Research workbench
Crystal structure of motif N of saccharomyces cerevisiae DBF4
Analyse Crystal structure of motif N of saccharomyces cerevisiae DBF4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OQ0
- Type
- protein
- Length
- 984 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DBF4
- UniProt
- P32325
- Pockets
- 12 · best druggability 0.63
Structure
x-ray diffraction · 5 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | DBF4 | protein | 101 | 43% helix, 15% strand | P32325 |
| B, G | DBF4 | protein | 93 | 46% helix, 18% strand | P32325 |
| C, H | DBF4 | protein | 100 | 40% helix, 17% strand | P32325 |
| D, I | DBF4 | protein | 103 | 47% helix, 15% strand | P32325 |
| E, J | DBF4 | protein | 95 | 44% helix, 13% strand | P32325 |
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 330 | 0.63 | 0.79 | 44 | empty |
| 2 | 295 | 0.60 | 0.79 | 46 | empty |
| 3 | 411 | 0.60 | 0.76 | 53 | empty |
| 4 | 414 | 0.60 | 0.76 | 61 | empty |
| 5 | 158 | 0.52 | 0.79 | 24 | empty |
Interfaces
12 interfaces between chains.
- B–C · 648 Ų buried · 12 hydrogen bonds · protein-protein
- G–H · 644 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 644 Ų buried · 11 hydrogen bonds · protein-protein
- H–I · 643 Ų buried · 13 hydrogen bonds · protein-protein
- F–G · 638 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 modified (engineered).
Compared structures
- 3OQ0 · Crystal Structure of motif N of Saccharomyces cerevisiae Dbf4 · the same entry in another collection · chain J against J, TM-score 1.00
- P32325 · AlphaFold monomer V2.0 prediction for ddk kinase regulatory subunit DBF4 (P32325) · a predicted model of the same protein · chain G against A, TM-score 0.98
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 P32325
- Elsewhere: RCSB PDB 3OQ0 · PDBe 3OQ0 · UniProt P32325
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.