Structure of PDB 4xbf Chain A Binding Site BS01

Receptor Information

>4xbf Chain A (length=666) Species: 9606 (Homo sapiens)

PSGVEGAAFQSRLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQL
WLDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHGLINFGIYKRI
KPLPTKKTGKVIIIGSGVSGLAAARQLQSFGMDVTLLEARDRVGGRVATF
RKGNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKCPLYEANGQAV
PKEKDEMVEQEFNRLLEATSYLSHQLDFNVLNNKPVSLGQALEVVIQLQE
KHVKDEQIEHWKKIVKTQEELKELLNKMVNLKEKIKELHQQYKEASEVKP
PRDITAEFLVKSKHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVY
LSSRDRQILDWHFANLEFANATPLSTLSLKHWDQDDDFEFTGSHLTVRNG
YSCVPVALAEGLDIKLNTAVRQVRYTASGCEVIAVNTRSTSQTFIYKCDA
VLCTLPLGVLKQQPPAVQFVPPLPEWKTSAVQRMGFGNLNKVVLCFDRVF
WDPSVNLFGHVGSTTASRGELFLFWNLYKAPILLALVAGEAAGIMENISD
DVIVGRCLAILKGIFGSSAVPQPKETVVSRWRADPWARGSYSYVAAGSSG
NDYDLMAQPITPGPSIPGAPQPIPRLFFAGEHTIRNYPATVHGALLSGLR
EAGRIADQFLGAMYTL

Ligand information

>4xbf Chain D (length=5)

uuagg

.....

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4xbf G-quadruplex RNA binding and recognition by the lysine-specific histone demethylase-1 enzyme.
• Resolution: 2.803 Å
• Binding residue (original residue number in PDB): K280 I615 Y616 K617 C618 D619
• Binding residue (residue number reindexed from 1): K110 I445 Y446 K447 C448 D449

Enzymatic activity

• Catalytic site (original residue number in PDB): T335 D553 K661
• Catalytic site (residue number reindexed from 1): T165 D383 K491
• Enzyme Commision number: 1.14.99.66: [histone-H3]-N(6),N(6)-dimethyl-L-lysine(4) FAD-dependent demethylase.

Gene Ontology

Molecular Function

• GO:0016491 oxidoreductase activity
• GO:0050660 flavin adenine dinucleotide binding

Biological Process

• GO:0006355 regulation of DNA-templated transcription

Cellular Component

• GO:0005634 nucleus

External links

• PDB: RCSB:4xbf, PDBe:4xbf, PDBj:4xbf
• PDBsum: 4xbf
• PubMed: 27277658
• UniProt: O60341|KDM1A_HUMAN Lysine-specific histone demethylase 1A (Gene Name=KDM1A)