Research workbench
Mammalian V-ATPase from rat brain membrane-embedded vo region rotational state 2 (from focused refinement)
Analyse Mammalian V-ATPase from rat brain membrane-embedded vo region rotational state… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VQG
- Type
- protein
- Length
- 2,813 residues
- Chains
- 18
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATPase H+-transporting V1 subunit D; V-type proton ATPase subunit F; V-type proton ATPase…
- UniProt
- Q6P503, P50408, P25286, B0K022, O54715, Q5M7T6, Q5EB76, D3ZIM6, P63081, Q6AXS4
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 10 distinct chains · 67% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | ATPase H+-transporting V1 subunit D | protein | 104 | 56% helix, 13% strand | Q6P503 |
| L | V-type proton ATPase subunit F | protein | 110 | 35% helix, 18% strand | P50408 |
| a | V-type proton ATPase 116 kda subunit a isoform 1 | protein | 441 | 67% helix, 2% strand | P25286 |
| b | ATPase, H+ transporting, V0 subunit B (predicted), isoform CRA_A | protein | 203 | 78% helix, 0% strand | B0K022 |
| c | V-type proton ATPase subunit S1 | protein | 41 | 61% helix, 0% strand | O54715 |
| d | V-type proton ATPase subunit | protein | 350 | 67% helix, 0% strand | Q5M7T6 |
| e | V-type proton ATPase subunit E 2 | protein | 78 | 65% helix, 1% strand | Q5EB76 |
| f | Ribonuclease K | protein | 84 | 74% helix, 0% strand | D3ZIM6 |
| g, h, i, j, k, l, m, n, o | V-type proton ATPase 16 kda proteolipid subunit | protein | 150 | 85% helix, 0% strand | P63081 |
| p | Renin receptor | protein | 52 | 60% helix, 0% strand | Q6AXS4 |
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1027 | 0.85 | 0.85 | 87 | empty |
| 2 | 1122 | 0.84 | 0.85 | 126 | empty |
| 3 | 1110 | 0.83 | 0.84 | 79 | empty |
| 4 | 812 | 0.82 | 0.84 | 82 | empty |
| 5 | 1055 | 0.80 | 0.81 | 90 | empty |
Interfaces
39 interfaces between chains.
- a–e · 2480 Ų buried · 19 hydrogen bonds · protein-protein
- b–o · 1816 Ų buried · 8 hydrogen bonds · protein-protein
- H–L · 1795 Ų buried · 13 hydrogen bonds · protein-protein
- b–g · 1620 Ų buried · 6 hydrogen bonds · protein-protein
- i–j · 1578 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6VQG · Mammalian V-ATPase from rat brain membrane-embedded Vo region rotational state 2 (from… · 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 Q6P503
- Every structure of UniProt P50408
- Every structure of UniProt P25286
- Every structure of UniProt B0K022
- Every structure of UniProt O54715
- Every structure of UniProt Q5M7T6
- Every structure of UniProt Q5EB76
- Every structure of UniProt D3ZIM6
- Every structure of UniProt P63081
- Every structure of UniProt Q6AXS4
- Elsewhere: RCSB PDB 6VQG · PDBe 6VQG · UniProt Q6P503 · UniProt P50408 · UniProt P25286 · UniProt B0K022 · UniProt O54715 · UniProt Q5M7T6 · UniProt Q5EB76 · UniProt D3ZIM6 · UniProt P63081 · UniProt Q6AXS4
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