Research workbench
Cryo-EM structure of V-ATPase from bovine brain, state 1
Analyse Cryo-EM structure of V-ATPase from bovine brain, state 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XBW
- Type
- protein
- Length
- 8,186 residues
- Chains
- 32
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- V-type proton ATPase catalytic subunit a; V-type proton ATPase subunit B, brain isoform…
- EC
- 7.1.2.2, 3.1.-.-
- UniProt
- P31404, P31408, P21282, A0A3Q1M4W9, P11019, Q28029, Q0VCV6, F1MZL6, F1MJV0, Q2TA24, P61420, Q2KIB5, P40682, P81134, P23956, Q3ZC23
- Ligands
- POV, ADP, OLA, NAG, MG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 22 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | V-type proton ATPase catalytic subunit a (EC 7.1.2.2) | protein | 589 | 33% helix, 23% strand | P31404 |
| B | V-type proton ATPase catalytic subunit a (EC 7.1.2.2) | protein | 590 | 30% helix, 25% strand | P31404 |
| C | V-type proton ATPase catalytic subunit a (EC 7.1.2.2) | protein | 597 | 32% helix, 25% strand | P31404 |
| D | V-type proton ATPase subunit B, brain isoform | protein | 461 | 29% helix, 23% strand | P31408 |
| E | V-type proton ATPase subunit B, brain isoform | protein | 458 | 32% helix, 23% strand | P31408 |
| F | V-type proton ATPase subunit B, brain isoform | protein | 459 | 31% helix, 22% strand | P31408 |
| G | V-type proton ATPase subunit C 1 | protein | 346 | 44% helix, 10% strand | P21282 |
| H | V-type proton ATPase subunit D | protein | 211 | 70% helix, 9% strand | A0A3Q1M4W9 |
| I, J | V-type proton ATPase subunit E 1 | protein | 218 | 68% helix, 8% strand | P11019 |
| K | V-type proton ATPase subunit E 1 | protein | 220 | 66% helix, 8% strand | P11019 |
| L | V-type proton ATPase subunit F | protein | 103 | 30% helix, 20% strand | Q28029 |
| M, N, O | V-type proton ATPase subunit G | protein | 108 | 80% helix, 0% strand | Q0VCV6 |
| P | V-type proton ATPase subunit H | protein | 368 | 66% helix, 0% strand | F1MZL6 |
| a | V-type proton ATPase subunit a | protein | 750 | 56% helix, 6% strand | F1MJV0 |
| b | V-type proton ATPase 21 kda proteolipid subunit | protein | 204 | 77% helix, 0% strand | Q2TA24 |
| d | V-type proton ATPase subunit D 1 | protein | 348 | 53% helix, 0% strand | P61420 |
| e | V-type proton ATPase subunit E 2 | protein | 73 | 53% helix, 1% strand | Q2KIB5 |
| s | V-type proton ATPase subunit S1 | protein | 205 | 14% helix, 36% strand | P40682 |
| r | Renin receptor | protein | 46 | 59% helix, 0% strand | P81134 |
| c, g, k, l, m, n | V-type proton ATPase 16 kda proteolipid subunit | protein | 150 | 84% helix, 0% strand | P23956 |
| o, p, q | V-type proton ATPase 16 kda proteolipid subunit | protein | 151 | 82% helix, 0% strand | P23956 |
| f | Ribonuclease kappa (EC 3.1.-.-) | protein | 45 | 71% helix, 0% strand | Q3ZC23 |
Ligands and binding sites
- POV · (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate · ligand · 9 copies · chains b, s, c, g, r, p, l, m, n, o, k, q
- ADP · Adenosine-5'-diphosphate · ligand · chains C, F
- OLA · Oleic acid · ligand · chains r, o, p
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains s, b
- MG · Magnesium ion · metal · chains C
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 | 991 | 0.86 | 0.87 | 98 | POV, OLA |
| 2 | 443 | 0.85 | 0.92 | 57 | empty |
| 3 | 715 | 0.85 | 0.88 | 89 | MG, ADP |
| 4 | 451 | 0.85 | 0.92 | 47 | empty |
| 5 | 368 | 0.84 | 0.93 | 78 | empty |
Interfaces
76 interfaces between chains.
- C–F · 3034 Ų buried · 35 hydrogen bonds · protein-protein
- B–E · 2656 Ų buried · 26 hydrogen bonds · protein-protein
- a–e · 2436 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 2367 Ų buried · 31 hydrogen bonds · protein-protein
- A–D · 2324 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 glycan, 2 covalent, 1 disulfide, 1 isopeptide (N-glycosylation, covalent ligand, disulfide, isopeptide).
Compared structures
- 6XBW · Cryo-EM structure of V-ATPase from bovine brain, state 1 · 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 P31404
- Every structure of UniProt P31408
- Every structure of UniProt P21282
- Every structure of UniProt A0A3Q1M4W9
- Every structure of UniProt P11019
- Every structure of UniProt Q28029
- Every structure of UniProt Q0VCV6
- Every structure of UniProt F1MZL6
- Every structure of UniProt F1MJV0
- Every structure of UniProt Q2TA24
- Every structure of UniProt P61420
- Every structure of UniProt Q2KIB5
- Every structure of UniProt P40682
- Every structure of UniProt P81134
- Every structure of UniProt P23956
- Every structure of UniProt Q3ZC23
- Elsewhere: RCSB PDB 6XBW · PDBe 6XBW · UniProt P31404 · UniProt P31408 · UniProt P21282 · UniProt A0A3Q1M4W9 · UniProt P11019 · UniProt Q28029 · UniProt Q0VCV6 · UniProt F1MZL6 · UniProt F1MJV0 · UniProt Q2TA24 · UniProt P61420 · UniProt Q2KIB5 · UniProt P40682 · UniProt P81134 · UniProt P23956 · UniProt Q3ZC23
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