Research workbench
Yeast vacuolar ATPase vo in lipid nanodisc
Analyse Yeast vacuolar ATPase vo in lipid nanodisc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6C6L
- Type
- protein
- Length
- 2,918 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…
- EC
- 3.6.3.14
- UniProt
- P32842, P23968, P53262, Q3E7B6, P25515, P32366, P32563, P0C5R9
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 9 distinct chains · 65% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | V-type proton ATPase subunit C' | protein | 157 | 76% helix, 0% strand | P32842 |
| C | V-type proton ATPase subunit C'' | protein | 200 | 75% helix, 0% strand | P23968 |
| N | V0 assembly protein 1 | protein | 52 | 46% helix, 0% strand | P53262 |
| M | V-type proton ATPase subunit E | protein | 69 | 58% helix, 0% strand | Q3E7B6 |
| E, F, G, I, J, L | V-type proton ATPase subunit C (EC 3.6.3.14) | protein | 159 | 79% helix, 0% strand | P25515 |
| B | V-type proton ATPase subunit D | protein | 344 | 63% helix, 0% strand | P32366 |
| H, K | V-type proton ATPase subunit C (EC 3.6.3.14) | protein | 160 | 78% helix, 0% strand | P25515 |
| A | V-type proton ATPase subunit a, vacuolar isoform | protein | 746 | 57% helix, 8% strand | P32563 |
| O | V-type proton ATPase subunit F | protein | 76 | 58% helix, 0% strand | P0C5R9 |
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 | 983 | 0.80 | 0.81 | 92 | empty |
| 2 | 1152 | 0.80 | 0.81 | 99 | empty |
| 3 | 681 | 0.76 | 0.81 | 56 | empty |
| 4 | 895 | 0.75 | 0.79 | 67 | empty |
| 5 | 817 | 0.75 | 0.79 | 87 | empty |
Interfaces
33 interfaces between chains.
- M–A · 2215 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 1843 Ų buried · 6 hydrogen bonds · protein-protein
- D–C · 1816 Ų buried · 2 hydrogen bonds · protein-protein
- K–L · 1810 Ų buried · 5 hydrogen bonds · protein-protein
- E–F · 1799 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6C6L · Yeast Vacuolar ATPase Vo in lipid nanodisc · the same entry in another collection · chain O against O, 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 P32366
- Every structure of UniProt P32563
- Every structure of UniProt P0C5R9
- Elsewhere: RCSB PDB 6C6L · PDBe 6C6L · UniProt P32842 · UniProt P23968 · UniProt P53262 · UniProt Q3E7B6 · UniProt P25515 · UniProt P32366 · UniProt P32563 · UniProt P0C5R9
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