Research workbench
Yeast V-ATPase state 3
Analyse Yeast V-ATPase state 3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3J9V
- Type
- protein
- Length
- 7,451 residues
- Chains
- 28
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- V-type proton ATPase subunit a, vacuolar isoform; V-type proton ATPase subunit C; V-type…
- EC
- 3.6.3.14, 3.1.-.-
- UniProt
- P32563, P31412, P32610, P39111, P17255, P16140, P32366, P48836, P22203, P41807, P25515
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 11 distinct chains · 55% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| b | V-type proton ATPase subunit a, vacuolar isoform | protein | 312 | 54% helix, 13% strand | P32563 |
| O | V-type proton ATPase subunit C | protein | 392 | 47% helix, 13% strand | P31412 |
| M | V-type proton ATPase subunit D | protein | 210 | 76% helix, 10% strand | P32610 |
| N | V-type proton ATPase subunit F | protein | 115 | 37% helix, 22% strand | P39111 |
| E, A, C | V-type proton ATPase catalytic subunit a (EC 3.6.3.14, 3.1.-.-) | protein | 593 | 37% helix, 25% strand | P17255 |
| F, B, D | V-type proton ATPase subunit B | protein | 457 | 36% helix, 23% strand | P16140 |
| Q | V-type proton ATPase subunit D | protein | 345 | 61% helix, 0% strand | P32366 |
| J, L, H | V-type proton ATPase subunit G | protein | 105 | 89% helix, 0% strand | P48836 |
| I, K, G | V-type proton ATPase subunit E | protein | 217 | 71% helix, 11% strand | P22203 |
| P | V-type proton ATPase subunit H | protein | 461 | 73% helix, 0% strand | P41807 |
| R, U, X, Y, W, Z, V, a, S, T | V-type proton ATPase subunit C | protein | 150 | 82% helix, 0% strand | P25515 |
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 | 669 | 0.86 | 0.90 | 78 | empty |
| 2 | 348 | 0.85 | 0.95 | 53 | empty |
| 3 | 260 | 0.84 | 0.96 | 32 | empty |
| 4 | 580 | 0.83 | 0.88 | 65 | empty |
| 5 | 213 | 0.81 | 0.95 | 41 | empty |
Interfaces
56 interfaces between chains.
- C–D · 3733 Ų buried · 45 hydrogen bonds · protein-protein
- A–B · 3534 Ų buried · 40 hydrogen bonds · protein-protein
- J–I · 2994 Ų buried · 13 hydrogen bonds · protein-protein
- H–G · 2946 Ų buried · 6 hydrogen bonds · protein-protein
- L–K · 2936 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- P17255 · AlphaFold monomer V2.0 prediction for V-type proton ATPase catalytic subunit a (P17255) · a predicted model of the same protein · chain E against A, TM-score 0.94
- P25515 · AlphaFold monomer V2.0 prediction for V-type proton ATPase subunit C (P25515) · a predicted model of the same protein · chain R against A, TM-score 0.93
- P16140 · AlphaFold monomer V2.0 prediction for V-type proton ATPase subunit B (P16140) · a predicted model of the same protein · chain F against A, TM-score 0.93
- P39111 · AlphaFold monomer V2.0 prediction for V-type proton ATPase subunit F (P39111) · a predicted model of the same protein · chain N against A, TM-score 0.92
- P32610 · AlphaFold monomer V2.0 prediction for V-type proton ATPase subunit D (P32610) · a predicted model of the same protein · chain M against A, TM-score 0.89
- P22203 · AlphaFold monomer V2.0 prediction for V-type proton ATPase subunit E (P22203) · a predicted model of the same protein · chain I against A, TM-score 0.85
- P41807 · AlphaFold monomer V2.0 prediction for V-type proton ATPase subunit H (P41807) · a predicted model of the same protein · chain P against A, TM-score 0.85
- P31412 · AlphaFold monomer V2.0 prediction for V-type proton ATPase subunit C (P31412) · a predicted model of the same protein · chain O against A, TM-score 0.84
- P32366 · AlphaFold monomer V2.0 prediction for V-type proton ATPase subunit D (P32366) · a predicted model of the same protein · chain Q against A, TM-score 0.80
- P48836 · AlphaFold monomer V2.0 prediction for V-type proton ATPase subunit G (P48836) · a predicted model of the same protein · chain J against A, TM-score 0.79
- P32563 · AlphaFold monomer V2.0 prediction for V-type proton ATPase subunit a, vacuolar isoform… · a predicted model of the same protein · chain b against A, TM-score 0.67
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 P32563
- Every structure of UniProt P31412
- Every structure of UniProt P32610
- Every structure of UniProt P39111
- Every structure of UniProt P17255
- Every structure of UniProt P16140
- Every structure of UniProt P32366
- Every structure of UniProt P48836
- Every structure of UniProt P22203
- Every structure of UniProt P41807
- Every structure of UniProt P25515
- Elsewhere: RCSB PDB 3J9V · PDBe 3J9V · UniProt P32563 · UniProt P31412 · UniProt P32610 · UniProt P39111 · UniProt P17255 · UniProt P16140 · UniProt P32366 · UniProt P48836 · UniProt P22203 · UniProt P41807 · UniProt P25515
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