Research workbench
Cryo-EM structure of the mammalian dp-state ATP synthase
Analyse Cryo-EM structure of the mammalian dp-state ATP synthase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6J5I
- Type
- protein
- Length
- 5,213 residues
- Chains
- 30
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP synthase subunit alpha, mitochondrial; ATP synthase subunit beta; ATPase inhibitor…
- EC
- 7.1.2.2
- UniProt
- P80021, K7GLT8, Q29307, A0A287A9I8, A0A286ZYL7, A5GFX4, Q2EN81, A0A286ZYM6, P13618, A0A287B4I0, Q95339, F1RFD4, Q35914, Q35915, Q4VT52
- Ligands
- ATP, ADP, MG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 23 distinct chains · 39% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP synthase subunit alpha, mitochondrial | protein | 509 | 27% helix, 17% strand | P80021 |
| B | ATP synthase subunit alpha, mitochondrial | protein | 481 | 32% helix, 18% strand | P80021 |
| C | ATP synthase subunit alpha, mitochondrial | protein | 502 | 34% helix, 16% strand | P80021 |
| D | ATP synthase subunit beta (EC 7.1.2.2) | protein | 471 | 27% helix, 17% strand | K7GLT8 |
| E | ATP synthase subunit beta (EC 7.1.2.2) | protein | 467 | 29% helix, 16% strand | K7GLT8 |
| F | ATP synthase subunit beta (EC 7.1.2.2) | protein | 468 | 21% helix, 16% strand | K7GLT8 |
| J | ATPase inhibitor, mitochondrial | protein | 55 | 42% helix, 0% strand | Q29307 |
| G | ATP synthase subunit gamma | protein | 272 | 53% helix, 12% strand | A0A287A9I8 |
| H | ATP synthase subunit delta, mitochondrial | protein | 132 | 27% helix, 22% strand | A0A286ZYL7 |
| I | ATP synthase F1 subunit epsilon | protein | 48 | 40% helix, 8% strand | A5GFX4 |
| S | ATP synthase subunit O, mitochondrial | protein | 187 | 47% helix, 7% strand | Q2EN81 |
| b | ATP synthase peripheral stalk-membrane subunit B | protein | 209 | 86% helix, 0% strand | A0A286ZYM6 |
| c | ATP synthase-coupling factor 6, mitochondrial | protein | 70 | 39% helix, 0% strand | P13618 |
| d | ATP synthase subunit D, mitochondrial | protein | 147 | 47% helix, 0% strand | A0A287B4I0 |
| e | ATP synthase subunit E | protein | 63 | 90% helix, 0% strand | — |
| f | ATP synthase subunit F, mitochondrial | protein | 80 | 53% helix, 0% strand | Q95339 |
| g | ATP synthase subunit G | protein | 84 | 61% helix, 0% strand | — |
| i | ATP synthase membrane subunit dapit | protein | 42 | 74% helix, 0% strand | F1RFD4 |
| k | Subunit K analog | protein | 29 | 55% helix, 0% strand | — |
| 8 | ATP synthase protein 8 | protein | 56 | 54% helix, 0% strand | Q35914 |
| a | ATP synthase subunit a | protein | 223 | 49% helix, 0% strand | Q35915 |
| K, L, M, N, O, P, Q, R | Mitochondrial H+ transporting ATP synthase subunit C isoform 1 | protein | 72 | 85% helix, 0% strand | Q4VT52 |
| u | ATP synthase membrane subunit 6.8PL | protein | 42 | 55% helix, 0% strand | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 3 copies · chains A, D, B, E, C, F
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains C, D, B, F
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, D, F
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 | 795 | 0.87 | 0.90 | 91 | ATP, MG |
| 2 | 841 | 0.86 | 0.89 | 106 | empty |
| 3 | 1124 | 0.85 | 0.85 | 107 | empty |
| 4 | 1187 | 0.84 | 0.85 | 122 | empty |
| 5 | 825 | 0.84 | 0.86 | 73 | empty |
Interfaces
87 interfaces between chains.
- A–D · 2507 Ų buried · 15 hydrogen bonds · protein-protein
- C–F · 2485 Ų buried · 21 hydrogen bonds · protein-protein
- B–F · 2289 Ų buried · 25 hydrogen bonds · protein-protein
- b–d · 1937 Ų buried · 10 hydrogen bonds · protein-protein
- B–E · 1921 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6J5I · Cryo-EM structure of the mammalian DP-state ATP synthase · the same entry in another collection · chain S against S, 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 P80021
- Every structure of UniProt K7GLT8
- Every structure of UniProt Q29307
- Every structure of UniProt A0A287A9I8
- Every structure of UniProt A0A286ZYL7
- Every structure of UniProt A5GFX4
- Every structure of UniProt Q2EN81
- Every structure of UniProt A0A286ZYM6
- Every structure of UniProt P13618
- Every structure of UniProt A0A287B4I0
- Every structure of UniProt Q95339
- Every structure of UniProt F1RFD4
- Every structure of UniProt Q35914
- Every structure of UniProt Q35915
- Every structure of UniProt Q4VT52
- Elsewhere: RCSB PDB 6J5I · PDBe 6J5I · UniProt P80021 · UniProt K7GLT8 · UniProt Q29307 · UniProt A0A287A9I8 · UniProt A0A286ZYL7 · UniProt A5GFX4 · UniProt Q2EN81 · UniProt A0A286ZYM6 · UniProt P13618 · UniProt A0A287B4I0 · UniProt Q95339 · UniProt F1RFD4 · UniProt Q35914 · UniProt Q35915 · UniProt Q4VT52
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