Research workbench
Mammalian V-ATPase from rat brain soluble V1 region rotational state 1 with sidk and ADP (from focused refinement)
Analyse Mammalian V-ATPase from rat brain soluble V1 region rotational state 1 with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VQ9
- Type
- protein
- Length
- 4,578 residues
- Chains
- 16
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATPase H+-transporting V1 subunit a; V-type proton ATPase subunit B, brain isoform…
- UniProt
- D4A133, P62815, Q6P503, Q6PCU2, Q8R2H0, Q5ZWW6
- Ligands
- ADP, MG
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 8 distinct chains · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | ATPase H+-transporting V1 subunit a | protein | 600 | 35% helix, 23% strand | D4A133 |
| D, E, F | V-type proton ATPase subunit B, brain isoform | protein | 459 | 36% helix, 23% strand | P62815 |
| H | ATPase H+-transporting V1 subunit D | protein | 109 | 88% helix, 0% strand | Q6P503 |
| I, J, K | V-type proton ATPase subunit E 1 | protein | 161 | 61% helix, 13% strand | Q6PCU2 |
| M, N, O | V-type proton ATPase subunit G | protein | 47 | 70% helix, 0% strand | Q8R2H0 |
| Q | Effector protein sidk | protein | 224 | 69% helix, 0% strand | Q5ZWW6 |
| R | Effector protein sidk | protein | 212 | 66% helix, 1% strand | Q5ZWW6 |
| S | Effector protein sidk | protein | 232 | 64% helix, 0% strand | Q5ZWW6 |
Ligands and binding sites
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 | 1030 | 0.89 | 0.91 | 131 | empty |
| 2 | 1038 | 0.88 | 0.89 | 105 | ADP, MG |
| 3 | 693 | 0.87 | 0.91 | 93 | empty |
| 4 | 968 | 0.86 | 0.87 | 106 | empty |
| 5 | 847 | 0.86 | 0.88 | 117 | empty |
Interfaces
35 interfaces between chains.
- C–F · 3317 Ų buried · 42 hydrogen bonds · protein-protein
- A–D · 2837 Ų buried · 39 hydrogen bonds · protein-protein
- B–E · 2337 Ų buried · 30 hydrogen bonds · protein-protein
- A–E · 2201 Ų buried · 21 hydrogen bonds · protein-protein
- D–I · 2037 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 6VQ9 · Mammalian V-ATPase from rat brain soluble V1 region rotational state 1 with SidK and ADP… · the same entry in another collection · chain S against S, 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 D4A133
- Every structure of UniProt P62815
- Every structure of UniProt Q6P503
- Every structure of UniProt Q6PCU2
- Every structure of UniProt Q8R2H0
- Every structure of UniProt Q5ZWW6
- Elsewhere: RCSB PDB 6VQ9 · PDBe 6VQ9 · UniProt D4A133 · UniProt P62815 · UniProt Q6P503 · UniProt Q6PCU2 · UniProt Q8R2H0 · UniProt Q5ZWW6
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