Research workbench
Inter-subunit interaction and quaternary rearrangement defined by the central stalk of prokaryotic V1-ATPase
Analyse Inter-subunit interaction and quaternary rearrangement defined by the central… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3A5C
- Type
- protein
- Length
- 6,532 residues
- Chains
- 16
- Method
- x-ray diffraction
- 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
- Ligands
- ADP
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, I, J, K | V-type ATP synthase alpha chain (EC 3.6.3.14) | protein | 561 | 36% helix, 22% strand | Q56403 |
| D, E, F, L, M, N | V-type ATP synthase beta chain (EC 3.6.3.14) | protein | 450 | 38% helix, 23% strand | Q56404 |
| G, O | V-type ATP synthase subunit D (EC 3.6.3.14) | protein | 129 | 92% helix, 0% strand | O87880 |
| H, P | V-type ATP synthase subunit F (EC 3.6.3.14) | protein | 104 | 41% helix, 17% strand | P74903 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, F, C, E, I, N, K, M
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 | 970 | 0.86 | 0.87 | 169 | empty |
| 2 | 931 | 0.86 | 0.88 | 172 | empty |
| 3 | 903 | 0.85 | 0.87 | 165 | empty |
| 4 | 1168 | 0.84 | 0.85 | 167 | empty |
| 5 | 1142 | 0.84 | 0.85 | 169 | empty |
Interfaces
30 interfaces between chains.
- I–N · 1002 Ų buried · 18 hydrogen bonds · protein-protein
- C–E · 978 Ų buried · 16 hydrogen bonds · protein-protein
- A–F · 961 Ų buried · 15 hydrogen bonds · protein-protein
- K–M · 950 Ų buried · 14 hydrogen bonds · protein-protein
- I–L · 893 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3A5C · Inter-subunit interaction and quaternary rearrangement defined by the central stalk of… · the same entry in another collection · chain P against P, 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
- Elsewhere: RCSB PDB 3A5C · PDBe 3A5C · UniProt Q56403 · UniProt Q56404 · UniProt O87880 · UniProt P74903
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