Structure of PDB 5egb Chain A

Receptor sequence

>5egbA (length=111) Species: 9606 (Homo sapiens)

EKPYVCRECGRGFSNKSHLLRHQRTHTGEKPYVCRECGRGFRDKSHLLRH
QRTHTGEKPYVCRECGRGFRDKSNLLSHQRTHTGEKPYVCRECGRGFSNK
SHLLRHQRTHT

3D structure

• PDB: 5egb Structural basis for human PRDM9 action at recombination hot spots.
• Chain: A
• Resolution: 1.977 Å

Enzymatic activity

• Enzyme Commision number: 2.1.1.-
  2.1.1.354: [histone H3]-lysine(4) N-trimethyltransferase.
  2.1.1.355: [histone H3]-lysine(9) N-trimethyltransferase.
  2.1.1.359: [histone H3]-lysine(36) N-trimethyltransferase.
  2.1.1.361: [histone H4]-lysine(20) N-methyltransferase.
  2.1.1.362: [histone H4]-N-methyl-L-lysine(20) N-methyltransferase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	dna	A	H733 R736 H737 T740 R754 F756 R757 H761 R764 H765 R782 R785 N789 H793 R810 F812 N814 H817 R820 H821	H18 R21 H22 T25 R39 F41 R42 H46 R49 H50 R67 R70 N74 H78 R95 F97 N99 H102 R105 H106	PDBbind-CN: Kd=0.034uM
BS02	dna	A	Y719 K731 S732 H733 K759 S760 H761 L763 R764 R767 Y775 D786 K787 S788 K815 S816 L819 R823	Y4 K16 S17 H18 K44 S45 H46 L48 R49 R52 Y60 D71 K72 S73 K100 S101 L104 R108	PDBbind-CN: Kd=0.034uM
BS03	ZN	A	C721 C724 H737 H741	C6 C9 H22 H26
BS04	ZN	A	C749 C752 H765 H769	C34 C37 H50 H54
BS05	ZN	A	C777 C780 H793 H797	C62 C65 H78 H82
BS06	ZN	A	C805 C808 H821 H825	C90 C93 H106 H110

External links

• PDB: RCSB:5egb, PDBe:5egb, PDBj:5egb
• PDBsum: 5egb
• PubMed: 26833727
• UniProt: Q9NQV7|PRDM9_HUMAN Histone-lysine N-methyltransferase PRDM9 (Gene Name=PRDM9)