Research workbench
Solution structure of mll cxxc domain in complex with palindromic cpg DNA
Analyse Solution structure of mll cxxc domain in complex with palindromic cpg DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2KKF
- Type
- protein + DNA
- Length
- 81 residues
- Chains
- 3
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase hrx; 5'-D(*CP*CP*CP*TP*GP*CP*GP*CP*AP*GP*GP*G)-3'
- EC
- 2.1.1.43
- UniProt
- Q03164
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.41
Structure
solution nmr · 2 distinct chains · 21% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase hrx (EC 2.1.1.43) | protein | 57 | 21% helix, 4% strand | Q03164 |
| B, C | 5'-D(*CP*CP*CP*TP*GP*CP*GP*CP*AP*GP*GP*G)-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
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 | 82 | 0.41 | 0.79 | 13 | empty |
| 2 | 88 | 0.32 | 0.74 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 613 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–C · 544 Ų buried · 10 hydrogen bonds · protein-nucleic
- B–C · 536 Ų buried · 44 hydrogen bonds · nucleic-nucleic
Compared structures
- 2KKF · Solution structure of MLL CXXC domain in complex with palindromic CPG DNA · the same entry in another collection · chain A against A, TM-score 1.00
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 Q03164
- Elsewhere: RCSB PDB 2KKF · PDBe 2KKF · UniProt Q03164
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