Research workbench
Fitted atomic models of thermus thermophilus V-ATPase subunits into cryo-EM MAP
Analyse Fitted atomic models of thermus thermophilus V-ATPase subunits into cryo-EM MAP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3J0J
- Type
- protein
- Length
- 4,154 residues
- Chains
- 13
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- V-type ATP synthase alpha chain; V-type ATP synthase beta chain; V-type ATP synthase…
- EC
- 3.6.3.14
- UniProt
- Q56403, Q56404, O87880, P74903, Q5SIT5, P74901, P74902
- Ligands
- ADP
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 7 distinct chains · 52% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | V-type ATP synthase alpha chain (EC 3.6.3.14) | protein | 561 | 36% helix, 22% strand | Q56403 |
| D, E, F | V-type ATP synthase beta chain | protein | 450 | 38% helix, 22% strand | Q56404 |
| G | V-type ATP synthase subunit D | protein | 129 | 92% helix, 0% strand | O87880 |
| H | V-type ATP synthase subunit F | protein | 104 | 42% helix, 17% strand | P74903 |
| I, K | V-type ATP synthase, subunit (vapc-therm) | protein | 100 | 89% helix, 0% strand | Q5SIT5 |
| J, L | V-type ATP synthase subunit E | protein | 184 | 59% helix, 7% strand | P74901 |
| M | V-type ATP synthase subunit C | protein | 320 | 69% helix, 0% strand | P74902 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, F, C, E
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 | 1190 | 0.85 | 0.87 | 208 | empty |
| 2 | 1089 | 0.84 | 0.85 | 153 | empty |
| 3 | 1164 | 0.84 | 0.85 | 180 | empty |
| 4 | 1041 | 0.83 | 0.85 | 157 | empty |
| 5 | 934 | 0.83 | 0.85 | 133 | empty |
Interfaces
20 interfaces between chains.
- I–J · 2472 Ų buried · 17 hydrogen bonds · protein-protein
- K–L · 2468 Ų buried · 17 hydrogen bonds · protein-protein
- A–F · 1004 Ų buried · 18 hydrogen bonds · protein-protein
- C–E · 951 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 894 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- 3J0J · Fitted atomic models of Thermus thermophilus V-ATPase subunits into cryo-EM map · the same entry in another collection · chain M against M, 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 Q56403
- Every structure of UniProt Q56404
- Every structure of UniProt O87880
- Every structure of UniProt P74903
- Every structure of UniProt Q5SIT5
- Every structure of UniProt P74901
- Every structure of UniProt P74902
- Elsewhere: RCSB PDB 3J0J · PDBe 3J0J · UniProt Q56403 · UniProt Q56404 · UniProt O87880 · UniProt P74903 · UniProt Q5SIT5 · UniProt P74901 · UniProt P74902
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