UniProt A0R050 · UniProt A0R057 · UniProt A0R1B6 · UniProt A0R1B5 · UniProt A0R0M4 · UniProt A0R056 · UniProt A0R049 · UniProt I7FGS8
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