Research workbench
Structural basis of selective binding of non-methylated cpg islands (DNA-tcga) by the cxxc domain of CFP1
Analyse Structural basis of selective binding of non-methylated cpg islands (DNA-tcga)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QMH
- Type
- protein + DNA
- Length
- 77 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cpg-binding protein; 5'-D(*GP*CP*CP*AP*TP*CP*GP*AP*TP*GP*GP*C)-3'
- UniProt
- Q9P0U4
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.35
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cpg-binding protein | protein | 53 | 26% helix, 0% strand | Q9P0U4 |
| B, C | 5'-D(*GP*CP*CP*AP*TP*CP*GP*AP*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 | 65 | 0.35 | 0.78 | 14 | empty |
| 2 | 61 | 0.32 | 0.76 | 13 | empty |
| 3 | 90 | 0.31 | 0.73 | 14 | empty |
Interfaces
3 interfaces between chains.
- B–C · 542 Ų buried · 57 hydrogen bonds · nucleic-nucleic
- A–B · 377 Ų buried · 6 hydrogen bonds · protein-nucleic
- A–C · 268 Ų buried · 4 hydrogen bonds · protein-nucleic
Compared structures
- 3QMH · Structural Basis of Selective Binding of Non-Methylated CpG islands (DNA-TCGA) by the… · 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 0.95
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 3QMH · PDBe 3QMH · UniProt Q9P0U4
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