Research workbench
Cryo-EM structure of archazolid a bound to yeast vo V-ATPase
Analyse Cryo-EM structure of archazolid a bound to yeast vo V-ATPase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TAP
- Type
- protein
- Length
- 2,915 residues
- Chains
- 15
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- V-type proton ATPase subunit C'; V-type proton ATPase subunit C''; V0 assembly protein 1…
- UniProt
- P32842, P23968, P53262, Q3E7B6, P25515, P0C5R9, P32366, P32563
- Ligands
- KJL
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 8 distinct chains · 69% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | V-type proton ATPase subunit C' | protein | 158 | 82% helix, 0% strand | P32842 |
| C | V-type proton ATPase subunit C'' | protein | 198 | 82% helix, 0% strand | P23968 |
| N | V0 assembly protein 1 | protein | 52 | 54% helix, 0% strand | P53262 |
| M | V-type proton ATPase subunit E | protein | 71 | 65% helix, 4% strand | Q3E7B6 |
| E, F, G, H, I, J, K, L | V-type proton ATPase subunit C | protein | 159 | 79% helix, 0% strand | P25515 |
| O | Yeast V-ATPase subunit F | protein | 69 | 81% helix, 1% strand | P0C5R9 |
| B | V-type proton ATPase subunit D | protein | 345 | 65% helix, 0% strand | P32366 |
| A | V-type proton ATPase subunit a, vacuolar isoform | protein | 750 | 63% helix, 9% strand | P32563 |
Ligands and binding sites
- KJL · Archazolid A · ligand · 8 copies · chains D, C, A, E, F, G, H, I, J, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 989 | 0.82 | 0.83 | 79 | empty |
| 2 | 1184 | 0.81 | 0.82 | 105 | empty |
| 3 | 1112 | 0.78 | 0.80 | 81 | empty |
| 4 | 1200 | 0.73 | 0.76 | 102 | empty |
| 5 | 564 | 0.69 | 0.78 | 49 | empty |
Interfaces
33 interfaces between chains.
- M–A · 2316 Ų buried · 22 hydrogen bonds · protein-protein
- D–E · 1894 Ų buried · 6 hydrogen bonds · protein-protein
- E–F · 1841 Ų buried · 7 hydrogen bonds · protein-protein
- J–K · 1830 Ų buried · 9 hydrogen bonds · protein-protein
- G–H · 1828 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7TAP · Cryo-EM structure of archazolid A bound to yeast VO V-ATPase · the same entry in another collection · chain A against A, 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 P32842
- Every structure of UniProt P23968
- Every structure of UniProt P53262
- Every structure of UniProt Q3E7B6
- Every structure of UniProt P25515
- Every structure of UniProt P0C5R9
- Every structure of UniProt P32366
- Every structure of UniProt P32563
- Elsewhere: RCSB PDB 7TAP · PDBe 7TAP · UniProt P32842 · UniProt P23968 · UniProt P53262 · UniProt Q3E7B6 · UniProt P25515 · UniProt P0C5R9 · UniProt P32366 · UniProt P32563
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