Research workbench
Bovine ATP synthase F1C8-peripheral stalk domain, state 3
Analyse Bovine ATP synthase F1C8-peripheral stalk domain, state 3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Z1U
- Type
- protein
- Length
- 4,239 residues
- Chains
- 21
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP synthase subunit alpha, mitochondrial; ATP synthase subunit beta, mitochondrial; ATP…
- EC
- 7.1.2.2
- UniProt
- P19483, P00829, P05631, P05630, P05632, P01096, P07926, P13621, P13619, P02721
- Ligands
- ATP, ADP, MG
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 14 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP synthase subunit alpha, mitochondrial | protein | 501 | 39% helix, 18% strand | P19483 |
| B | ATP synthase subunit alpha, mitochondrial | protein | 502 | 39% helix, 18% strand | P19483 |
| C | ATP synthase subunit alpha, mitochondrial | protein | 483 | 36% helix, 18% strand | P19483 |
| D | ATP synthase subunit beta, mitochondrial (EC 7.1.2.2) | protein | 469 | 35% helix, 19% strand | P00829 |
| E, F | ATP synthase subunit beta, mitochondrial (EC 7.1.2.2) | protein | 467 | 36% helix, 17% strand | P00829 |
| G | ATP synthase subunit gamma, mitochondrial | protein | 272 | 62% helix, 15% strand | P05631 |
| H | ATP synthase subunit delta, mitochondrial | protein | 131 | 27% helix, 37% strand | P05630 |
| I | ATP synthase subunit epsilon, mitochondrial | protein | 47 | 57% helix, 9% strand | P05632 |
| J | ATPase inhibitor, mitochondrial | protein | 47 | 68% helix, 0% strand | P01096 |
| K, L, P | ATP synthase F(0) complex subunit C2, mitochondrial | protein | 74 | 95% helix, 0% strand | P07926 |
| M, N, Q, R, O | ATP synthase F(0) complex subunit C2, mitochondrial | protein | 75 | 92% helix, 0% strand | P07926 |
| S | ATP synthase subunit O, mitochondrial | protein | 187 | 55% helix, 14% strand | P13621 |
| b | ATP synthase F(0) complex subunit B1, mitochondrial | protein | 47 | 83% helix, 0% strand | P13619 |
| h | ATP synthase-coupling factor 6, mitochondrial | protein | 22 | 68% helix, 0% strand | P02721 |
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
- 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 | 916 | 0.88 | 0.90 | 119 | ATP, MG |
| 2 | 900 | 0.88 | 0.90 | 104 | ATP, MG |
| 3 | 700 | 0.87 | 0.91 | 83 | ATP, MG |
| 4 | 630 | 0.83 | 0.87 | 96 | empty |
| 5 | 388 | 0.83 | 0.91 | 55 | empty |
Interfaces
55 interfaces between chains.
- C–F · 2486 Ų buried · 28 hydrogen bonds · protein-protein
- A–D · 2453 Ų buried · 28 hydrogen bonds · protein-protein
- B–F · 2246 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 2102 Ų buried · 19 hydrogen bonds · protein-protein
- B–E · 2056 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (methylation).
Compared structures
- 6Z1U · bovine ATP synthase F1c8-peripheral stalk domain, state 3 · the same entry in another collection · chain I against I, 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 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 P07926
- Every structure of UniProt P13621
- Every structure of UniProt P13619
- Every structure of UniProt P02721
- Elsewhere: RCSB PDB 6Z1U · PDBe 6Z1U · UniProt P19483 · UniProt P00829 · UniProt P05631 · UniProt P05630 · UniProt P05632 · UniProt P01096 · UniProt P07926 · UniProt P13621 · UniProt P13619 · UniProt P02721
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