Structure of PDB 5fy4 Chain A Binding Site BS02

Receptor Information

>5fy4 Chain A (length=454) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

SMFLPPPECPVFEPSWEEFADPFAFIHKIRPIAEQTGICKVRPPPDWQPP
FACDVDKLHFTPRIQRLNELEAQTRVKRDYTLRTFGEMADAFKSDYFNMP
VHMVPTELVEKEFWRLVSTIEEDVTVEYGADIASKEFGSGFPVRDIKLSP
EEEEYLDSGWNLNNMPVMEQSVLAHITADICGMKLPWLYVGMCFSSFCWH
IEDHWSYSINYLHWGEPKTWYGVPGYAAEQLENVMKKLAPELFVSQPDLL
HQLVTIMNPNTLMTHEVPVYRTNQCAGEFVITFPRAYHSGFNQGFNFAEA
VNFCTVDWLPLGRQCVEHYRLLHRYCVFSHDEMICKMASKADVLDVVVAS
TVQKDMAIMIEDEKALRETVRKLGVIDSERMDFELLPDDERQCVKCKTTC
FMSAISCSCKPGLLVCLHHVKELCSCPPYKYKLRYRYTLDDLYPMMNALK
LRAE

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

5fy4 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	5fy4 Crystal Structure of the Catalytic Domain of Human Jarid1B in Complex with Succinate
Resolution	2.1 Å
Binding residue (original residue number in PDB)	L90 L413 V414 T416 E419
Binding residue (residue number reindexed from 1)	L67 L116 V117 T119 E122
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)	G182 Y189 H200 E202 H288 A300
Enzyme Commision number	1.14.11.67: [histone H3]-trimethyl-L-lysine(4) demethylase.

External links

PDB	RCSB:5fy4, PDBe:5fy4, PDBj:5fy4
PDBsum	5fy4
PubMed
UniProt	Q9UGL1\|KDM5B_HUMAN Lysine-specific demethylase 5B (Gene Name=KDM5B)

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