MolNFT v1 · #172060 · protein
Bovine ATP synthase monomer state 1 (combined)
6ZPO · ATP synthase protein 8: “Bovine ATP synthase monomer state 1 (combined)”. Electron microscopy, 5 ligands (ATP, ADP, CDL), 20 pockets (best druggability 0.88). MolNFT v1 #172060 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6ZPO
- Type
- protein
- Length
- 5,150 residues
- Chains
- 29
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP synthase protein 8; ATP synthase subunit alpha, mitochondrial; ATP synthase subunit…
- EC
- 7.1.2.2
- UniProt
- P03929, P19483, P00829, P05631, P05630, P05632, P01096, P32876, P13621, P00847, P13619, P13620, Q00361, Q28851, Q28852, P02721, P14790, Q3ZBI7
- Ligands
- ATP, ADP, CDL, LHG, MG
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 22 distinct chains · 51% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 8 | ATP synthase protein 8 | protein | 41 | 66% helix, 0% strand | P03929 |
| A | ATP synthase subunit alpha, mitochondrial | protein | 508 | 40% helix, 20% strand | P19483 |
| B | ATP synthase subunit alpha, mitochondrial | protein | 477 | 41% helix, 20% strand | P19483 |
| C | ATP synthase subunit alpha, mitochondrial | protein | 498 | 41% helix, 19% strand | P19483 |
| D | ATP synthase subunit beta, mitochondrial (EC 7.1.2.2) | protein | 469 | 37% helix, 19% strand | P00829 |
| E, F | ATP synthase subunit beta, mitochondrial (EC 7.1.2.2) | protein | 467 | 39% helix, 19% strand | P00829 |
| G | ATP synthase subunit gamma, mitochondrial | protein | 272 | 62% helix, 15% strand | P05631 |
| H | ATP synthase subunit delta, mitochondrial | protein | 132 | 30% helix, 34% strand | P05630 |
| I | ATP synthase subunit epsilon, mitochondrial | protein | 47 | 53% helix, 9% strand | P05632 |
| J | ATPase inhibitor, mitochondrial | protein | 47 | 74% helix, 0% strand | P01096 |
| K, L, P | ATP synthase F(0) complex subunit C1, mitochondrial | protein | 74 | 85% helix, 0% strand | P32876 |
| M, N, O, Q, R | ATP synthase F(0) complex subunit C1, mitochondrial | protein | 75 | 95% helix, 0% strand | P32876 |
| S | ATP synthase subunit O, mitochondrial | protein | 188 | 57% helix, 13% strand | P13621 |
| a | ATP synthase subunit a | protein | 226 | 75% helix, 0% strand | P00847 |
| b | ATP synthase F(0) complex subunit B1, mitochondrial | protein | 209 | 83% helix, 2% strand | P13619 |
| d | ATP synthase subunit D, mitochondrial | protein | 156 | 62% helix, 1% strand | P13620 |
| e | ATP synthase subunit E, mitochondrial | protein | 41 | 83% helix, 0% strand | Q00361 |
| f | ATP synthase subunit F, mitochondrial | protein | 83 | 60% helix, 2% strand | Q28851 |
| g | ATP synthase subunit G, mitochondrial | protein | 79 | 76% helix, 1% strand | Q28852 |
| h | ATP synthase-coupling factor 6, mitochondrial | protein | 62 | 56% helix, 0% strand | P02721 |
| j | ATP synthase subunit ATP5MPL, mitochondrial | protein | 48 | 83% helix, 0% strand | P14790 |
| k | ATP synthase membrane subunit dapit, mitochondrial | protein | 36 | 81% helix, 0% strand | Q3ZBI7 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 3 copies · chains A, D, B, E, C, F
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains C, D, E, B, F
- CDL · Cardiolipin · ligand · 3 copies · chains a, b, f, g, 8, j
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 2 copies · chains f, g, b
- 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 | 871 | 0.88 | 0.91 | 116 | ATP, MG |
| 2 | 950 | 0.88 | 0.90 | 110 | ATP, MG |
| 3 | 792 | 0.86 | 0.89 | 92 | empty |
| 4 | 693 | 0.83 | 0.87 | 97 | ADP, MG |
| 5 | 1119 | 0.82 | 0.83 | 114 | ADP, MG |
Interfaces
80 interfaces between chains.
- b–d · 3162 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 2562 Ų buried · 26 hydrogen bonds · protein-protein
- C–F · 2332 Ų buried · 25 hydrogen bonds · protein-protein
- B–F · 2184 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 2144 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified, 1 covalent (methylation, covalent ligand).
Compared structures
- 6ZPO · bovine ATP synthase monomer state 1 (combined) · the same entry in another collection · chain J against J, 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 P03929
- Every structure of UniProt P19483
- Every structure of UniProt P00829
- Every structure of UniProt P05631
- Every structure of UniProt P05630
- Every structure of UniProt P05632
- Every structure of UniProt P01096
- Every structure of UniProt P32876
- Every structure of UniProt P13621
- Every structure of UniProt P00847
- Every structure of UniProt P13619
- Every structure of UniProt P13620
- Every structure of UniProt Q00361
- Every structure of UniProt Q28851
- Every structure of UniProt Q28852
- Every structure of UniProt P02721
- Every structure of UniProt P14790
- Every structure of UniProt Q3ZBI7
- Elsewhere: RCSB PDB 6ZPO · PDBe 6ZPO · UniProt P03929 · UniProt P19483 · UniProt P00829 · UniProt P05631 · UniProt P05630 · UniProt P05632 · UniProt P01096 · UniProt P32876 · UniProt P13621 · UniProt P00847 · UniProt P13619 · UniProt P13620 · UniProt Q00361 · UniProt Q28851 · UniProt Q28852 · UniProt P02721 · UniProt P14790 · UniProt Q3ZBI7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.