Research workbench
Yeast ATP synthase state 3CATALYTIC(D) with 10 mm ATP backbone model
Analyse Yeast ATP synthase state 3CATALYTIC(D) with 10 mm ATP backbone model in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TKR
- Type
- protein
- Length
- 5,056 residues
- Chains
- 27
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP synthase subunit 9; ATP synthase subunit alpha; ATP synthase subunit beta; ATP…
- EC
- 7.1.2.2
- UniProt
- P61829, P07251, P00830, P38077, Q12165, P21306, P09457, P00854, P05626, P30902, Q06405, Q12349, P81450, P00856
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 20 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 0, 1, 2, 4, 5, 8 | ATP synthase subunit 9 | protein | 75 | 96% helix, 0% strand | P61829 |
| 3, 6, 9 | ATP synthase subunit 9 | protein | 74 | 91% helix, 0% strand | P61829 |
| 7 | ATP synthase subunit 9 | protein | 73 | 92% helix, 0% strand | P61829 |
| A | ATP synthase subunit alpha | protein | 499 | 38% helix, 16% strand | P07251 |
| B | ATP synthase subunit alpha | protein | 507 | 39% helix, 19% strand | P07251 |
| C | ATP synthase subunit alpha | protein | 496 | 39% helix, 19% strand | P07251 |
| D | ATP synthase subunit beta (EC 7.1.2.2) | protein | 468 | 36% helix, 20% strand | P00830 |
| E | ATP synthase subunit beta (EC 7.1.2.2) | protein | 469 | 34% helix, 19% strand | P00830 |
| F | ATP synthase subunit beta (EC 7.1.2.2) | protein | 470 | 37% helix, 19% strand | P00830 |
| G | ATP synthase subunit gamma | protein | 265 | 63% helix, 12% strand | P38077 |
| H | ATP synthase subunit delta | protein | 120 | 25% helix, 39% strand | Q12165 |
| I | ATP synthase subunit epsilon | protein | 48 | 35% helix, 13% strand | P21306 |
| O | ATP synthase subunit 5 | protein | 187 | 47% helix, 8% strand | P09457 |
| T | ATP synthase subunit a | protein | 224 | 70% helix, 0% strand | P00854 |
| U | ATP synthase subunit 4 | protein | 155 | 94% helix, 0% strand | P05626 |
| V | ATP synthase subunit D | protein | 171 | 58% helix, 0% strand | P30902 |
| W | ATP synthase subunit F | protein | 85 | 42% helix, 1% strand | Q06405 |
| X | ATP synthase subunit H | protein | 62 | 45% helix, 2% strand | Q12349 |
| Y | ATP synthase subunit J | protein | 37 | 57% helix, 0% strand | P81450 |
| Z | ATP synthase protein 8 | protein | 48 | 79% helix, 0% strand | P00856 |
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 | 0.80 | 0.83 | 122 | empty |
| 2 | 859 | 0.80 | 0.84 | 129 | empty |
| 3 | 785 | 0.74 | 0.80 | 135 | empty |
| 4 | 718 | 0.74 | 0.81 | 121 | empty |
| 5 | 448 | 0.74 | 0.84 | 62 | empty |
Interfaces
53 interfaces between chains.
- B–F · 575 Ų buried · 9 hydrogen bonds · protein-protein
- B–E · 534 Ų buried · 3 hydrogen bonds · protein-protein
- A–E · 520 Ų buried · 7 hydrogen bonds · protein-protein
- 1–2 · 452 Ų buried · 0 hydrogen bonds · protein-protein
- 0–1 · 450 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7TKR · Yeast ATP synthase State 3catalytic(d) with 10 mM ATP backbone model · the same entry in another collection · chain 2 against 2, 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 P61829
- 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 P09457
- Every structure of UniProt P00854
- Every structure of UniProt P05626
- Every structure of UniProt P30902
- Every structure of UniProt Q06405
- Every structure of UniProt Q12349
- Every structure of UniProt P81450
- Every structure of UniProt P00856
- Elsewhere: RCSB PDB 7TKR · PDBe 7TKR · UniProt P61829 · UniProt P07251 · UniProt P00830 · UniProt P38077 · UniProt Q12165 · UniProt P21306 · UniProt P09457 · UniProt P00854 · UniProt P05626 · UniProt P30902 · UniProt Q06405 · UniProt Q12349 · UniProt P81450 · UniProt P00856
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