Research workbench
Cryo-EM structure of bedaquiline-saturated mycobacterium smegmatis ATP synthase rotational state 1 (backbone model)
Analyse Cryo-EM structure of bedaquiline-saturated mycobacterium smegmatis ATP synthase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JG8
- Type
- protein
- Length
- 4,827 residues
- Chains
- 20
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP synthase subunit alpha; ATP synthase subunit beta; ATP synthase gamma chain; ATP…
- EC
- 7.1.2.2
- UniProt
- A0A0D6IV93, A0A0D6IU77, A0A0D6IUE3, A0A0D6IU73, A0R206, A0A0D6IV98, A0R203, Q5TIX5
- Ligands
- BQ1
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · 10 distinct chains · 54% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP synthase subunit alpha (EC 7.1.2.2) | protein | 523 | 43% helix, 21% strand | A0A0D6IV93 |
| B | ATP synthase subunit alpha (EC 7.1.2.2) | protein | 508 | 44% helix, 19% strand | A0A0D6IV93 |
| C | ATP synthase subunit alpha (EC 7.1.2.2) | protein | 506 | 42% helix, 20% strand | A0A0D6IV93 |
| D, E, F | ATP synthase subunit beta (EC 7.1.2.2) | protein | 464 | 42% helix, 22% strand | A0A0D6IU77 |
| G | ATP synthase gamma chain | protein | 279 | 63% helix, 18% strand | A0A0D6IUE3 |
| H | ATP synthase epsilon chain | protein | 117 | 18% helix, 46% strand | A0A0D6IU73 |
| a | ATP synthase subunit a | protein | 207 | 81% helix, 0% strand | A0R206 |
| b | ATP synthase subunit B | protein | 138 | 95% helix, 0% strand | A0A0D6IV98 |
| d | ATP synthase subunit B-delta | protein | 428 | 78% helix, 5% strand | A0R203 |
| 1, 2, 3, 4, 5, 6, 7, 8, 9 | ATP synthase subunit C | protein | 81 | 90% helix, 0% strand | Q5TIX5 |
Ligands and binding sites
- BQ1 · Bedaquiline · ligand · 7 copies · chains a, 1, 9, 2, 3, 4, 5, 6, 7
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 | 757 | 0.78 | 0.83 | 123 | empty |
| 2 | 867 | 0.76 | 0.80 | 142 | empty |
| 3 | 826 | 0.74 | 0.80 | 120 | empty |
| 4 | 560 | 0.74 | 0.83 | 121 | empty |
| 5 | 352 | 0.74 | 0.86 | 63 | empty |
Interfaces
36 interfaces between chains.
- A–D · 727 Ų buried · 7 hydrogen bonds · protein-protein
- b–d · 553 Ų buried · 0 hydrogen bonds · protein-protein
- B–E · 490 Ų buried · 6 hydrogen bonds · protein-protein
- 7–8 · 481 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 479 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 7JG8 · Cryo-EM structure of bedaquiline-saturated Mycobacterium smegmatis ATP synthase… · the same entry in another collection · chain 9 against 9, 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 A0A0D6IV93
- Every structure of UniProt A0A0D6IU77
- Every structure of UniProt A0A0D6IUE3
- Every structure of UniProt A0A0D6IU73
- Every structure of UniProt A0R206
- Every structure of UniProt A0A0D6IV98
- Every structure of UniProt A0R203
- Every structure of UniProt Q5TIX5
- Elsewhere: RCSB PDB 7JG8 · PDBe 7JG8 · UniProt A0A0D6IV93 · UniProt A0A0D6IU77 · UniProt A0A0D6IUE3 · UniProt A0A0D6IU73 · UniProt A0R206 · UniProt A0A0D6IV98 · UniProt A0R203 · UniProt Q5TIX5
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