Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4GUS

Crystal structure of LSD2-NPAC with H3 in space group P3221

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000786	cellular_component	nucleosome
A	0003682	molecular_function	chromatin binding
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	0006338	biological_process	chromatin remodeling
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	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	34
Details	BINDING SITE FOR RESIDUE FAD A 901

Chain	Residue
A	ILE388
A	GLY419
A	ARG420
A	GLY435
A	ALA436
A	GLN437
A	ILE438
A	VAL598
A	VAL627
A	PRO628
A	ILE659
A	GLY389
A	TRP757
A	TRP762
A	ALA766
A	GLY794
A	GLU795
A	GLN803
A	THR804
A	VAL805
A	ALA808
A	HOH1102
A	GLY391
A	HOH1119
A	HOH1126
A	HOH1160
A	HOH1253
A	HOH1342
A	PRO392
A	ALA393
A	LEU411
A	GLU412
A	ALA413
A	LYS414

site_id	AC2
Number of Residues	1
Details	BINDING SITE FOR RESIDUE IOD A 904

Chain	Residue
A	LYS128

site_id	AC3
Number of Residues	1
Details	BINDING SITE FOR RESIDUE IOD A 906

Chain	Residue
A	LYS128

site_id	AC4
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL A 908

Chain	Residue
A	TRP422
A	ARG434
A	THR755
A	ARG756
A	TRP757
A	ASP760
A	HOH1186

site_id	AC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL A 909

Chain	Residue
A	LEU730
A	GLN731
A	MET734
A	ARG738
A	ASP748
A	PRO749

site_id	AC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN A 910

Chain	Residue
A	CYS53
A	CYS58
A	HIS84
A	HIS90

site_id	AC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN A 911

Chain	Residue
A	CYS65
A	CYS73
A	CYS92
A	CYS95

site_id	AC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN A 912

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	1
Details	MOD_RES: Citrulline; alternate => ECO:0000269\|PubMed:16567635

Chain	Residue	Details
C	ARG2

site_id	SWS_FT_FI2
Number of Residues	1
Details	MOD_RES: Phosphothreonine; by HASPIN => ECO:0000269\|PubMed:15681610, ECO:0000269\|PubMed:16185088

Chain	Residue	Details
C	THR3
A	GLN803
A	CYS58
A	CYS65
A	CYS73
A	HIS84
A	HIS90
A	CYS92
A	CYS95
A	VAL598

site_id	SWS_FT_FI3
Number of Residues	1
Details	MOD_RES: N6-methyllysine; alternate => ECO:0000269\|PubMed:16185088, ECO:0000269\|PubMed:16267050, ECO:0000269\|PubMed:16457588, ECO:0000269\|PubMed:17194708

Chain	Residue	Details
C	MET4
A	CYS147
A	CYS169
A	CYS185

site_id	SWS_FT_FI4
Number of Residues	1
Details	MOD_RES: 5-glutamyl serotonin; alternate => ECO:0000269\|PubMed:30867594

Chain	Residue	Details
C	GLN5
B	LYS179
B	LYS201
B	LYS211
B	LYS240

site_id	SWS_FT_FI5
Number of Residues	1
Details	MOD_RES: Phosphothreonine; by PKC => ECO:0000269\|PubMed:20228790

Chain	Residue	Details
C	THR6
B	LYS237

site_id	SWS_FT_FI6
Number of Residues	1
Details	MOD_RES: Symmetric dimethylarginine; by PRMT5; alternate => ECO:0000250\|UniProtKB:P84244

Chain	Residue	Details
C	ARG8

site_id	SWS_FT_FI7
Number of Residues	1
Details	MOD_RES: N6-methyllysine; alternate => ECO:0000269\|PubMed:11242053, ECO:0000269\|PubMed:16185088, ECO:0000269\|PubMed:16267050, ECO:0000269\|PubMed:16457588, ECO:0000269\|PubMed:17194708, ECO:0000269\|PubMed:7309716

Chain	Residue	Details
C	LYS9

site_id	SWS_FT_FI8
Number of Residues	1
Details	MOD_RES: Phosphoserine; alternate; by AURKB, AURKC, RPS6KA3, RPS6KA4 and RPS6KA5 => ECO:0000269\|PubMed:10464286, ECO:0000269\|PubMed:11856369, ECO:0000269\|PubMed:12560483, ECO:0000269\|PubMed:15681610, ECO:0000269\|PubMed:15851689, ECO:0000269\|PubMed:16185088

Chain	Residue	Details
C	SER10

site_id	SWS_FT_FI9
Number of Residues	1
Details	MOD_RES: Phosphothreonine; by PKC => ECO:0000269\|PubMed:12560483, ECO:0000269\|PubMed:18066052, ECO:0000269\|PubMed:22901803

Chain	Residue	Details
C	THR11

site_id	SWS_FT_FI10
Number of Residues	1
Details	MOD_RES: N6-succinyllysine; alternate => ECO:0000269\|PubMed:22389435

Chain	Residue	Details
C	LYS14

site_id	SWS_FT_FI11
Number of Residues	1
Details	MOD_RES: Citrulline; alternate => ECO:0000269\|PubMed:15345777, ECO:0000269\|PubMed:16497732, ECO:0000269\|PubMed:16567635

Chain	Residue	Details
C	ARG17

site_id	SWS_FT_FI12
Number of Residues	1
Details	MOD_RES: N6-methyllysine; alternate => ECO:0000269\|PubMed:16267050, ECO:0000269\|PubMed:17194708

Chain	Residue	Details
C	LYS18

site_id	SWS_FT_FI13
Number of Residues	1
Details	LIPID: N6-decanoyllysine => ECO:0000269\|PubMed:35939806

Chain	Residue	Details
C	LYS18

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