MolNFT v1 · #167613 · protein
Mammalian V-ATPase from rat brain - composite model of rotational state 2 bound to ADP and sidk (built from focused refinement models)
6VQ7 · ATPase H+-transporting V1 subunit a: “Mammalian V-ATPase from rat brain - composite model of rotational state 2 bound to ADP and sidk (built from…”. Electron microscopy, 2 ligands (ADP, MG), 20 pockets (best druggability 0.89).…
- PDB
- 6VQ7
- Type
- protein
- Length
- 8,454 residues
- Chains
- 34
- 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, Q5FVI6, Q6P503, Q6PCU2, P50408, Q8R2H0, Q5ZWW6, P25286, B0K022, O54715, Q5M7T6, Q5EB76, D3ZIM6, P63081, Q6AXS4
- Ligands
- ADP, MG
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 18 distinct chains · 59% helix, 9% 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 | 35% helix, 24% strand | P62815 |
| G | V-type proton ATPase subunit C 1 | protein | 360 | 52% helix, 14% strand | Q5FVI6 |
| H | ATPase H+-transporting V1 subunit D | protein | 214 | 74% helix, 7% strand | Q6P503 |
| I, J, K | V-type proton ATPase subunit E 1 | protein | 225 | 72% helix, 8% strand | Q6PCU2 |
| L | V-type proton ATPase subunit F | protein | 110 | 35% helix, 18% strand | P50408 |
| M, N, O | V-type proton ATPase subunit G | protein | 114 | 88% helix, 0% strand | Q8R2H0 |
| Q | Effector protein sidk | protein | 212 | 66% helix, 1% strand | Q5ZWW6 |
| R | Effector protein sidk | protein | 232 | 64% helix, 0% strand | Q5ZWW6 |
| S | Effector protein sidk | protein | 224 | 69% helix, 0% strand | Q5ZWW6 |
| a | V-type proton ATPase 116 kda subunit a isoform 1 | protein | 750 | 63% helix, 7% 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 |
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 | 853 | 0.89 | 0.92 | 119 | empty |
| 2 | 844 | 0.88 | 0.91 | 103 | empty |
| 3 | 912 | 0.86 | 0.88 | 106 | empty |
| 4 | 935 | 0.86 | 0.87 | 98 | empty |
| 5 | 661 | 0.85 | 0.89 | 77 | empty |
Interfaces
82 interfaces between chains.
- B–E · 3339 Ų buried · 36 hydrogen bonds · protein-protein
- C–F · 2900 Ų buried · 39 hydrogen bonds · protein-protein
- a–e · 2479 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 2387 Ų buried · 33 hydrogen bonds · protein-protein
- I–M · 2271 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6VQ7 · Mammalian V-ATPase from rat brain - composite model of rotational state 2 bound to ADP… · the same entry in another collection · chain K against K, 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 Q5FVI6
- Every structure of UniProt Q6P503
- Every structure of UniProt Q6PCU2
- Every structure of UniProt P50408
- Every structure of UniProt Q8R2H0
- Every structure of UniProt Q5ZWW6
- 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 6VQ7 · PDBe 6VQ7 · UniProt D4A133 · UniProt P62815 · UniProt Q5FVI6 · UniProt Q6P503 · UniProt Q6PCU2 · UniProt P50408 · UniProt Q8R2H0 · UniProt Q5ZWW6 · UniProt P25286 · UniProt B0K022 · UniProt O54715 · UniProt Q5M7T6 · UniProt Q5EB76 · UniProt D3ZIM6 · UniProt P63081 · UniProt Q6AXS4
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