Research workbench
Model of the yeast F1FO-ATP synthase dimer based on subtomogram average
Analyse Model of the yeast F1FO-ATP synthase dimer based on subtomogram average in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4B2Q
- Type
- protein
- Length
- 9,028 residues
- Chains
- 46
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP synthase subunit alpha, mitochondrial; ATP synthase subunit beta, mitochondrial; ATP…
- EC
- 3.6.3.14
- UniProt
- P07251, P00830, P38077, Q12165, P21306, P61829, P13619, P13620, P02721, P13621
- Ligands
- ATP, ADP, MG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 13 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, a, c | ATP synthase subunit alpha, mitochondrial | protein | 485 | 39% helix, 19% strand | P07251 |
| B, b | ATP synthase subunit alpha, mitochondrial | protein | 485 | 40% helix, 19% strand | P07251 |
| D, d | ATP synthase subunit beta, mitochondrial (EC 3.6.3.14) | protein | 470 | 35% helix, 19% strand | P00830 |
| E, e | ATP synthase subunit beta, mitochondrial (EC 3.6.3.14) | protein | 473 | 37% helix, 22% strand | P00830 |
| F, f | ATP synthase subunit beta, mitochondrial (EC 3.6.3.14) | protein | 472 | 36% helix, 21% strand | P00830 |
| G, g | ATP synthase subunit gamma, mitochondrial | protein | 269 | 58% helix, 12% strand | P38077 |
| H, h | ATP synthase subunit delta, mitochondrial | protein | 132 | 27% helix, 37% strand | Q12165 |
| I, i | ATP synthase subunit epsilon, mitochondrial | protein | 59 | 29% helix, 15% strand | P21306 |
| J, K, L, M, N, O, P, Q, R, S, j, k, l, m, n, o, p, q, r, s | ATP synthase subunit 9, mitochondrial | protein | 76 | 76% helix, 0% strand | P61829 |
| T, t | ATP synthase subunit B, mitochondrial (EC 3.6.3.14) | protein | 129 | 95% helix, 0% strand | P13619 |
| U, u | ATP synthase subunit D, mitochondrial | protein | 120 | 64% helix, 0% strand | P13620 |
| V, v | ATP synthase-coupling factor 6, mitochondrial | protein | 65 | 43% helix, 0% strand | P02721 |
| W, w | ATP synthase subunit O, mitochondrial (EC 3.6.3.14) | protein | 110 | 60% helix, 0% strand | P13621 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 6 copies · chains A, D, B, C, F, a, d, b, c, f
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains C, D, B, F, c, d, b, f
- MG · Magnesium ion · metal · 10 copies · chains A, B, C, D, F, 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 | 885 | 0.87 | 0.89 | 109 | empty |
| 2 | 796 | 0.86 | 0.89 | 90 | ATP, MG |
| 3 | 986 | 0.85 | 0.86 | 100 | ADP, MG |
| 4 | 516 | 0.84 | 0.91 | 62 | MG |
| 5 | 1079 | 0.84 | 0.85 | 107 | ADP, MG |
Interfaces
104 interfaces between chains.
- b–f · 3114 Ų buried · 42 hydrogen bonds · protein-protein
- B–F · 3106 Ų buried · 42 hydrogen bonds · protein-protein
- t–u · 2881 Ų buried · 21 hydrogen bonds · protein-protein
- T–U · 2874 Ų buried · 21 hydrogen bonds · protein-protein
- a–d · 2482 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 4B2Q · Model of the yeast F1Fo-ATP synthase dimer based on subtomogram average · the same entry in another collection · chain J against J, 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 P07251
- Every structure of UniProt P00830
- Every structure of UniProt P38077
- Every structure of UniProt Q12165
- Every structure of UniProt P21306
- Every structure of UniProt P61829
- Every structure of UniProt P13619
- Every structure of UniProt P13620
- Every structure of UniProt P02721
- Every structure of UniProt P13621
- Elsewhere: RCSB PDB 4B2Q · PDBe 4B2Q · UniProt P07251 · UniProt P00830 · UniProt P38077 · UniProt Q12165 · UniProt P21306 · UniProt P61829 · UniProt P13619 · UniProt P13620 · UniProt P02721 · UniProt P13621
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