Structure of PDB 6wc6 Chain A Binding Site BS01

Receptor Information

>6wc6 Chain A (length=666) Species: 9606 (Homo sapiens)

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

Ligand information

>6wc6 Chain C (length=15) Species: 9606 (Homo sapiens)

SEEERNAKAEKEKKL

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6wc6 Identification of structure and nucleosome binding within the N-terminus of lysine specific demethylase 1
• Resolution: 3.1 Å
• Binding residue (original residue number in PDB): R591 T607 R608 S609 T610 S719 D720 R750
• Binding residue (residue number reindexed from 1): R421 T437 R438 S439 T440 S549 D550 R580

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:6wc6, PDBe:6wc6, PDBj:6wc6
• PDBsum: 6wc6
• UniProt: O60341|KDM1A_HUMAN Lysine-specific histone demethylase 1A (Gene Name=KDM1A)