MolNFT v1 · #42489 · protein + DNA
Solution structure of mll cxxc domain in complex with palindromic cpg DNA
2KKF · Histone-lysine N-methyltransferase hrx: “Solution structure of mll cxxc domain in complex with palindromic cpg DNA”. Solution nmr, 1 ligand (ZN), 2 pockets (best druggability 0.41). MolNFT v1 #42489 on GenesisL1: 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
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.