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Ternary complex of the mixed lineage leukaemia (MLL1) set domain with the cofactor product S-adenosylhomocysteine and histone peptide.
Analyse Ternary complex of the mixed lineage leukaemia (MLL1) set domain with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2W5Z
- Type
- protein
- Length
- 188 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase hrx; Histone peptide
- EC
- 2.1.1.43
- UniProt
- Q03164
- Ligands
- SAH, ZN
- Pockets
- 2 · best druggability 0.48
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase hrx (EC 2.1.1.43) | protein | 180 | 19% helix, 28% strand | Q03164 |
| C | Histone peptide (EC 2.1.1.43) | protein | 8 | 0% helix, 13% strand | — |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · chains A, C
- ZN · Zinc ion · metal · chains A
- GOL · Glycerol · 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 | 189 | 0.48 | 0.76 | 22 | SAH |
| 2 | 69 | 0.36 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–C · 713 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (methylation).
Compared structures
- 2W5Z · Ternary Complex of the Mixed Lineage Leukaemia (MLL1) SET Domain with the cofactor… · 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 2W5Z · PDBe 2W5Z · UniProt Q03164
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