Structure of PDB 5t0m Chain A

Receptor sequence

>5t0mA (length=260) Species: 9606 (Homo sapiens)

IICRDVARGYENVPIPCVNGVDGEPCPEDYKYISENCETSTMNIDRNITH
LQHCTCVDDCSSSNCLCGQLSIRCWYDKDGRLLQEFNKIEPPLIFECNQA
CSCWRNCKNRVVQSGIKVRLQLYRTAKMGWGVRALQTIPQGTFICEYVGE
LISDAEADVREDDSYLFDLDEVYCIDARYYGNISRFINHLCDPNIIPVRV
FMLHQDLRFPRIAFFSSRDIRTGEELGFDYGDRFWDIKSKYFTCQCGSEK
CKHSAEAIAL

3D structure

• PDB: 5t0m A histone H3K9M mutation traps histone methyltransferase Clr4 to prevent heterochromatin spreading.
• Chain: A
• Resolution: 1.896 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): Y1067 Y1154
• Catalytic site (residue number reindexed from 1): Y147 Y230
• Enzyme Commision number: 2.1.1.-
  2.1.1.367: [histone H3]-lysine(9) 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	peptide	A	Y1067 D1074 A1077 D1078 D1083 L1086 F1087 D1088 Y1154 R1157 F1158 I1161	Y147 D154 A157 D158 D163 L166 F167 D168 Y230 R233 F234 I237
BS02	ZN	A	C974 C987 C1017 C1021	C54 C67 C97 C101
BS03	ZN	A	C980 C1017 C1023 C1027	C60 C97 C103 C107
BS04	ZN	A	C974 C976 C980 C985	C54 C56 C60 C65
BS05	ZN	A	C1115 C1168 C1170 C1175	C191 C244 C246 C251
BS06	SAM	A	M1048 W1050 S1084 Y1085 R1109 F1110 N1112 H1113 Y1154 F1166 C1168 Q1169	M128 W130 S164 Y165 R185 F186 N188 H189 Y230 F242 C244 Q245
BS07	SAH	A	M1048 W1050 S1084 Y1085 R1109 F1110 N1112 H1113 Y1154 F1166 C1168 Q1169	M128 W130 S164 Y165 R185 F186 N188 H189 Y230 F242 C244 Q245	BindingDB: Ki=570nM,IC50=2000nM

Gene Ontology

Molecular Function

• GO:0002039 p53 binding
• GO:0008270 zinc ion binding
• GO:0016279 protein-lysine N-methyltransferase activity
• GO:0042054 histone methyltransferase activity

Cellular Component

• GO:0005634 nucleus

External links

• PDB: RCSB:5t0m, PDBe:5t0m, PDBj:5t0m
• PDBsum: 5t0m
• PubMed: 27648579
• UniProt: Q96KQ7|EHMT2_HUMAN Histone-lysine N-methyltransferase EHMT2 (Gene Name=EHMT2)