MolNFT v1 · #76493 · protein + DNA
Structural basis of selective binding of non-methylated cpg islands (DNA-acgt) by the cxxc domain of CFP1
3QMI · Cpg-binding protein: “Structural basis of selective binding of non-methylated cpg islands (DNA-acgt) by the cxxc domain of CFP1”. X-ray diffraction, 2 ligands (ZN, PO4), 2 pockets (best druggability 0.33). MolNFT v1 #76493 on…
- PDB
- 3QMI
- Type
- protein + DNA
- Length
- 76 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*AP*CP*GP*TP*TP*GP*GP*C)-3'
- UniProt
- Q9P0U4
- Ligands
- ZN, PO4
- Pockets
- 2 · best druggability 0.33
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cpg-binding protein | protein | 52 | 35% helix, 0% strand | Q9P0U4 |
| B, C | 5'-D(*GP*CP*CP*AP*AP*CP*GP*TP*TP*GP*GP*C)-3' | dna | 12 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A
- PO4 · Phosphate ion · ion · chains C
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 50 | 0.33 | 0.79 | 14 | empty |
| 2 | 53 | 0.23 | 0.72 | 10 | empty |
Interfaces
3 interfaces between chains.
- B–C · 550 Ų buried · 50 hydrogen bonds · nucleic-nucleic
- A–B · 372 Ų buried · 5 hydrogen bonds · protein-nucleic
- A–C · 263 Ų buried · 4 hydrogen bonds · protein-nucleic
Compared structures
- 3QMI · Structural Basis of Selective Binding of Non-Methylated CpG islands (DNA-ACGT) 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 0.97
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 3QMI · PDBe 3QMI · UniProt Q9P0U4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.