Research workbench
Structure of VPS34 complex II from S. cerevisiae.
Analyse Structure of VPS34 complex II from S. cerevisiae. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DFZ
- Type
- protein
- Length
- 2,853 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vacuolar protein sorting-associated protein 38; Phosphatidylinositol 3-kinase VPS34…
- EC
- 2.7.1.137, 2.7.11.1
- UniProt
- Q05919, P22543, P22219, Q02948
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 6 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vacuolar protein sorting-associated protein 38 | protein | 343 | 49% helix, 18% strand | Q05919 |
| C | Phosphatidylinositol 3-kinase VPS34 (EC 2.7.1.137) | protein | 783 | 43% helix, 12% strand | P22543 |
| B | SERINE/THREONINE-protein kinase VPS15 (EC 2.7.11.1) | protein | 1224 | 39% helix, 17% strand | P22219 |
| E | Nanobody binding S. cerevisiae VPS34 | protein | 113 | 3% helix, 52% strand | — |
| D | Vacuolar protein sorting-associated protein 30 | protein | 341 | 63% helix, 8% strand | Q02948 |
| G | Putative N-terminal domain of S. cerevisiae VPS30 | protein | 49 | 49% helix, 0% strand | — |
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 | 852 | 0.81 | 0.84 | 131 | empty |
| 2 | 727 | 0.79 | 0.84 | 98 | empty |
| 3 | 541 | 0.79 | 0.86 | 94 | empty |
| 4 | 1195 | 0.79 | 0.81 | 129 | empty |
| 5 | 879 | 0.75 | 0.79 | 105 | empty |
Interfaces
7 interfaces between chains.
- C–B · 1412 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 943 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 735 Ų buried · 1 hydrogen bond · protein-protein
- C–E · 314 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 306 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5DFZ · Structure of Vps34 complex II from S. cerevisiae. · the same entry in another collection · chain G against G, TM-score 1.00
- P22543 · AlphaFold monomer V2.0 prediction for phosphatidylinositol 3-kinase VPS34 (P22543) · a predicted model of the same protein · chain C against A, TM-score 0.87
- Q02948 · AlphaFold monomer V2.0 prediction for vacuolar protein sorting- associated protein 30… · a predicted model of the same protein · chain D against A, TM-score 0.81
- P22219 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase VPS15 (P22219) · a predicted model of the same protein · chain B against A, TM-score 0.62
- Q05919 · AlphaFold monomer V2.0 prediction for vacuolar protein sorting- associated protein 38… · a predicted model of the same protein · chain A against A, TM-score 0.38
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 Q05919
- Every structure of UniProt P22543
- Every structure of UniProt P22219
- Every structure of UniProt Q02948
- Elsewhere: RCSB PDB 5DFZ · PDBe 5DFZ · UniProt Q05919 · UniProt P22543 · UniProt P22219 · UniProt Q02948
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