Research workbench
The MG.ADP inhibited state of the yeast F1C10 ATP synthase
Analyse The MG.ADP inhibited state of the yeast F1C10 ATP synthase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WPD
- Type
- protein
- Length
- 4,090 residues
- Chains
- 19
- Method
- x-ray diffraction
- 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
- Ligands
- ATP, ADP, MG
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 9 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | ATP synthase subunit alpha, mitochondrial | protein | 485 | 39% helix, 19% strand | P07251 |
| B | ATP synthase subunit alpha, mitochondrial | protein | 485 | 40% helix, 19% strand | P07251 |
| D | ATP synthase subunit beta, mitochondrial (EC 3.6.3.14) | protein | 470 | 35% helix, 19% strand | P00830 |
| E | ATP synthase subunit beta, mitochondrial (EC 3.6.3.14) | protein | 473 | 37% helix, 22% strand | P00830 |
| F | ATP synthase subunit beta, mitochondrial (EC 3.6.3.14) | protein | 472 | 36% helix, 21% strand | P00830 |
| G | ATP synthase subunit gamma, mitochondrial | protein | 269 | 58% helix, 12% strand | P38077 |
| H | ATP synthase subunit delta, mitochondrial | protein | 132 | 27% helix, 37% strand | Q12165 |
| I | ATP synthase subunit epsilon, mitochondrial | protein | 59 | 29% helix, 15% strand | P21306 |
| J, K, L, M, N, O, P, Q, R, S | ATP synthase subunit 9, mitochondrial (EC 3.6.3.14) | protein | 76 | 76% helix, 0% strand | P61829 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 3 copies · chains A, D, B, C, F
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains C, D, B, F
- 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 | 945 | 0.88 | 0.89 | 126 | empty |
| 2 | 779 | 0.86 | 0.89 | 86 | ATP, MG |
| 3 | 1032 | 0.85 | 0.86 | 110 | ADP, MG |
| 4 | 699 | 0.84 | 0.88 | 83 | ADP, MG |
| 5 | 1063 | 0.83 | 0.84 | 81 | ATP, MG |
Interfaces
39 interfaces between chains.
- B–F · 3114 Ų buried · 42 hydrogen bonds · protein-protein
- A–D · 2480 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 2314 Ų buried · 25 hydrogen bonds · protein-protein
- C–F · 2314 Ų buried · 25 hydrogen bonds · protein-protein
- A–E · 1918 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 2WPD · The Mg.ADP inhibited state of the yeast F1c10 ATP synthase · 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
- Elsewhere: RCSB PDB 2WPD · PDBe 2WPD · UniProt P07251 · UniProt P00830 · UniProt P38077 · UniProt Q12165 · UniProt P21306 · UniProt P61829
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