2W5Z: Histone-lysine N-methyltransferase hrx

Name: PDB 2W5Z: Ternary Complex of the Mixed Lineage Leukaemia (MLL1) SET Domain with the cofactor product S-Adenosylhomocysteine and histone peptide.
Published: 2009-02-10
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Ternary Complex of the Mixed Lineage Leukaemia (MLL1) SET Domain with the cofactor product S-Adenosylhomocysteine and histone peptide. Determined by X-ray diffraction at 2.2 Å resolution. Released 10 Feb 2009.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: HOMO SAPIENS
Chains: 2
Atoms: 1,628
Mol. weight: 23.94 kDa
Ligands: SAH, ZN
Released: 10 Feb 2009

Explore 2W5Z in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2W5Z contains 12 α-helices and 16 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 11 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	3801-3802	2
α-helix	3805-3808	4
α-helix	3809-3811	3
α-helix	3816-3820	5
α-helix	3823-3830	8
β-strand	3831-3835	5	1
β-strand	3841-3845	5	1
β-strand	3849	1	2
β-strand	3854-3857	4	3
β-strand	3861-3864	4	4
α-helix	3865-3867	3
α-helix	3868-3878	11
β-strand	3884-3886	3	4
β-strand	3891-3894	4	4
α-helix	3901-3904	4
α-helix	3905	1
β-strand	3906-3907	2	5
β-strand	3913-3920	8	3
β-strand	3923-3930	8	3
β-strand	3934	1	2
α-helix	3938	1
β-strand	3939-3940	2	1
β-strand	3941-3942	2	5
α-helix	3954-3955	2
β-strand	3956	1	6
β-strand	3967	1	6

Chain C: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	4	1	4
α-helix	6-8	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-lysine N-methyltransferase hrx	A	protein	192	HOMO SAPIENS	Q03164
Histone peptide	C	protein	9	HOMO SAPIENS	P68433 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2W5Z_1 HISTONE-LYSINE N-METHYLTRANSFERASE HRX (chains A)
GPLGSHMHRQPPEYNPNDEEEEEVQLKSARRATSMDLPMPMRFRHLKKTSKEAVGVYRSP
IHGRGLFCKRNIDAGEMVIEYAGNVIRSIQTDKREKYYDSKGIGCYMFRIDDSEVVDATM
HGNAARFINHSCEPNCYSRVINIDGQKHIVIFAMRKIYRGEELTYDYKFPIEDASNKLPC
NCGAKKCRKFLN

Sequence of entity 2 (C), FASTA

>2W5Z_2 HISTONE PEPTIDE (chains C)
ARTKQTARY

Ligands and cofactors

ID	Name	Formula	Copies
SAH	S-adenosyl-L-homocysteine	C14 H20 N6 O5 S	1
ZN	Zinc ion	Zn	1

Water and common crystallization additives (GOL) are not listed.

Primary citation

Structural Basis for the Requirement of Additional Factors for Mll1 Set Domain Activity and Recognition of Epigenetic Marks. Southall, S.M., Wong, P.S., Odho, Z. et al. Mol Cell (2009) 33:181. DOI 10.1016/J.MOLCEL.2008.12.029 · PubMed

Other PDB entries of the same protein (UniProt Q03164), best resolution first:

3EMH 1.37 Å, Structural basis of WDR5-MLL interaction
9C4T 1.46 Å, menin mutant M327I in complex with MLL peptide
9C4V 1.47 Å, Menin mutant G331D in complex with MLL peptide
7S79 1.53 Å, Structure of HLA-B*07:02 in complex with synthetic phosphono-mll peptide analog
9C4S 1.54 Å, Menin mutant G331R in complex with MLL peptide
4GQ6 1.55 Å, Human menin in complex with MLL peptide
7S7D 1.56 Å, Structure of HLA-B*07:02 in complex with synthetic sulfo-mll peptide analog
9C4U 1.57 Å, Menin mutant T349M in complex with MLL peptide
7S8E 1.6 Å, Structure of HLA-B*07:02 in complex with MLL(747-755) phosphopeptide and bound glycerol
4ESG 1.7 Å, X-ray structure of WDR5-MLL1 Win motif peptide binary complex
3EG6 1.72 Å, Structure of WDR5 bound to MLL1 peptide
3LQH 1.72 Å, Crystal structure of MLL1 PHD3-Bromo in the free form

Browse structure collections

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