Research workbench
Yeast ATP synthase state 2CATALYTIC(D) with 10 mm ATP backbone model
Analyse Yeast ATP synthase state 2CATALYTIC(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
- 7TKJ
- Type
- protein
- Length
- 5,051 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 0.81
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 | 91% helix, 0% strand | P61829 |
| 3, 6, 9 | ATP synthase subunit 9 | protein | 74 | 92% helix, 0% strand | P61829 |
| 7 | ATP synthase subunit 9 | protein | 73 | 92% helix, 0% strand | P61829 |
| A | ATP synthase subunit alpha | protein | 501 | 39% helix, 19% strand | P07251 |
| B | ATP synthase subunit alpha | protein | 505 | 38% helix, 18% strand | P07251 |
| C | ATP synthase subunit alpha | protein | 493 | 38% helix, 18% strand | P07251 |
| D | ATP synthase subunit beta (EC 7.1.2.2) | protein | 469 | 34% helix, 22% strand | P00830 |
| E | ATP synthase subunit beta (EC 7.1.2.2) | protein | 470 | 35% helix, 19% strand | P00830 |
| F | ATP synthase subunit beta (EC 7.1.2.2) | protein | 468 | 35% helix, 20% strand | P00830 |
| G | ATP synthase subunit gamma | protein | 265 | 65% helix, 10% strand | P38077 |
| H | ATP synthase subunit delta | protein | 118 | 26% helix, 38% strand | Q12165 |
| I | ATP synthase subunit epsilon | protein | 48 | 35% helix, 10% strand | P21306 |
| O | ATP synthase subunit 5 | protein | 187 | 48% helix, 13% strand | P09457 |
| T | ATP synthase subunit a | protein | 224 | 70% helix, 0% strand | P00854 |
| U | ATP synthase subunit 4 | protein | 155 | 95% helix, 0% strand | P05626 |
| V | ATP synthase subunit D | protein | 171 | 63% helix, 0% strand | P30902 |
| W | ATP synthase subunit F | protein | 85 | 44% helix, 0% strand | Q06405 |
| X | ATP synthase subunit H | protein | 62 | 45% helix, 0% strand | Q12349 |
| Y | ATP synthase subunit J | protein | 37 | 57% helix, 0% strand | P81450 |
| Z | ATP synthase protein 8 | protein | 48 | 81% 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 | 675 | 0.81 | 0.86 | 108 | empty |
| 2 | 1106 | 0.80 | 0.83 | 128 | empty |
| 3 | 921 | 0.77 | 0.80 | 149 | empty |
| 4 | 775 | 0.75 | 0.81 | 104 | empty |
| 5 | 1115 | 0.74 | 0.78 | 142 | empty |
Interfaces
51 interfaces between chains.
- A–E · 604 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 553 Ų buried · 8 hydrogen bonds · protein-protein
- B–E · 494 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 478 Ų buried · 4 hydrogen bonds · protein-protein
- 2–3 · 444 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7TKJ · Yeast ATP synthase State 2catalytic(d) with 10 mM ATP backbone model · the same entry in another collection · chain 0 against 0, 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 7TKJ · PDBe 7TKJ · 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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