Structure of PDB 5fyb Chain A

Receptor sequence
>5fybA (length=455) Species: 9606 (Homo sapiens) [Search protein sequence]
SMFLPPPECPVFEPSWEEFADPFAFIHKIRPIAEQTGICKVRPPPDWQPP
FACDVDKLHFTPRIQRLNELEAQTRVKLRDYTLRTFGEMADAFKSDYFNM
PVHMVPTELVEKEFWRLVSTIEEDVTVEYGADIASKEFGSGFPVRDIKLS
PEEEEYLDSGWNLNNMPVMEQSVLAHITADICGMKLPWLYVGMCFSSFCW
HIEDHWSYSINYLHWGEPKTWYGVPGYAAEQLENVMKKLAPELFVSQPDL
LHQLVTIMNPNTLMTHEVPVYRTNQCAGEFVITFPRAYHSGFNQGFNFAE
AVNFCTVDWLPLGRQCVEHYRLLHRYCVFSHDEMICKMASKADVLDVVVA
STVQKDMAIMIEDEKALRETVRKLGVIDSERMDFELLPDDERQCVKCKTT
CFMSAISCSCKPGLLVCLHHVKELCSCPPYKYKLRYRYTLDDLYPMMNAL
KLRAE
3D structure
PDB5fyb Crystal Structure of the Catalytic Domain of Human Jarid1B in Complex with Mc1648
ChainA
Resolution1.87 Å
3D
structure
Catalytic site residues are labeled in the structure
[Spin on]
[Spin off]
[Reset orientation]

[High quality]
[Low quality]

[White background]
[Black background]

[Download]
[Download structure with residue number starting from 1]
Enzymatic activity
Catalytic site (original residue number in PDB) G481 Y488 H499 E501 H587 A599
Catalytic site (residue number reindexed from 1) G183 Y190 H201 E203 H289 A301
Enzyme Commision number 1.14.11.67: [histone H3]-trimethyl-L-lysine(4) demethylase.
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 C692 C695 C715 H718 C394 C397 C417 H420
BS02 ZN A C706 C708 C723 C725 C408 C410 C425 C427
BS03 MN A H499 E501 H587 H201 E203 H289
BS04 77J A E31 P33 V34 I55 E8 P10 V11 I32
BS05 77J A Y488 F496 H499 E501 S507 N509 K517 H587 Y190 F198 H201 E203 S209 N211 K219 H289
External links
PDB RCSB:5fyb, PDBe:5fyb, PDBj:5fyb
PDBsum5fyb
PubMed
UniProtQ9UGL1|KDM5B_HUMAN Lysine-specific demethylase 5B (Gene Name=KDM5B)

[Back to BioLiP]