MolNFT v1 · #115677 · protein + DNA
Crystal structure of the drosophila zeste DNA binding domain in complex with DNA
5CQQ · Regulatory protein zeste: “Crystal structure of the drosophila zeste DNA binding domain in complex with DNA”. X-ray diffraction, 5 pockets (best druggability 0.60). MolNFT v1 #115677 on GenesisL1: 3D structure, binding sites and…
- 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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