Structure of PDB 3m5a Chain A

Receptor sequence

>3m5aA (length=246) Species: 9606 (Homo sapiens)

RHGVCWIYYPDGGSLVGEVNEDGEMTGEKIAYVYPDERTALYGKFIDGEM
IEGKLATLMSTEEGRPHFELMPGNSVYHFDKSTSSCISTNALLPDPYESE
RVYVAESLISSAGEGLFSKVAVGPNTVMSFANGVRITHQEVDSRDWALNG
NTLSLDEETVIDVPEPYNHVSKYCASLGHKANHSFTPNCIYDMFVHPRFG
PIKCIRTLRAVEADEELTVAYGYDHSPGPEAPEWYQVELKAFQATQ

3D structure

• PDB: 3m5a SET7/9 catalytic mutants reveal the role of active site water molecules in lysine multiple methylation.
• Chain: A
• Resolution: 1.75 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): A245 H293 H297 Y305 Y335
• Catalytic site (residue number reindexed from 1): A131 H179 H183 Y191 Y221
• Enzyme Commision number: 2.1.1.364: [histone H3]-lysine(4) 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	H252 V255 D256 R258 W260 N263 N265 T266 L267 S268 E271 Y305 K317 Y335 Y337 D338 E348	H138 V141 D142 R144 W146 N149 N151 T152 L153 S154 E157 Y191 K203 Y221 Y223 D224 E230
BS02	SAH	A	A226 E228 H293 K294 N296 H297 Y335 W352 E356	A112 E114 H179 K180 N182 H183 Y221 W234 E238
BS03	CO	A	E351 W352	E233 W234
BS04	CO	A	R323 A324	R209 A210
BS05	CO	A	H283 S285	H169 S171

Gene Ontology

Molecular Function

• GO:0016279 protein-lysine N-methyltransferase activity
• GO:0140945 histone H3K4 monomethyltransferase activity

Biological Process

• GO:0006355 regulation of DNA-templated transcription

Cellular Component

• GO:0005694 chromosome

External links

• PDB: RCSB:3m5a, PDBe:3m5a, PDBj:3m5a
• PDBsum: 3m5a
• PubMed: 20675860
• UniProt: Q8WTS6|SETD7_HUMAN Histone-lysine N-methyltransferase SETD7 (Gene Name=SETD7)