Research workbench
Bovine ATP synthase monomer state 3 (combined)
Analyse Bovine ATP synthase monomer state 3 (combined) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZQN
- Type
- protein
- Length
- 5,165 residues
- Chains
- 29
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP synthase subunit alpha, mitochondrial; ATP synthase subunit beta, mitochondrial; ATP…
- EC
- 7.1.2.2
- UniProt
- P19483, P00829, P05631, P05630, P05632, P01096, P07926, P13621, P03929, P00847, P13620, Q28851, Q28852, P14790, P13619, P02721, Q3ZBI7, Q00361
- Ligands
- ATP, ADP, CDL, LHG, MG
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 22 distinct chains · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP synthase subunit alpha, mitochondrial | protein | 501 | 38% helix, 17% strand | P19483 |
| B | ATP synthase subunit alpha, mitochondrial | protein | 502 | 40% helix, 18% strand | P19483 |
| C | ATP synthase subunit alpha, mitochondrial | protein | 483 | 37% helix, 18% strand | P19483 |
| D | ATP synthase subunit beta, mitochondrial (EC 7.1.2.2) | protein | 469 | 37% helix, 19% strand | P00829 |
| E, F | ATP synthase subunit beta, mitochondrial (EC 7.1.2.2) | protein | 467 | 35% helix, 18% strand | P00829 |
| G | ATP synthase subunit gamma, mitochondrial | protein | 272 | 62% helix, 14% strand | P05631 |
| H | ATP synthase subunit delta, mitochondrial | protein | 131 | 29% helix, 39% strand | P05630 |
| I | ATP synthase subunit epsilon, mitochondrial | protein | 47 | 55% helix, 9% strand | P05632 |
| J | ATPase inhibitor, mitochondrial | protein | 47 | 68% helix, 0% strand | P01096 |
| K, L, P | ATP synthase F(0) complex subunit C2, mitochondrial | protein | 74 | 85% helix, 0% strand | P07926 |
| M, N, R, O, Q | ATP synthase F(0) complex subunit C2, mitochondrial | protein | 75 | 85% helix, 0% strand | P07926 |
| S | ATP synthase subunit O, mitochondrial | protein | 187 | 56% helix, 14% strand | P13621 |
| 8 | ATP synthase protein 8 | protein | 41 | 66% helix, 0% strand | P03929 |
| a | ATP synthase subunit a | protein | 226 | 74% helix, 0% strand | P00847 |
| d | ATP synthase subunit D, mitochondrial | protein | 155 | 57% helix, 1% strand | P13620 |
| f | ATP synthase subunit F, mitochondrial | protein | 83 | 66% helix, 0% strand | Q28851 |
| g | ATP synthase subunit G, mitochondrial | protein | 79 | 78% helix, 0% strand | Q28852 |
| j | ATP synthase subunit ATP5MPL, mitochondrial | protein | 48 | 83% helix, 0% strand | P14790 |
| b | ATP synthase F(0) complex subunit B1, mitochondrial | protein | 209 | 84% helix, 2% strand | P13619 |
| h | ATP synthase-coupling factor 6, mitochondrial | protein | 62 | 55% helix, 0% strand | P02721 |
| k | ATP synthase membrane subunit dapit, mitochondrial | protein | 36 | 75% helix, 0% strand | Q3ZBI7 |
| e | ATP synthase subunit E, mitochondrial | protein | 56 | 88% helix, 0% strand | Q00361 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 3 copies · chains A, D, B, E, C, F
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains C, D, E, B, F
- CDL · Cardiolipin · ligand · 3 copies · chains 8, a, f, j, g, b
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 2 copies · chains f, b
- 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 | 766 | 0.88 | 0.91 | 97 | ATP, MG |
| 2 | 458 | 0.85 | 0.93 | 72 | ATP, MG |
| 3 | 646 | 0.83 | 0.88 | 85 | empty |
| 4 | 313 | 0.82 | 0.93 | 63 | ATP, MG |
| 5 | 543 | 0.82 | 0.88 | 82 | ADP, MG |
Interfaces
81 interfaces between chains.
- d–b · 3068 Ų buried · 32 hydrogen bonds · protein-protein
- A–D · 2509 Ų buried · 29 hydrogen bonds · protein-protein
- C–F · 2477 Ų buried · 31 hydrogen bonds · protein-protein
- B–F · 2232 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 2075 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (methylation).
Compared structures
- 6ZQN · bovine ATP synthase monomer state 3 (combined) · the same entry in another collection · chain K against K, 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 P19483
- Every structure of UniProt P00829
- Every structure of UniProt P05631
- Every structure of UniProt P05630
- Every structure of UniProt P05632
- Every structure of UniProt P01096
- Every structure of UniProt P07926
- Every structure of UniProt P13621
- Every structure of UniProt P03929
- Every structure of UniProt P00847
- Every structure of UniProt P13620
- Every structure of UniProt Q28851
- Every structure of UniProt Q28852
- Every structure of UniProt P14790
- Every structure of UniProt P13619
- Every structure of UniProt P02721
- Every structure of UniProt Q3ZBI7
- Every structure of UniProt Q00361
- Elsewhere: RCSB PDB 6ZQN · PDBe 6ZQN · UniProt P19483 · UniProt P00829 · UniProt P05631 · UniProt P05630 · UniProt P05632 · UniProt P01096 · UniProt P07926 · UniProt P13621 · UniProt P03929 · UniProt P00847 · UniProt P13620 · UniProt Q28851 · UniProt Q28852 · UniProt P14790 · UniProt P13619 · UniProt P02721 · UniProt Q3ZBI7 · UniProt Q00361
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