MolNFT v1 · #171623 · protein
Bovine ATP synthase fo domain
6ZBB · ATP synthase protein 8: “Bovine ATP synthase fo domain”. Electron microscopy, 2 ligands (CDL, LHG), 14 pockets (best druggability 0.87). MolNFT v1 #171623 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6ZBB
- Type
- protein
- Length
- 1,328 residues
- Chains
- 17
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP synthase protein 8; ATP synthase F(0) complex subunit C1, mitochondrial; ATP synthase…
- UniProt
- P03929, P32876, P00847, P13619, P13620, Q00361, Q28851, Q28852, P14790, Q3ZBI7
- Ligands
- CDL, LHG
- Pockets
- 14 · best druggability 0.87
Structure
electron microscopy · 11 distinct chains · 75% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 8 | ATP synthase protein 8 | protein | 41 | 63% helix, 0% strand | P03929 |
| K, L, P | ATP synthase F(0) complex subunit C1, mitochondrial | protein | 74 | 89% helix, 0% strand | P32876 |
| M, N, O, Q, R | ATP synthase F(0) complex subunit C1, mitochondrial | protein | 75 | 95% helix, 0% strand | P32876 |
| a | ATP synthase subunit a | protein | 224 | 75% helix, 0% strand | P00847 |
| b | ATP synthase F(0) complex subunit B1, mitochondrial | protein | 112 | 75% helix, 4% strand | P13619 |
| d | ATP synthase subunit D, mitochondrial | protein | 51 | 45% helix, 2% strand | P13620 |
| e | ATP synthase subunit E, mitochondrial | protein | 57 | 86% helix, 0% strand | Q00361 |
| f | ATP synthase subunit F, mitochondrial | protein | 83 | 57% helix, 1% strand | Q28851 |
| g | ATP synthase subunit G, mitochondrial | protein | 79 | 78% helix, 1% strand | Q28852 |
| j | ATP synthase subunit ATP5MPL, mitochondrial | protein | 48 | 81% helix, 0% strand | P14790 |
| k | ATP synthase membrane subunit dapit, mitochondrial | protein | 36 | 75% helix, 0% strand | Q3ZBI7 |
Ligands and binding sites
- CDL · Cardiolipin · ligand · 3 copies · chains 8, a, f, j, b, g
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 2 copies · chains f, b
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 682 | 0.87 | 0.91 | 85 | empty |
| 2 | 565 | 0.78 | 0.84 | 60 | empty |
| 3 | 913 | 0.76 | 0.79 | 74 | CDL |
| 4 | 148 | 0.67 | 0.88 | 33 | empty |
| 5 | 402 | 0.65 | 0.78 | 36 | empty |
Interfaces
34 interfaces between chains.
- Q–R · 1581 Ų buried · 15 hydrogen bonds · protein-protein
- L–M · 1578 Ų buried · 5 hydrogen bonds · protein-protein
- N–O · 1553 Ų buried · 5 hydrogen bonds · protein-protein
- M–N · 1552 Ų buried · 6 hydrogen bonds · protein-protein
- K–R · 1550 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (methylation).
Compared structures
- 6ZBB · bovine ATP synthase Fo domain · the same entry in another collection · chain b against b, 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 P32876
- 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 P14790
- Every structure of UniProt Q3ZBI7
- Elsewhere: RCSB PDB 6ZBB · PDBe 6ZBB · UniProt P03929 · UniProt P32876 · UniProt P00847 · UniProt P13619 · UniProt P13620 · UniProt Q00361 · UniProt Q28851 · UniProt Q28852 · UniProt P14790 · UniProt Q3ZBI7
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