Research workbench
Cryo-EM structure of bafilomycin A1-bound intact V-ATPase from bovine brain
Analyse Cryo-EM structure of bafilomycin A1-bound intact V-ATPase from bovine brain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KHR
- Type
- protein
- Length
- 8,212 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, WEV, ADP, WJP, OLA, NAG, MAN, GLC, BMA, MG
- Pockets
- 20 · best druggability 0.90
Structure
electron microscopy · 21 distinct chains · 44% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | V-type proton ATPase catalytic subunit a (EC 7.1.2.2) | protein | 589 | 30% helix, 22% strand | P31404 |
| B | V-type proton ATPase catalytic subunit a (EC 7.1.2.2) | protein | 591 | 30% helix, 24% strand | P31404 |
| C | V-type proton ATPase catalytic subunit a (EC 7.1.2.2) | protein | 600 | 31% helix, 24% strand | P31404 |
| D | V-type proton ATPase subunit B, brain isoform | protein | 461 | 27% helix, 22% strand | P31408 |
| E, F | V-type proton ATPase subunit B, brain isoform | protein | 458 | 31% helix, 22% strand | P31408 |
| G | V-type proton ATPase subunit C 1 | protein | 346 | 43% helix, 9% strand | P21282 |
| H | V-type proton ATPase subunit D | protein | 212 | 63% helix, 9% strand | A0A3Q1M4W9 |
| I, J | V-type proton ATPase subunit E 1 | protein | 218 | 68% helix, 6% strand | P11019 |
| K | V-type proton ATPase subunit E 1 | protein | 220 | 67% helix, 8% strand | P11019 |
| L | V-type proton ATPase subunit F | protein | 103 | 23% helix, 22% strand | Q28029 |
| M, N, O | V-type proton ATPase subunit G | protein | 109 | 72% helix, 0% strand | Q0VCV6 |
| P | V-type proton ATPase subunit H | protein | 368 | 62% helix, 0% strand | F1MZL6 |
| a | V-type proton ATPase subunit a | protein | 750 | 49% helix, 6% strand | F1MJV0 |
| b | V-type proton ATPase 21 kda proteolipid subunit | protein | 204 | 74% helix, 0% strand | Q2TA24 |
| d | V-type proton ATPase subunit D 1 | protein | 348 | 48% helix, 0% strand | P61420 |
| e | V-type proton ATPase subunit E 2 | protein | 73 | 45% helix, 3% strand | Q2KIB5 |
| s | V-type proton ATPase subunit S1 | protein | 204 | 11% helix, 36% strand | P40682 |
| r | Renin receptor | protein | 46 | 57% helix, 0% strand | P81134 |
| c, g, k, l, m, n | V-type proton ATPase 16 kda proteolipid subunit | protein | 150 | 83% helix, 0% strand | P23956 |
| o, p, q | V-type proton ATPase 16 kda proteolipid subunit | protein | 151 | 78% helix, 0% strand | P23956 |
| f | Ribonuclease kappa (EC 3.1.-.-) | protein | 65 | 82% helix, 0% strand | Q3ZC23 |
Ligands and binding sites
- POV · (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate · ligand · 8 copies · chains b, s, r, g, k, c, p, q, n, o, l, m
- WEV · (5R)-2,4-dideoxy-1-C-{(2S,3R,4S)-3-hydroxy-4-[(2R,3S, 4E,6E,9R,10S,11R,12E,14Z)-10-hydroxy-3,15-dimethoxy-7, 9,11,13-tetramethyl-16-oxo-1-oxacyclohexadeca-4,6,12, 14-tetraen-2-yl]pentan-2-yl}-4-methyl-5-propan-2-yl-alpha-D-threo-pentopyranose · ligand · 6 copies · chains c, g, k, l, m, o, p, q
- ADP · Adenosine-5'-diphosphate · ligand · chains C, F
- WJP · Methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6, 10,14,18-tetraen-1-yl dihydrogen diphosphate · ligand · chains a, n, o
- OLA · Oleic acid · ligand · chains r, o, p
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains a, e, s, b
- MAN · alpha-D-mannopyranose · sugar · 5 copies · chains a, e
- GLC · alpha-D-glucopyranose · sugar · 3 copies · chains a
- BMA · beta-D-mannopyranose · sugar · chains a
- 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 | 1178 | 0.90 | 0.92 | 179 | empty |
| 2 | 646 | 0.87 | 0.92 | 77 | empty |
| 3 | 994 | 0.86 | 0.86 | 101 | POV, OLA |
| 4 | 690 | 0.85 | 0.89 | 80 | empty |
| 5 | 456 | 0.84 | 0.92 | 55 | empty |
Interfaces
74 interfaces between chains.
- C–F · 3131 Ų buried · 39 hydrogen bonds · protein-protein
- B–E · 2679 Ų buried · 29 hydrogen bonds · protein-protein
- B–D · 2480 Ų buried · 25 hydrogen bonds · protein-protein
- a–e · 2462 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 2304 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 glycan, 1 covalent, 1 disulfide, 1 isopeptide (N-glycosylation, covalent ligand, disulfide, glycosylation, isopeptide).
Compared structures
- 7KHR · Cryo-EM structure of bafilomycin A1-bound intact V-ATPase from bovine brain · 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 7KHR · PDBe 7KHR · 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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