Structure of PDB 3swc Chain B

Receptor sequence

>3swcB (length=261) Species: 9606 (Homo sapiens)

VERIVSRDIARGYERIPIPCVNAVDSEPCPSNYKYVSQNCVTSPMNIDRN
ITHLQYCVCIDDCSSSNCMCGQLSMRCWYDKDGRLLPEFNMAEPPLIFEC
NHACSCWRNCRNRVVQNGLRARLQLYRTRDMGWGVRSLQDIPPGTFVCEY
VGELISDSEADVREEDSYLFDLDNKDGEVYCIDARFYGNVSRFINHHCEP
NLVPVRVFMAHQDLRFPRIAFFSTRLIEAGEQLGFDYGERFWDIKGKLFS
CRCGSPKCRHS

3D structure

• PDB: 3swc MPP8 mediates the interactions between DNA methyltransferase Dnmt3a and H3K9 methyltransferase GLP/G9a.
• Chain: B
• Resolution: 2.332 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): Y1124 Y1211
• Catalytic site (residue number reindexed from 1): Y150 Y237
• 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	B	Y1124 D1131 A1134 D1135 D1140 S1141 Y1142 L1143 F1144 D1145 D1147 V1153 F1209 Y1211 R1214 F1215 I1218 K1219	Y150 D157 A160 D161 D166 S167 Y168 L169 F170 D171 D173 V179 F235 Y237 R240 F241 I244 K245
BS02	ZN	B	C1031 C1044 C1074 C1078	C57 C70 C100 C104
BS03	ZN	B	C1037 C1074 C1080 C1084	C63 C100 C106 C110
BS04	ZN	B	C1031 C1033 C1037 C1042	C57 C59 C63 C68
BS05	ZN	B	C1172 C1225 C1227 C1232	C198 C251 C253 C258
BS06	SAH	B	M1105 W1107 S1141 Y1142 R1166 F1167 N1169 H1170 Y1211 F1215 F1223 C1225	M131 W133 S167 Y168 R192 F193 N195 H196 Y237 F241 F249 C251	BindingDB: IC50=230nM

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
• GO:0046974 histone H3K9 methyltransferase activity

Cellular Component

• GO:0005634 nucleus

External links

• PDB: RCSB:3swc, PDBe:3swc, PDBj:3swc
• PDBsum: 3swc
• PubMed: 22086334
• UniProt: Q9H9B1|EHMT1_HUMAN Histone-lysine N-methyltransferase EHMT1 (Gene Name=EHMT1)