Research workbench
Zinc finger region of MLL2 in complex with cpg DNA
Analyse Zinc finger region of MLL2 in complex with cpg DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PZI
- Type
- protein + DNA
- Length
- 85 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase 2B; DNA (5'-D(*GP*CP*CP*AP*CP*CP*GP*GP*TP*GP*GP*C)-3')
- EC
- 2.1.1.43
- UniProt
- Q9UMN6
- Ligands
- ZN, UNX
- Pockets
- 3 · best druggability 0.48
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase 2B (EC 2.1.1.43) | protein | 61 | 39% helix, 0% strand | Q9UMN6 |
| B, C | DNA (5'-D(*GP*CP*CP*AP*CP*CP*GP*GP*TP*GP*GP*C)-3') | dna | 12 | — | — |
Ligands and binding sites
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 | 169 | 0.48 | 0.76 | 20 | UNX |
| 2 | 193 | 0.47 | 0.76 | 20 | empty |
| 3 | 73 | 0.35 | 0.77 | 11 | empty |
Interfaces
3 interfaces between chains.
- B–C · 565 Ų buried · 59 hydrogen bonds · nucleic-nucleic
- A–C · 504 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–B · 454 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 4PZI · Zinc finger region of MLL2 in complex with 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 Q9UMN6
- Elsewhere: RCSB PDB 4PZI · PDBe 4PZI · UniProt Q9UMN6
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