Research workbench
Yeast V-ATPase in complex with legionella pneumophila effector sidk (rotational state 2)
Analyse Yeast V-ATPase in complex with legionella pneumophila effector sidk (rotational… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VOY
- Type
- protein
- Length
- 8,691 residues
- Chains
- 33
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- V-type proton ATPase catalytic subunit A,V-type proton ATPase catalytic subunit a; V-type…
- EC
- 3.6.3.14, 3.1.-.-
- UniProt
- P17255, P16140, P22203, P48836, P32610, P39111, P31412, P41807, P32366, P23968, P32842, P25515, P32563, Q3E7B6, G8UUS6
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 19 distinct chains · 58% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | V-type proton ATPase catalytic subunit A,V-type proton ATPase catalytic subunit a (EC 3.6.3.14, 3.1.-.-) | protein | 593 | 33% helix, 22% strand | P17255 |
| B, D, F | V-type proton ATPase subunit B | protein | 457 | 35% helix, 19% strand | P16140 |
| G | V-type proton ATPase subunit E | protein | 218 | 68% helix, 10% strand | P22203 |
| H, J, L | V-type proton ATPase subunit G | protein | 105 | 89% helix, 0% strand | P48836 |
| I, K | V-type proton ATPase subunit E | protein | 217 | 71% helix, 7% strand | P22203 |
| M | V-type proton ATPase subunit D | protein | 210 | 74% helix, 9% strand | P32610 |
| N | V-type proton ATPase subunit F | protein | 115 | 37% helix, 23% strand | P39111 |
| O | V-type proton ATPase subunit C | protein | 392 | 45% helix, 12% strand | P31412 |
| P | V-type proton ATPase subunit H | protein | 462 | 69% helix, 0% strand | P41807 |
| Q | V-type proton ATPase subunit D | protein | 345 | 60% helix, 0% strand | P32366 |
| R | V-type proton ATPase subunit C'' | protein | 213 | 64% helix, 0% strand | P23968 |
| S | V-type proton ATPase subunit C' | protein | 147 | 67% helix, 0% strand | P32842 |
| T, U, W, X, Y | V-type proton ATPase subunit C | protein | 150 | 75% helix, 0% strand | P25515 |
| V | V-type proton ATPase subunit C | protein | 149 | 76% helix, 0% strand | P25515 |
| Z, a | V-type proton ATPase subunit C | protein | 148 | 76% helix, 0% strand | P25515 |
| b | V-type proton ATPase subunit a, vacuolar isoform | protein | 634 | 60% helix, 6% strand | P32563 |
| c | V-type proton ATPase subunit E | protein | 57 | 46% helix, 0% strand | Q3E7B6 |
| d | V-type proton ATPase subunit F | protein | 54 | 83% helix, 0% strand | — |
| e, f, g | Effector protein sidk | protein | 250 | 70% helix, 0% strand | G8UUS6 |
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 | 874 | 0.83 | 0.86 | 173 | empty |
| 2 | 537 | 0.78 | 0.86 | 106 | empty |
| 3 | 710 | 0.76 | 0.82 | 167 | empty |
| 4 | 897 | 0.76 | 0.80 | 130 | empty |
| 5 | 625 | 0.76 | 0.83 | 153 | empty |
Interfaces
55 interfaces between chains.
- A–B · 1091 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 862 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 627 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 597 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 564 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5VOY · Yeast V-ATPase in complex with Legionella pneumophila effector SidK (rotational 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 P17255
- Every structure of UniProt P16140
- Every structure of UniProt P22203
- Every structure of UniProt P48836
- Every structure of UniProt P32610
- Every structure of UniProt P39111
- Every structure of UniProt P31412
- Every structure of UniProt P41807
- Every structure of UniProt P32366
- Every structure of UniProt P23968
- Every structure of UniProt P32842
- Every structure of UniProt P25515
- Every structure of UniProt P32563
- Every structure of UniProt Q3E7B6
- Every structure of UniProt G8UUS6
- Elsewhere: RCSB PDB 5VOY · PDBe 5VOY · UniProt P17255 · UniProt P16140 · UniProt P22203 · UniProt P48836 · UniProt P32610 · UniProt P39111 · UniProt P31412 · UniProt P41807 · UniProt P32366 · UniProt P23968 · UniProt P32842 · UniProt P25515 · UniProt P32563 · UniProt Q3E7B6 · UniProt G8UUS6
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