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Cryo-EM structure of polytomella F-ATP synthase, rotary substate 1C, monomer-masked refinement
Analyse Cryo-EM structure of polytomella F-ATP synthase, rotary substate 1C… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RDN
- Type
- protein
- Length
- 7,103 residues
- Chains
- 31
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Asa-10: polytomella F-ATP synthase associated subunit 10; ATP synthase associated protein…
- EC
- 7.1.2.2
- UniProt
- Q85JD5, K0J903, D7NIZ2, A0A024FSR7, D7P897, D8V7I2, D8V7I7, D7P7X5, H8PGG3, D8V7I1, D7P7X6, Q4LDE7, A0ZW40, A0ZW41
- Ligands
- ATP, ADP, MG, ZN
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 21 distinct chains · 47% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 0 | Asa-10: polytomella F-ATP synthase associated subunit 10 | protein | 81 | 33% helix, 2% strand | — |
| 1 | ATP synthase associated protein ASA1 | protein | 595 | 63% helix, 1% strand | Q85JD5 |
| 2 | Asa-2: polytomella F-ATP synthase associated subunit 2 | protein | 441 | 61% helix, 5% strand | — |
| 3 | Mitochondrial F1F0 ATP synthase associated 32 kda protein | protein | 245 | 63% helix, 2% strand | K0J903 |
| 4 | Mitochondrial ATP synthase associated protein ASA4 | protein | 290 | 69% helix, 1% strand | D7NIZ2 |
| 5 | Mitochondrial F1F0 ATP synthase associated 14 kda protein | protein | 123 | 67% helix, 0% strand | A0A024FSR7 |
| 6 | Mitochondrial ATP synthase subunit ASA6 | protein | 124 | 55% helix, 0% strand | D7P897 |
| 7 | Mitochondrial ATP synthase associated protein ASA7 | protein | 176 | 43% helix, 13% strand | D8V7I2 |
| 8 | Mitochondrial ATP synthase subunit ASA8 | protein | 88 | 57% helix, 0% strand | D8V7I7 |
| 9 | Asa-9: polytomella F-ATP synthase associated subunit 9 | protein | 97 | 49% helix, 0% strand | — |
| A, B, C, D, E, F, G, H, I, J | Mitochondrial ATP synthase subunit C | protein | 74 | 88% helix, 0% strand | D7P7X5 |
| M | Mitochondrial ATP synthase subunit 6 | protein | 217 | 67% helix, 2% strand | H8PGG3 |
| P | Mitochondrial ATP synthase subunit oscp | protein | 193 | 47% helix, 8% strand | D8V7I1 |
| Q | Epsilon: polytomella F-ATP synthase epsilon subunit | protein | 72 | 28% helix, 18% strand | — |
| R | Mitochondrial ATP synthase subunit delta | protein | 177 | 27% helix, 27% strand | D7P7X6 |
| S | ATP synthase gamma chain, mitochondrial | protein | 277 | 55% helix, 14% strand | Q4LDE7 |
| T, U | ATP synthase subunit alpha | protein | 523 | 38% helix, 20% strand | A0ZW40 |
| V | ATP synthase subunit alpha | protein | 520 | 37% helix, 19% strand | A0ZW40 |
| X | ATP synthase subunit beta (EC 7.1.2.2) | protein | 542 | 33% helix, 18% strand | A0ZW41 |
| Y | ATP synthase subunit beta (EC 7.1.2.2) | protein | 521 | 35% helix, 17% strand | A0ZW41 |
| Z | ATP synthase subunit beta (EC 7.1.2.2) | protein | 538 | 34% helix, 18% strand | A0ZW41 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 3 copies · chains T, X, U, Z, V, Y
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains U, X, T, Y
- MG · Magnesium ion · metal · 5 copies · chains T, U, V, X, Y
- ZN · Zinc ion · metal · chains 6, M
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 | 1115 | 0.89 | 0.90 | 97 | empty |
| 2 | 713 | 0.85 | 0.88 | 90 | ATP, MG |
| 3 | 953 | 0.84 | 0.86 | 101 | ADP, MG |
| 4 | 399 | 0.84 | 0.92 | 54 | empty |
| 5 | 793 | 0.83 | 0.86 | 92 | ATP, MG |
Interfaces
99 interfaces between chains.
- U–X · 4133 Ų buried · 45 hydrogen bonds · protein-protein
- 1–5 · 3943 Ų buried · 31 hydrogen bonds · protein-protein
- V–Z · 3674 Ų buried · 29 hydrogen bonds · protein-protein
- T–Y · 3444 Ų buried · 26 hydrogen bonds · protein-protein
- 4–7 · 3068 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 6RDN · Cryo-EM structure of Polytomella F-ATP synthase, Rotary substate 1C, monomer-masked… · the same entry in another collection · chain 9 against 9, 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 Q85JD5
- Every structure of UniProt K0J903
- Every structure of UniProt D7NIZ2
- Every structure of UniProt A0A024FSR7
- Every structure of UniProt D7P897
- Every structure of UniProt D8V7I2
- Every structure of UniProt D8V7I7
- Every structure of UniProt D7P7X5
- Every structure of UniProt H8PGG3
- Every structure of UniProt D8V7I1
- Every structure of UniProt D7P7X6
- Every structure of UniProt Q4LDE7
- Every structure of UniProt A0ZW40
- Every structure of UniProt A0ZW41
- Elsewhere: RCSB PDB 6RDN · PDBe 6RDN · UniProt Q85JD5 · UniProt K0J903 · UniProt D7NIZ2 · UniProt A0A024FSR7 · UniProt D7P897 · UniProt D8V7I2 · UniProt D8V7I7 · UniProt D7P7X5 · UniProt H8PGG3 · UniProt D8V7I1 · UniProt D7P7X6 · UniProt Q4LDE7 · UniProt A0ZW40 · UniProt A0ZW41
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