Research workbench
Mycobacterium smegmatis ATP synthase state 1A
Analyse Mycobacterium smegmatis ATP synthase state 1A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NJK
- Type
- protein
- Length
- 4,934 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
- A0R202, A0R200, A0R201, A0R1Z9, A0R205, A0R206, A0R204, A0R203
- Ligands
- ATP, ADP, MG
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 12 distinct chains · 50% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP synthase subunit alpha (EC 7.1.2.2) | protein | 507 | 41% helix, 20% strand | A0R202 |
| B | ATP synthase subunit alpha (EC 7.1.2.2) | protein | 504 | 42% helix, 20% strand | A0R202 |
| C | ATP synthase subunit alpha (EC 7.1.2.2) | protein | 531 | 42% helix, 21% strand | A0R202 |
| D | ATP synthase subunit beta (EC 7.1.2.2) | protein | 468 | 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 | 469 | 41% helix, 22% strand | A0R200 |
| G | ATP synthase gamma chain | protein | 296 | 61% helix, 16% strand | A0R201 |
| H | ATP synthase epsilon chain | protein | 118 | 20% helix, 46% strand | A0R1Z9 |
| L, M, N, O, P, Q, R, S, T | ATP synthase subunit C | protein | 84 | 89% helix, 0% strand | A0R205 |
| a | ATP synthase subunit a | protein | 238 | 70% helix, 5% strand | A0R206 |
| b | ATP synthase subunit B | protein | 145 | 90% helix, 0% strand | A0R204 |
| d | ATP synthase subunit B-delta | protein | 438 | 76% helix, 5% strand | A0R203 |
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 | 991 | 0.89 | 0.91 | 120 | empty |
| 2 | 1074 | 0.88 | 0.89 | 135 | ATP, MG |
| 3 | 1134 | 0.86 | 0.86 | 81 | empty |
| 4 | 735 | 0.84 | 0.88 | 86 | ATP, MG |
| 5 | 1114 | 0.84 | 0.85 | 105 | ATP, MG |
Interfaces
48 interfaces between chains.
- C–D · 2868 Ų buried · 41 hydrogen bonds · protein-protein
- b–d · 2534 Ų buried · 15 hydrogen bonds · protein-protein
- B–F · 2256 Ų buried · 35 hydrogen bonds · protein-protein
- A–E · 2238 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 2199 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 7NJK · Mycobacterium smegmatis ATP synthase state 1a · the same entry in another collection · chain N against N, 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 A0R202
- Every structure of UniProt A0R200
- Every structure of UniProt A0R201
- Every structure of UniProt A0R1Z9
- Every structure of UniProt A0R205
- Every structure of UniProt A0R206
- Every structure of UniProt A0R204
- Every structure of UniProt A0R203
- Elsewhere: RCSB PDB 7NJK · PDBe 7NJK · UniProt A0R202 · UniProt A0R200 · UniProt A0R201 · UniProt A0R1Z9 · UniProt A0R205 · UniProt A0R206 · UniProt A0R204 · UniProt A0R203
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