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
- 3OQ4
- Type
- protein
- Length
- 520 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DBF4
- UniProt
- P32325
- Pockets
- 8 · best druggability 0.47
Structure
x-ray diffraction · 5 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DBF4 | protein | 124 | 45% helix, 12% strand | P32325 |
| B | DBF4 | protein | 102 | 46% helix, 17% strand | P32325 |
| C | DBF4 | protein | 99 | 44% helix, 17% strand | P32325 |
| D | DBF4 | protein | 99 | 43% helix, 17% strand | P32325 |
| E | DBF4 | protein | 96 | 38% helix, 17% strand | P32325 |
Pockets
8 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 102 | 0.47 | 0.80 | 22 | empty |
| 2 | 72 | 0.45 | 0.82 | 21 | empty |
| 3 | 92 | 0.44 | 0.79 | 23 | empty |
| 4 | 91 | 0.42 | 0.79 | 22 | empty |
| 5 | 69 | 0.34 | 0.76 | 11 | empty |
Interfaces
4 interfaces between chains.
- B–C · 657 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 651 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 645 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 622 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3OQ4 · Crystal Structure of motif N of Saccharomyces cerevisiae Dbf4 · the same entry in another collection · chain E against E, 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 C 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 3OQ4 · PDBe 3OQ4 · UniProt P32325
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