Structure of PDB 3fpd Chain B

Receptor sequence

>3fpdB (length=260) Species: 9606 (Homo sapiens)

ERIVSRDIARGYERIPIPCVNAVDSEPCPSNYKYVSQNCVTSPMNIDRNI
THLQYCVCIDDCSSSNCMCGQLSMRCWYDKDGRLLPEFNMAEPPLIFECN
HACSCWRNCRNRVVQNGLRARLQLYRTRDMGWGVRSLQDIPPGTFVCEYV
GELISDSEADVREEDSYLFDLDNKDGEVYCIDARFYGNVSRFINHHCEPN
LVPVRVFMAHQDLRFPRIAFFSTRLIEAGEQLGFDYGERFWDIKGKLFSC
RCGSPKCRHS

3D structure

• PDB: 3fpd Structural basis for G9a-like protein lysine methyltransferase inhibition by BIX-01294.
• Chain: B
• Resolution: 2.4 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): Y1124 Y1211
• Catalytic site (residue number reindexed from 1): Y149 Y236
• 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	SAH	B	M1105 W1107 S1141 Y1142 R1166 N1169 H1170 Y1211 F1215	M130 W132 S166 Y167 R191 N194 H195 Y236 F240	BindingDB: IC50=230nM
BS02	Q4A	B	D1131 A1134 D1135 V1136 E1138 D1140 L1143 D1145 R1214 F1215	D156 A159 D160 V161 E163 D165 L168 D170 R239 F240	MOAD: ic50=0.7uM BindingDB: IC50=700nM
BS03	ZN	B	C1031 C1044 C1074 C1078	C56 C69 C99 C103
BS04	ZN	B	C1037 C1074 C1080 C1084	C62 C99 C105 C109
BS05	ZN	B	C1031 C1033 C1037 C1042	C56 C58 C62 C67
BS06	ZN	B	C1172 C1225 C1227 C1232	C197 C250 C252 C257

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:3fpd, PDBe:3fpd, PDBj:3fpd
• PDBsum: 3fpd
• PubMed: 19219047
• UniProt: Q9H9B1|EHMT1_HUMAN Histone-lysine N-methyltransferase EHMT1 (Gene Name=EHMT1)