Research workbench
Mammalian V-ATPase from rat brain collar and peripheral stalks rotational state 3 (from focused refinement)
Analyse Mammalian V-ATPase from rat brain collar and peripheral stalks rotational state… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VQK
- Type
- protein
- Length
- 1,060 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- V-type proton ATPase subunit C 1; V-type proton ATPase subunit E 1; V-type proton ATPase…
- UniProt
- Q5FVI6, Q6PCU2, Q8R2H0, P25286
- Pockets
- 10 · best druggability 0.74
Structure
electron microscopy · 6 distinct chains · 66% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | V-type proton ATPase subunit C 1 | protein | 360 | 53% helix, 14% strand | Q5FVI6 |
| I, K | V-type proton ATPase subunit E 1 | protein | 64 | 94% helix, 0% strand | Q6PCU2 |
| J | V-type proton ATPase subunit E 1 | protein | 63 | 95% helix, 0% strand | Q6PCU2 |
| M, N | V-type proton ATPase subunit G | protein | 67 | 96% helix, 0% strand | Q8R2H0 |
| O | V-type proton ATPase subunit G | protein | 66 | 97% helix, 0% strand | Q8R2H0 |
| a | V-type proton ATPase 116 kda subunit a isoform 1 | protein | 309 | 58% helix, 12% strand | P25286 |
Pockets
10 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 462 | 0.74 | 0.83 | 76 | empty |
| 2 | 930 | 0.73 | 0.77 | 121 | empty |
| 3 | 321 | 0.67 | 0.82 | 52 | empty |
| 4 | 260 | 0.65 | 0.82 | 60 | empty |
| 5 | 494 | 0.64 | 0.77 | 70 | empty |
Interfaces
11 interfaces between chains.
- K–O · 581 Ų buried · 0 hydrogen bonds · protein-protein
- J–N · 381 Ų buried · 0 hydrogen bonds · protein-protein
- I–M · 316 Ų buried · 0 hydrogen bonds · protein-protein
- G–a · 174 Ų buried · 0 hydrogen bonds · protein-protein
- G–O · 156 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6VQK · Mammalian V-ATPase from rat brain collar and peripheral stalks rotational state 3 (from… · the same entry in another collection · chain a against a, TM-score 1.00
- Q5FVI6 · AlphaFold monomer V2.0 prediction for V-type proton ATPase subunit C 1 (Q5FVI6) · a predicted model of the same protein · chain G against A, TM-score 0.94
- P25286 · AlphaFold monomer V2.0 prediction for V-type proton ATPase 116 kda subunit A1 (P25286) · a predicted model of the same protein · chain a against A, TM-score 0.88
- Q6PCU2 · AlphaFold monomer V2.0 prediction for V-type proton ATPase subunit E 1 (Q6PCU2) · a predicted model of the same protein · chain J against A, TM-score 0.83
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 Q5FVI6
- Every structure of UniProt Q6PCU2
- Every structure of UniProt Q8R2H0
- Every structure of UniProt P25286
- Elsewhere: RCSB PDB 6VQK · PDBe 6VQK · UniProt Q5FVI6 · UniProt Q6PCU2 · UniProt Q8R2H0 · UniProt P25286
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