Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4GUR

Crystal structure of LSD2-NPAC with H3 in space group P21

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000786	cellular_component	nucleosome
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005654	cellular_component	nucleoplasm
A	0005694	cellular_component	chromosome
A	0006325	biological_process	chromatin organization
A	0008270	molecular_function	zinc ion binding
A	0016491	molecular_function	oxidoreductase activity
A	0032452	molecular_function	histone demethylase activity
A	0032453	molecular_function	histone H3K4 demethylase activity
A	0040029	biological_process	epigenetic regulation of gene expression
A	0042393	molecular_function	histone binding
A	0044726	biological_process	epigenetic programing of female pronucleus
A	0046872	molecular_function	metal ion binding
A	0050660	molecular_function	flavin adenine dinucleotide binding
A	0071514	biological_process	genomic imprinting
A	0071949	molecular_function	FAD binding
A	0140682	molecular_function	FAD-dependent H3K4me/H3K4me3 demethylase activity
C	0000786	cellular_component	nucleosome
C	0003677	molecular_function	DNA binding
C	0030527	molecular_function	structural constituent of chromatin

Functional Information from PDB Data

site_id	AC1
Number of Residues	31
Details	BINDING SITE FOR RESIDUE FAD A 901

Chain	Residue
A	ILE388
A	ARG420
A	ARG434
A	GLY435
A	ALA436
A	GLN437
A	ILE438
A	VAL598
A	VAL627
A	PRO628
A	TRP757
A	GLY389
A	TRP762
A	ALA766
A	GLY794
A	GLU795
A	GLN803
A	THR804
A	VAL805
A	ALA808
A	HOH1105
A	HOH1109
A	PRO392
A	HOH1110
A	HOH1134
A	ALA393
A	LEU411
A	GLU412
A	ALA413
A	LYS414
A	GLY419

site_id	AC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE GOL A 902

Chain	Residue
A	TRP422
A	ARG434
A	ARG756
A	ASP760

site_id	AC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN A 903

Chain	Residue
A	CYS53
A	CYS58
A	HIS84
A	HIS90

site_id	AC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN A 904

Chain	Residue
A	CYS65
A	CYS73
A	CYS92
A	CYS95

site_id	AC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN A 905

Chain	Residue
A	CYS142
A	CYS147
A	CYS169
A	CYS185

Functional Information from PROSITE/UniProt

site_id	PS00322
Number of Residues	7
Details	HISTONE_H3_1 Histone H3 signature 1. KAPRKQL

Chain	Residue	Details
C	LYS14-LEU20

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	98
Details	Domain: {"description":"SWIRM","evidences":[{"source":"PROSITE-ProRule","id":"PRU00247","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	37
Details	Region: {"description":"GLYR1-binding","evidences":[{"source":"PubMed","id":"23260659","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4GUR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4GUS","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4GUT","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4GUU","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	74
Details	Region: {"description":"Histone H3-binding","evidences":[{"source":"PubMed","id":"23260659","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23266887","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4FWF","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4GUR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4GUS","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	11
Details	Binding site: {"evidences":[{"source":"PubMed","id":"23260659","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23266887","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23357850","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"30970244","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4FWE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4FWF","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4FWJ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4GU0","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4GU1","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4GUR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4GUS","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4GUT","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4GUU","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4HSU","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6R1U","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6R25","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU00454","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"23260659","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23266887","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23357850","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"30970244","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4FWE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4FWF","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4FWJ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4GU0","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4GU1","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4GUR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4GUS","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4GUT","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4GUU","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4HSU","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6R1U","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6R25","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	56
Details	Binding site: {"evidences":[{"evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"23260659","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23266887","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23357850","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"30970244","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4FWE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4FWF","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4FWJ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4GU0","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4GU1","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4GUR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4GUS","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4GUT","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4GUU","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4HSU","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6R1U","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6R25","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	1
Details	Binding site: {"evidences":[{"source":"PubMed","id":"23260659","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23266887","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"30970244","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4FWE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4FWF","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4FWJ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4GU1","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4GUS","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4GUT","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4GUU","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6R1U","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6R25","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	3
Details	Region: {"description":"Interaction with histone H3","evidences":[{"source":"PubMed","id":"23260659","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	9
Details	Region: {"description":"Interaction with KDM1B","evidences":[{"source":"PubMed","id":"23260659","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4GUR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4GUS","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4GUT","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4GUU","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI10
Number of Residues	1
Details	Site: {"description":"Required to promote KDM1B demethylase activity toward histone H3K4me1 and H3K4me2","evidences":[{"source":"PubMed","id":"23260659","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI11
Number of Residues	1
Details	Modified residue: {"description":"Citrulline; alternate","evidences":[{"source":"PubMed","id":"16567635","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI12
Number of Residues	1
Details	Modified residue: {"description":"Phosphothreonine; by HASPIN and VRK1","evidences":[{"source":"PubMed","id":"15681610","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16185088","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"31527692","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI13
Number of Residues	1
Details	Modified residue: {"description":"N6-methyllysine; alternate","evidences":[{"source":"PubMed","id":"16185088","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16267050","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16457588","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17194708","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI14
Number of Residues	1
Details	Modified residue: {"description":"5-glutamyl serotonin; alternate","evidences":[{"source":"PubMed","id":"30867594","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI15
Number of Residues	1
Details	Modified residue: {"description":"Phosphothreonine; by PKC","evidences":[{"source":"PubMed","id":"20228790","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI16
Number of Residues	1
Details	Modified residue: {"description":"Symmetric dimethylarginine; by PRMT5; alternate","evidences":[{"source":"UniProtKB","id":"P84244","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI17
Number of Residues	1
Details	Modified residue: {"description":"N6-methyllysine; alternate","evidences":[{"source":"PubMed","id":"11242053","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16185088","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16267050","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16457588","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17194708","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"7309716","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI18
Number of Residues	1
Details	Modified residue: {"description":"Phosphoserine; alternate; by AURKB, AURKC, RPS6KA3, RPS6KA4 and RPS6KA5","evidences":[{"source":"PubMed","id":"10464286","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"11856369","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"12560483","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15681610","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15851689","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16185088","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI19
Number of Residues	1
Details	Modified residue: {"description":"Phosphothreonine; by PKC","evidences":[{"source":"PubMed","id":"12560483","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"18066052","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"22901803","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI20
Number of Residues	1
Details	Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"PubMed","id":"22389435","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI21
Number of Residues	1
Details	Modified residue: {"description":"Citrulline; alternate","evidences":[{"source":"PubMed","id":"15345777","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16497732","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16567635","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI22
Number of Residues	1
Details	Modified residue: {"description":"N6-methyllysine; alternate","evidences":[{"source":"PubMed","id":"16267050","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17194708","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI23
Number of Residues	1
Details	Lipidation: {"description":"N6-decanoyllysine","evidences":[{"source":"PubMed","id":"35939806","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)