Structure of PDB 6nm4 Chain A

Receptor sequence
>6nm4A (length=185) Species: 9606 (Homo sapiens) [Search protein sequence]
SEPQDDDYLYCEMCQNFFIDSCAAHGPPTFVKDSAVDKGHPNRSALSLPP
GLRIGPSGIPQAGLGVWNEASDLPLGLHFGPYEGRITEDEEAANNGYSWL
ITKGRNCYEYVDGKDKSWANWMRYVNCARDDEEQNLVAFQYHRQIFYRTC
RVIRPGCELLVWYGDEYGQELGIKWGSKWKKELMA
3D structure
PDB6nm4 Discovery of a chemical probe for PRDM9.
ChainA
Resolution2.58 Å
3D
structure
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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 ZN A C205 C208 C216 H219 C11 C14 C22 H25
BS02 SAM A A256 L258 G290 Y291 R317 Y318 N320 C321 A62 L64 G96 Y97 R123 Y124 N126 C127
BS03 KS7 A W293 C321 A322 D324 W356 W99 C127 A128 D130 W162 PDBbind-CN: -logKd/Ki=7.06,Kd=87nM
BS04 KS7 A D214 S215 A217 A218 P221 D20 S21 A23 A24 P27 PDBbind-CN: -logKd/Ki=7.06,Kd=87nM
Gene Ontology
Molecular Function
GO:0042054 histone methyltransferase activity

View graph for
Molecular Function
External links
PDB RCSB:6nm4, PDBe:6nm4, PDBj:6nm4
PDBsum6nm4
PubMed31848333
UniProtQ9NQV7|PRDM9_HUMAN Histone-lysine N-methyltransferase PRDM9 (Gene Name=PRDM9)

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