Research workbench
Crystal structure of the drosophila zeste DNA binding domain in complex with DNA
Analyse Crystal structure of the drosophila zeste DNA binding domain in complex with DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CQQ
- Type
- protein + DNA
- Length
- 225 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Regulatory protein zeste; DNA (5'- D(*CP*TP*GP*TP*TP*TP*TP*CP*CP*AP*CP*TP*CP*GP*TP*TP*TP*T…
- UniProt
- P09956
- Pockets
- 5 · best druggability 0.60
Structure
x-ray diffraction · 4 distinct chains · 64% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Regulatory protein zeste | protein | 74 | 65% helix, 0% strand | P09956 |
| B | Regulatory protein zeste | protein | 75 | 63% helix, 0% strand | P09956 |
| C, E | DNA (5'- D(*CP*TP*GP*TP*TP*TP*TP*CP*CP*AP*CP*TP*CP*GP*TP*TP*TP*TP*T)-3') | dna | 19 | — | — |
| D, F | DNA (5'- D(*AP*AP*AP*AP*AP*CP*GP*AP*GP*TP*GP*GP*AP*AP*AP*AP*CP*AP*G)-3') | dna | 19 | — | — |
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 305 | 0.60 | 0.79 | 35 | empty |
| 2 | 201 | 0.54 | 0.79 | 23 | empty |
| 3 | 97 | 0.38 | 0.76 | 16 | empty |
| 4 | 74 | 0.34 | 0.76 | 12 | empty |
| 5 | 73 | 0.30 | 0.74 | 10 | empty |
Interfaces
9 interfaces between chains.
- C–D · 839 Ų buried · 88 hydrogen bonds · nucleic-nucleic
- E–F · 835 Ų buried · 83 hydrogen bonds · nucleic-nucleic
- A–D · 572 Ų buried · 13 hydrogen bonds · protein-nucleic
- B–F · 529 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–C · 415 Ų buried · 3 hydrogen bonds · protein-nucleic
Compared structures
- 5CQQ · Crystal structure of the Drosophila Zeste DNA binding domain in complex with DNA · the same entry in another collection · chain F against F, TM-score 1.00
- P09956 · AlphaFold monomer V2.0 prediction for regulatory protein zeste (P09956) · a predicted model of the same protein · chain B 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 P09956
- Elsewhere: RCSB PDB 5CQQ · PDBe 5CQQ · UniProt P09956
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