Research workbench
Cryo-EM structure of V-ATPase from bovine brain, state 2
Analyse Cryo-EM structure of V-ATPase from bovine brain, state 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XBY
- Type
- protein
- Length
- 7,765 residues
- Chains
- 30
- 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
- UniProt
- P31404, P31408, P21282, A0A3Q1M4W9, P11019, Q28029, Q0VCV6, F1MZL6, F1MJV0, Q2TA24, P61420, P23956, P40682, P81134
- Ligands
- POV, ADP, NAG, MG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 20 distinct chains · 45% 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 | 597 | 31% helix, 23% strand | P31404 |
| B | V-type proton ATPase catalytic subunit a (EC 7.1.2.2) | protein | 577 | 31% helix, 23% strand | P31404 |
| C | V-type proton ATPase catalytic subunit a (EC 7.1.2.2) | protein | 583 | 30% helix, 23% strand | P31404 |
| D | V-type proton ATPase subunit B, brain isoform | protein | 457 | 28% helix, 21% strand | P31408 |
| E | V-type proton ATPase subunit B, brain isoform | protein | 457 | 28% helix, 22% strand | P31408 |
| F | V-type proton ATPase subunit B, brain isoform | protein | 454 | 28% helix, 24% strand | P31408 |
| G | V-type proton ATPase subunit C 1 | protein | 343 | 48% helix, 8% strand | P21282 |
| H | V-type proton ATPase subunit D | protein | 212 | 64% helix, 9% strand | A0A3Q1M4W9 |
| I, J | V-type proton ATPase subunit E 1 | protein | 218 | 68% helix, 9% strand | P11019 |
| K | V-type proton ATPase subunit E 1 | protein | 220 | 66% helix, 9% strand | P11019 |
| L | V-type proton ATPase subunit F | protein | 101 | 31% helix, 19% strand | Q28029 |
| M, N, O | V-type proton ATPase subunit G | protein | 108 | 76% helix, 0% strand | Q0VCV6 |
| P | V-type proton ATPase subunit H | protein | 370 | 64% helix, 0% strand | F1MZL6 |
| a | V-type proton ATPase subunit a | protein | 494 | 59% helix, 7% strand | F1MJV0 |
| b | V-type proton ATPase 21 kda proteolipid subunit | protein | 203 | 78% helix, 0% strand | Q2TA24 |
| d | V-type proton ATPase subunit D 1 | protein | 336 | 55% helix, 0% strand | P61420 |
| q, p, o | V-type proton ATPase 16 kda proteolipid subunit | protein | 151 | 79% helix, 0% strand | P23956 |
| c, g, k, l, m, n | V-type proton ATPase 16 kda proteolipid subunit | protein | 150 | 86% helix, 0% strand | P23956 |
| s | V-type proton ATPase subunit S1 | protein | 205 | 11% helix, 32% strand | P40682 |
| r | Renin receptor | protein | 43 | 56% helix, 0% strand | P81134 |
Ligands and binding sites
- POV · (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate · ligand · 7 copies · chains b, c, g, s, l, m, n, o, r, q, p
- ADP · Adenosine-5'-diphosphate · ligand · chains A, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains s, b
- MG · Magnesium ion · metal · chains A
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 | 1028 | 0.87 | 0.88 | 127 | empty |
| 2 | 1186 | 0.87 | 0.88 | 130 | empty |
| 3 | 989 | 0.86 | 0.87 | 96 | POV |
| 4 | 635 | 0.85 | 0.90 | 80 | MG, ADP |
| 5 | 407 | 0.84 | 0.92 | 48 | empty |
Interfaces
71 interfaces between chains.
- A–D · 3157 Ų buried · 30 hydrogen bonds · protein-protein
- C–F · 2787 Ų buried · 29 hydrogen bonds · protein-protein
- C–E · 2370 Ų buried · 27 hydrogen bonds · protein-protein
- B–E · 2368 Ų buried · 24 hydrogen bonds · protein-protein
- K–O · 1994 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 glycan, 3 covalent, 1 disulfide (N-glycosylation, covalent ligand, disulfide).
Compared structures
- 6XBY · Cryo-EM structure of V-ATPase from bovine brain, state 2 · 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 P23956
- Every structure of UniProt P40682
- Every structure of UniProt P81134
- Elsewhere: RCSB PDB 6XBY · PDBe 6XBY · UniProt P31404 · UniProt P31408 · UniProt P21282 · UniProt A0A3Q1M4W9 · UniProt P11019 · UniProt Q28029 · UniProt Q0VCV6 · UniProt F1MZL6 · UniProt F1MJV0 · UniProt Q2TA24 · UniProt P61420 · UniProt P23956 · UniProt P40682 · UniProt P81134
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