Research workbench
Mycobacterium smegmatis ATP synthase Fo combined class 2
Analyse Mycobacterium smegmatis ATP synthase Fo combined class 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NJV
- Type
- protein
- Length
- 1,118 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.9
- Source
- Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)
- Molecule
- ATP synthase subunit c; ATP synthase subunit a; ATP synthase subunit b; ATP synthase…
- UniProt
- A0R205, A0R206, A0R204, A0R203
- Ligands
- BQ1
- Pockets
- 10 · best druggability 0.86
Structure
electron microscopy · resolution 2.9 · 4 distinct chains · 79% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, M, N, O, P, Q, R, S, T | ATP synthase subunit c | protein | 84 | 86% helix, 0% strand | A0R205 |
| a | ATP synthase subunit a | protein | 238 | 72% helix, 5% strand | A0R206 |
| b | ATP synthase subunit b | protein | 63 | 84% helix, 0% strand | A0R204 |
| d | ATP synthase subunit b-delta | protein | 61 | 95% helix, 0% strand | A0R203 |
Ligands and binding sites
- BQ1 · Bedaquiline · ligand · chains M, N, a
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1198 | 0.86 | 0.86 | 85 | empty |
| 2 | 261 | 0.78 | 0.91 | 49 | empty |
| 3 | 101 | 0.72 | 0.94 | 23 | empty |
| 4 | 561 | 0.64 | 0.75 | 55 | empty |
| 5 | 294 | 0.57 | 0.76 | 26 | empty |
Interfaces
17 interfaces between chains.
- a–b · 1712 Ų buried · 11 hydrogen bonds · protein-protein
- Q–R · 1700 Ų buried · 6 hydrogen bonds · protein-protein
- L–T · 1697 Ų buried · 8 hydrogen bonds · protein-protein
- L–M · 1678 Ų buried · 9 hydrogen bonds · protein-protein
- R–S · 1675 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 7NJV · Mycobacterium smegmatis ATP synthase fo combined class 2 · the same entry in another collection · chain d against d, 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 A0R205
- Every structure of UniProt A0R206
- Every structure of UniProt A0R204
- Every structure of UniProt A0R203
- Elsewhere: RCSB PDB 7NJV · PDBe 7NJV · UniProt A0R205 · UniProt A0R206 · UniProt A0R204 · UniProt A0R203
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