Research workbench
Structural basis of selective binding of nonmethylated cpg islands by the cxxc domain of CFP1
Analyse Structural basis of selective binding of nonmethylated cpg islands by the cxxc… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QMD
- Type
- protein + DNA
- Length
- 77 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cpg-binding protein; DNA (5'-D(*GP*CP*CP*AP*AP*CP*GP*AP*TP*GP*GP*C)-3'); DNA…
- UniProt
- Q9P0U4
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.37
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cpg-binding protein | protein | 53 | 34% helix, 0% strand | Q9P0U4 |
| B | DNA (5'-D(*GP*CP*CP*AP*AP*CP*GP*AP*TP*GP*GP*C)-3') | dna | 12 | — | — |
| C | DNA (5'-D(*GP*CP*CP*AP*TP*CP*GP*TP*TP*GP*GP*C)-3') | dna | 12 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 63 | 0.37 | 0.79 | 15 | empty |
| 2 | 62 | 0.36 | 0.79 | 15 | empty |
| 3 | 81 | 0.29 | 0.73 | 14 | empty |
Interfaces
3 interfaces between chains.
- B–C · 550 Ų buried · 54 hydrogen bonds · nucleic-nucleic
- A–C · 404 Ų buried · 6 hydrogen bonds · protein-nucleic
- A–B · 250 Ų buried · 4 hydrogen bonds · protein-nucleic
Compared structures
- 3QMD · Structural Basis of Selective Binding of Nonmethylated CpG Islands by the CXXC Domain of… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9P0U4 · AlphaFold monomer V2.0 prediction for cxxc-type zinc finger protein 1 (Q9P0U4) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q9P0U4
- Elsewhere: RCSB PDB 3QMD · PDBe 3QMD · UniProt Q9P0U4
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