Structure of PDB 5fy9 Chain A Binding Site BS02

Receptor Information

>5fy9 Chain A (length=460) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

SMFLPPPECPVFEPSWEEFADPFAFIHKIRPIAEQTGICKVRPPPDWQPP
FACDVDKLHFTPRIQRLNELEAQTRVKLGGGGARDYTLRTFGEMADAFKS
DYFNMPVHMVPTELVEKEFWRLVSTIEEDVTVEYGADIASKEFGSGFPVR
DIKLSPEEEEYLDSGWNLNNMPVMEQSVLAHITADICGMKLPWLYVGMCF
SSFCWHIEDHWSYSINYLHWGEPKTWYGVPGYAAEQLENVMKKLAPELFV
SQPDLLHQLVTIMNPNTLMTHEVPVYRTNQCAGEFVITFPRAYHSGFNQG
FNFAEAVNFCTVDWLPLGRQCVEHYRLLHRYCVFSHDEMICKMASKADVL
DVVVASTVQKDMAIMIEDEKALRETVRKLGVIDSERMDFELLPDDERQCV
KCKTTCFMSAISCSCKPGLLVCLHHVKELCSCPPYKYKLRYRYTLDDLYP
MMNALKLRAE

Ligand information

Ligand ID

InChI

InChI=1S/Mn/q+2

InChIKey

WAEMQWOKJMHJLA-UHFFFAOYSA-N

SMILES

Software	SMILES
ACDLabs 10.04 OpenEye OEToolkits 1.5.0	[Mn+2]
CACTVS 3.341	[Mn++]

Formula

Name

MANGANESE (II) ION

PDB chain

5fy9 Chain A Residue 1755 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	5fy9 Crystal Structure of the Catalytic Domain of Human Jarid1B in Complex with Pyruvate
Resolution	2.03 Å
Binding residue (original residue number in PDB)	H499 E501 H587
Binding residue (residue number reindexed from 1)	H206 E208 H294
Annotation score	1

Enzymatic activity

Catalytic site (original residue number in PDB)	G481 Y488 H499 E501 H587 A599
Catalytic site (residue number reindexed from 1)	G188 Y195 H206 E208 H294 A306
Enzyme Commision number	1.14.11.67: [histone H3]-trimethyl-L-lysine(4) demethylase.

External links

PDB	RCSB:5fy9, PDBe:5fy9, PDBj:5fy9
PDBsum	5fy9
PubMed
UniProt	Q9UGL1\|KDM5B_HUMAN Lysine-specific demethylase 5B (Gene Name=KDM5B)

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