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
- 3A5D
- 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
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 19% 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 | 35% 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, 22% 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 |
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 | 911 | 0.85 | 0.87 | 173 | empty |
| 2 | 688 | 0.85 | 0.90 | 161 | empty |
| 3 | 923 | 0.85 | 0.87 | 159 | empty |
| 4 | 1174 | 0.84 | 0.86 | 168 | empty |
| 5 | 989 | 0.83 | 0.85 | 143 | empty |
Interfaces
30 interfaces between chains.
- I–N · 1011 Ų buried · 19 hydrogen bonds · protein-protein
- C–E · 993 Ų buried · 19 hydrogen bonds · protein-protein
- K–M · 977 Ų buried · 13 hydrogen bonds · protein-protein
- A–F · 932 Ų buried · 12 hydrogen bonds · protein-protein
- I–L · 862 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3A5D · 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 3A5D · PDBe 3A5D · UniProt Q56403 · UniProt Q56404 · UniProt O87880 · UniProt P74903
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