Research workbench
Yeast ATP synthase state 2BINDING(B) with 10 mm ATP backbone model
Analyse Yeast ATP synthase state 2BINDING(B) 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
- 7TKF
- 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 0.81
Structure
electron microscopy · 20 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 0, 1, 2, 4, 5, 8 | ATP synthase subunit 9 | protein | 75 | 92% helix, 0% strand | P61829 |
| 3, 6, 9 | ATP synthase subunit 9 | protein | 74 | 89% helix, 0% strand | P61829 |
| 7 | ATP synthase subunit 9 | protein | 73 | 92% helix, 0% strand | P61829 |
| A | ATP synthase subunit alpha | protein | 501 | 41% helix, 19% strand | P07251 |
| B | ATP synthase subunit alpha | protein | 505 | 41% helix, 20% strand | P07251 |
| C | ATP synthase subunit alpha | protein | 496 | 38% helix, 20% strand | P07251 |
| D | ATP synthase subunit beta (EC 7.1.2.2) | protein | 469 | 36% helix, 21% strand | P00830 |
| E | ATP synthase subunit beta (EC 7.1.2.2) | protein | 470 | 37% helix, 19% strand | P00830 |
| F | ATP synthase subunit beta (EC 7.1.2.2) | protein | 468 | 36% helix, 19% strand | P00830 |
| G | ATP synthase subunit gamma | protein | 265 | 64% helix, 11% strand | P38077 |
| H | ATP synthase subunit delta | protein | 120 | 27% helix, 36% strand | Q12165 |
| I | ATP synthase subunit epsilon | protein | 48 | 35% helix, 10% strand | P21306 |
| O | ATP synthase subunit 5 | protein | 187 | 49% helix, 9% 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 | 61% helix, 0% strand | P30902 |
| W | ATP synthase subunit F | protein | 85 | 45% helix, 0% strand | Q06405 |
| X | ATP synthase subunit H | protein | 62 | 42% helix, 0% 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 | 1099 | 0.81 | 0.84 | 125 | empty |
| 2 | 448 | 0.78 | 0.87 | 65 | empty |
| 3 | 843 | 0.75 | 0.80 | 136 | empty |
| 4 | 709 | 0.74 | 0.81 | 115 | empty |
| 5 | 739 | 0.74 | 0.80 | 126 | empty |
Interfaces
44 interfaces between chains.
- U–V · 547 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 503 Ų buried · 7 hydrogen bonds · protein-protein
- 6–7 · 497 Ų buried · 0 hydrogen bonds · protein-protein
- 0–9 · 485 Ų buried · 0 hydrogen bonds · protein-protein
- 8–9 · 484 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7TKF · Yeast ATP synthase State 2binding(b) with 10 mM ATP backbone model · the same entry in another collection · chain Z against Z, 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 7TKF · PDBe 7TKF · 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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