Research workbench
Mycobacterium smegmatis ATP synthase F1 state 3
Analyse Mycobacterium smegmatis ATP synthase F1 state 3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NKJ
- Type
- protein
- Length
- 2,945 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP synthase subunit alpha; ATP synthase subunit beta; ATP synthase gamma chain
- EC
- 7.1.2.2
- UniProt
- A0R202, A0R200, A0R201
- Ligands
- ATP, ADP, MG
- Pockets
- 20 · best druggability 0.90
Structure
electron microscopy · 7 distinct chains · 43% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP synthase subunit alpha (EC 7.1.2.2) | protein | 495 | 42% helix, 21% strand | A0R202 |
| B | ATP synthase subunit alpha (EC 7.1.2.2) | protein | 476 | 41% helix, 21% strand | A0R202 |
| C | ATP synthase subunit alpha (EC 7.1.2.2) | protein | 486 | 42% helix, 21% strand | A0R202 |
| D | ATP synthase subunit beta (EC 7.1.2.2) | protein | 467 | 40% helix, 22% strand | A0R200 |
| E | ATP synthase subunit beta (EC 7.1.2.2) | protein | 464 | 41% helix, 23% strand | A0R200 |
| F | ATP synthase subunit beta (EC 7.1.2.2) | protein | 467 | 42% helix, 22% strand | A0R200 |
| G | ATP synthase gamma chain | protein | 90 | 86% helix, 0% strand | A0R201 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, D, B, E, C, F
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains C, D, E
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, D, F
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 | 1021 | 0.90 | 0.91 | 153 | ATP, MG |
| 2 | 722 | 0.86 | 0.90 | 87 | empty |
| 3 | 1068 | 0.84 | 0.85 | 86 | ATP, MG |
| 4 | 1199 | 0.84 | 0.85 | 105 | ATP, MG |
| 5 | 467 | 0.81 | 0.89 | 77 | ADP, MG |
Interfaces
13 interfaces between chains.
- C–D · 2960 Ų buried · 39 hydrogen bonds · protein-protein
- C–F · 2255 Ų buried · 22 hydrogen bonds · protein-protein
- A–E · 2248 Ų buried · 30 hydrogen bonds · protein-protein
- B–F · 2219 Ų buried · 37 hydrogen bonds · protein-protein
- A–D · 2157 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 7NKJ · Mycobacterium smegmatis ATP synthase F1 state 3 · the same entry in another collection · chain G against G, TM-score 1.00
- A0R202 · AlphaFold monomer V2.0 prediction for ATP synthase subunit alpha (A0R202) · a predicted model of the same protein · chain C against A, TM-score 0.99
- A0R200 · AlphaFold monomer V2.0 prediction for ATP synthase subunit beta (A0R200) · a predicted model of the same protein · chain E against A, TM-score 0.97
- A0R201 · AlphaFold monomer V2.0 prediction for ATP synthase gamma chain (A0R201) · a predicted model of the same protein · chain G against A, TM-score 0.96
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 A0R202
- Every structure of UniProt A0R200
- Every structure of UniProt A0R201
- Elsewhere: RCSB PDB 7NKJ · PDBe 7NKJ · UniProt A0R202 · UniProt A0R200 · UniProt A0R201
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