Research workbench
Crystal structure of bovine F1-C8 sub-complex of ATP synthase
Analyse Crystal structure of bovine F1-C8 sub-complex of ATP synthase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XND
- Type
- protein
- Length
- 3,892 residues
- Chains
- 17
- 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
- P19483, P00829, P05631, P05630, P05632, P32876
- Ligands
- ANP, MG, SO4
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 7 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | ATP synthase subunit alpha, mitochondrial (EC 3.6.3.14) | protein | 492 | 42% helix, 20% strand | P19483 |
| D | ATP synthase subunit beta, mitochondrial (EC 3.6.3.14) | protein | 467 | 37% helix, 22% strand | P00829 |
| E, F | ATP synthase subunit beta, mitochondrial (EC 3.6.3.14) | protein | 466 | 35% helix, 21% strand | P00829 |
| G | ATP synthase subunit gamma, mitochondrial (EC 3.6.3.14) | protein | 263 | 58% helix, 12% strand | P05631 |
| H | ATP synthase subunit delta, mitochondrial (EC 3.6.3.14) | protein | 131 | 23% helix, 37% strand | P05630 |
| I | ATP synthase subunit epsilon, mitochondrial (EC 3.6.3.14) | protein | 47 | 40% helix, 4% strand | P05632 |
| J, K, L, M, N, O, P, Q | ATP synthase lipid-binding protein, mitochondrial (EC 3.6.3.14) | protein | 72 | 67% helix, 0% strand | P32876 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 5 copies · chains A, D, B, E, C, F
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, D, F
- SO4 · Sulfate ion · ion · chains A, E
- GOL · Glycerol · additive · chains B
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 | 746 | 0.87 | 0.90 | 97 | ANP, MG |
| 2 | 450 | 0.84 | 0.91 | 49 | empty |
| 3 | 361 | 0.83 | 0.92 | 43 | empty |
| 4 | 628 | 0.83 | 0.88 | 66 | empty |
| 5 | 1062 | 0.83 | 0.84 | 98 | ANP, MG |
Interfaces
33 interfaces between chains.
- C–D · 3157 Ų buried · 48 hydrogen bonds · protein-protein
- A–D · 2532 Ų buried · 32 hydrogen bonds · protein-protein
- C–F · 2392 Ų buried · 28 hydrogen bonds · protein-protein
- B–F · 2305 Ų buried · 32 hydrogen bonds · protein-protein
- A–E · 2139 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 2XND · Crystal structure of bovine F1-c8 sub-complex of ATP Synthase · 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 P32876
- Elsewhere: RCSB PDB 2XND · PDBe 2XND · UniProt P19483 · UniProt P00829 · UniProt P05631 · UniProt P05630 · UniProt P05632 · UniProt P32876
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