Research workbench
Yeast F1 ATPase in the absence of bound nucleotides
Analyse Yeast F1 ATPase in the absence of bound nucleotides in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FKS
- Type
- protein
- Length
- 9,507 residues
- Chains
- 27
- 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
- Ligands
- PO4
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 24 distinct chains · 37% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP synthase subunit alpha, mitochondrial (EC 3.6.3.14) | protein | 484 | 41% helix, 21% strand | P07251 |
| B | ATP synthase subunit alpha, mitochondrial (EC 3.6.3.14) | protein | 479 | 35% helix, 20% strand | P07251 |
| C, L | ATP synthase subunit alpha, mitochondrial (EC 3.6.3.14) | protein | 484 | 40% helix, 19% strand | P07251 |
| D | ATP synthase subunit beta, mitochondrial (EC 3.6.3.14) | protein | 466 | 29% helix, 19% strand | P00830 |
| E | ATP synthase subunit beta, mitochondrial (EC 3.6.3.14) | protein | 468 | 35% helix, 19% strand | P00830 |
| F | ATP synthase subunit beta, mitochondrial (EC 3.6.3.14) | protein | 471 | 36% helix, 20% strand | P00830 |
| G | ATP synthase subunit gamma, mitochondrial (EC 3.6.3.14) | protein | 268 | 59% helix, 11% strand | P38077 |
| H | ATP synthase subunit delta, mitochondrial (EC 3.6.3.14) | protein | 116 | 8% helix, 35% strand | Q12165 |
| I | ATP synthase subunit epsilon, mitochondrial (EC 3.6.3.14) | protein | 46 | 24% helix, 13% strand | P21306 |
| J | ATP synthase subunit alpha, mitochondrial (EC 3.6.3.14) | protein | 481 | 38% helix, 20% strand | P07251 |
| K | ATP synthase subunit alpha, mitochondrial (EC 3.6.3.14) | protein | 484 | 37% helix, 20% strand | P07251 |
| M, O, X | ATP synthase subunit beta, mitochondrial (EC 3.6.3.14) | protein | 469 | 35% helix, 19% strand | P00830 |
| N | ATP synthase subunit beta, mitochondrial (EC 3.6.3.14) | protein | 466 | 35% helix, 19% strand | P00830 |
| P | ATP synthase subunit gamma, mitochondrial (EC 3.6.3.14) | protein | 235 | 58% helix, 8% strand | P38077 |
| Q | ATP synthase subunit delta, mitochondrial (EC 3.6.3.14) | protein | 68 | 9% helix, 3% strand | Q12165 |
| R | ATP synthase subunit epsilon, mitochondrial (EC 3.6.3.14) | protein | 25 | 0% helix, 4% strand | P21306 |
| S | ATP synthase subunit alpha, mitochondrial (EC 3.6.3.14) | protein | 481 | 40% helix, 20% strand | P07251 |
| T | ATP synthase subunit alpha, mitochondrial (EC 3.6.3.14) | protein | 473 | 33% helix, 18% strand | P07251 |
| U | ATP synthase subunit alpha, mitochondrial (EC 3.6.3.14) | protein | 477 | 39% helix, 19% strand | P07251 |
| V | ATP synthase subunit beta, mitochondrial (EC 3.6.3.14) | protein | 455 | 31% helix, 19% strand | P00830 |
| W | ATP synthase subunit beta, mitochondrial (EC 3.6.3.14) | protein | 466 | 35% helix, 18% strand | P00830 |
| Y | ATP synthase subunit gamma, mitochondrial (EC 3.6.3.14) | protein | 187 | 70% helix, 3% strand | P38077 |
| Z | ATP synthase subunit delta, mitochondrial (EC 3.6.3.14) | protein | 11 | 45% helix, 0% strand | Q12165 |
| 1 | ATP synthase subunit epsilon, mitochondrial (EC 3.6.3.14) | protein | 25 | 16% helix, 0% strand | P21306 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 15 copies · chains A, B, C, D, F, J, K, L, M, N, O, S, T, U, X
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 | 978 | 0.89 | 0.91 | 121 | PO4 |
| 2 | 1001 | 0.88 | 0.90 | 122 | empty |
| 3 | 958 | 0.87 | 0.88 | 107 | empty |
| 4 | 761 | 0.86 | 0.89 | 83 | PO4 |
| 5 | 711 | 0.85 | 0.89 | 70 | PO4 |
Interfaces
54 interfaces between chains.
- L–M · 3187 Ų buried · 34 hydrogen bonds · protein-protein
- T–X · 2962 Ų buried · 39 hydrogen bonds · protein-protein
- K–O · 2912 Ų buried · 37 hydrogen bonds · protein-protein
- B–F · 2841 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 2689 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 3FKS · Yeast F1 ATPase in the absence of bound nucleotides · 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 P07251
- Every structure of UniProt P00830
- Every structure of UniProt P38077
- Every structure of UniProt Q12165
- Every structure of UniProt P21306
- Elsewhere: RCSB PDB 3FKS · PDBe 3FKS · UniProt P07251 · UniProt P00830 · UniProt P38077 · UniProt Q12165 · UniProt P21306
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