Histone-lysine N-methyltransferase 2D
Homo sapiens
State in the Current Structure
| Assembly | Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Associated Components | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|
| 1 | Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count | Chain B； UniProt 1503–1562 | Fragment：residues 1503-1562 | Histone H4 × 1 ZN ZINC ION × 2 | SOLUTION NMR NMR measurement conditions：pH 7；298 K；Ionic strength (raw mmCIF value) 100；Pressure 1 NMR sample composition：2.5 mM [U-13C; U-15N] MLL4 PHD6, 7.5 mM histone H4K16ac (11-21) peptide, 93% H2O/7% D2O | 93% H2O/7% D2O | Resolution not provided |
Other States of the Same Protein in the Database
Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.
| Other PDB | Difference from Current Entry 6O7G | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 3UVK Crystal structure of WDR5 in complex with the WDR5-interacting motif of MLL2 Deposited 2011-11-30 | Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
5337–5347（11 aa）
Fragment：WDR5-interacting motif (UNP residues 5337-5347)
|
Not recorded | BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；323 K；0.1 M ammonium sulfate, 24% PEG3350, 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 323K
|
Resolution 1.40 Å R-free 0.192 |
| 4ERQ X-ray structure of WDR5-MLL2 Win motif peptide binary complex Deposited 2012-04-20 | Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
5333–5346（14 aa）
Fragment：UNP residues 5333-5346
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
hanging drop；pH 7.3；294 K；PEG3350, Ammonium Sulfate, HEPES, pH 7.3, hanging drop, temperature 294K
|
Resolution 1.91 Å R-free 0.200 |
| 4ERQ X-ray structure of WDR5-MLL2 Win motif peptide binary complex Deposited 2012-04-20 | Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
5333–5346（14 aa）
Fragment：UNP residues 5333-5346
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
hanging drop；pH 7.3；294 K；PEG3350, Ammonium Sulfate, HEPES, pH 7.3, hanging drop, temperature 294K
|
Resolution 1.91 Å R-free 0.200 |
| 4ERQ X-ray structure of WDR5-MLL2 Win motif peptide binary complex Deposited 2012-04-20 | Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain F
5333–5346（14 aa）
Fragment：UNP residues 5333-5346
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
hanging drop；pH 7.3；294 K；PEG3350, Ammonium Sulfate, HEPES, pH 7.3, hanging drop, temperature 294K
|
Resolution 1.91 Å R-free 0.200 |
| 4Z4P Structure of the MLL4 SET Domain Deposited 2015-04-02 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
5385–5539（155 aa）
Fragment：UNP residues 5385-5539
|
Not recorded | ZN ZINC ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；100 mM Tris-HCl
20 % Ethanol
|
Resolution 2.20 Å R-free 0.242 |
| 8U2Y Solution structure of the PHD6 finger of MLL4 bound to TET3 Deposited 2023-09-06 | Different construct Different experimental conditions | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1503–1562（60 aa）
|
Not recorded | ZN ZINC ION × 2 |
SOLUTION NMR
NMR measurement conditions
pH 7；298 K；Ionic strength (raw mmCIF value) 150；Pressure 1
NMR sample composition
2.0 mM [U-13C; U-15N] Protein, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 9ATN NMR structure of the MLL4 PHD2/3 fingers in complex with ASXL2 Deposited 2024-02-27 | Different construct Different ligand/ion Different experimental conditions | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
227–322（96 aa）
|
Not recorded | ZN ZINC ION × 4 |
SOLUTION NMR
NMR measurement conditions
pH 7；298 K；Ionic strength (raw mmCIF value) 150；Pressure 1
NMR sample composition
1.5 mM 13C, 15N MLL4 PHD2,3, 25 mM TRIS, 150 mM sodium chloride, 3 mM DTT, 93% H2O/7% D2O | 93% H2O/7% D2O
|
Resolution not provided |
| 9YL3 State 1 MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-08 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 15 PDB declaration: 17-meric |
Chain K
4507–5537（1031 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions | Resolution 3.50 Å |
| 9YLE State 3 MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-08 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 15 PDB declaration: 17-meric |
Chain K
4507–5537（1031 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions | Resolution 3.63 Å |
| 9YLY MLL4FC bound to a nucleosome with p53 RE Deposited 2025-10-09 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 14 PDB declaration: 16-meric |
Chain K
4507–5537（1031 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions | Resolution 3.77 Å |
| 9YM8 State 2 focused on PHD FYR of MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-09 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: 18-meric |
Chain K
4507–5537（1031 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions | Resolution 3.43 Å |
| 9YMF State 2 focused on H3 N terminal tail of MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-09 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: 18-meric |
Chain K
4507–5537（1031 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions | Resolution 3.45 Å |
10 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | KMT2D_HUMAN |
| Isoform | O14686-3 |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain B； PDBConstruct 5–64； UniProt 1503–1562 |
