Research workbench
Mammalian V-ATPase from rat brain - composite model of rotational state 3 bound to ADP and sidk (built from focused refinement models)
Analyse Mammalian V-ATPase from rat brain - composite model of rotational state 3 bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VQ8
- Type
- protein
- Length
- 8,451 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
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 20 distinct chains · 60% 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 | 36% helix, 22% strand | P62815 |
| G | V-type proton ATPase subunit C 1 | protein | 360 | 53% helix, 14% strand | Q5FVI6 |
| H | ATPase H+-transporting V1 subunit D | protein | 214 | 74% helix, 7% strand | Q6P503 |
| I, K | V-type proton ATPase subunit E 1 | protein | 225 | 72% helix, 9% strand | Q6PCU2 |
| J | V-type proton ATPase subunit E 1 | protein | 224 | 71% helix, 9% strand | Q6PCU2 |
| L | V-type proton ATPase subunit F | protein | 110 | 35% helix, 18% strand | P50408 |
| M, N | V-type proton ATPase subunit G | protein | 114 | 86% helix, 0% strand | Q8R2H0 |
| O | V-type proton ATPase subunit G | protein | 113 | 88% helix, 0% strand | Q8R2H0 |
| Q | Effector protein sidk | protein | 232 | 64% helix, 0% strand | Q5ZWW6 |
| R | Effector protein sidk | protein | 224 | 69% helix, 0% strand | Q5ZWW6 |
| S | Effector protein sidk | protein | 212 | 66% helix, 1% strand | Q5ZWW6 |
| a | V-type proton ATPase 116 kda subunit a isoform 1 | protein | 749 | 64% helix, 6% strand | P25286 |
| b | ATPase, H+ transporting, V0 subunit B (predicted), isoform CRA_A | protein | 203 | 79% 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 | 66% 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
- ADP · Adenosine-5'-diphosphate · ligand · chains A, D
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 | 693 | 0.87 | 0.91 | 93 | empty |
| 2 | 950 | 0.86 | 0.88 | 108 | empty |
| 3 | 481 | 0.86 | 0.93 | 64 | empty |
| 4 | 1087 | 0.86 | 0.87 | 117 | empty |
| 5 | 977 | 0.86 | 0.87 | 163 | empty |
Interfaces
84 interfaces between chains.
- A–D · 3353 Ų buried · 39 hydrogen bonds · protein-protein
- B–E · 2900 Ų buried · 37 hydrogen bonds · protein-protein
- C–F · 2406 Ų buried · 36 hydrogen bonds · protein-protein
- K–O · 2290 Ų buried · 18 hydrogen bonds · protein-protein
- B–F · 2191 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 6VQ8 · Mammalian V-ATPase from rat brain - composite model of rotational state 3 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 6VQ8 · PDBe 6VQ8 · 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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