4GU0

Crystal structure of LSD2 with H3

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	0006351	biological_process	DNA-templated transcription
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	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
B	0000786	cellular_component	nucleosome
B	0005515	molecular_function	protein binding
B	0005634	cellular_component	nucleus
B	0005654	cellular_component	nucleoplasm
B	0005694	cellular_component	chromosome
B	0006325	biological_process	chromatin organization
B	0006351	biological_process	DNA-templated transcription
B	0008270	molecular_function	zinc ion binding
B	0016491	molecular_function	oxidoreductase activity
B	0032452	molecular_function	histone demethylase activity
B	0032453	molecular_function	histone H3K4 demethylase activity
B	0040029	biological_process	epigenetic regulation of gene expression
B	0042393	molecular_function	histone binding
B	0046872	molecular_function	metal ion binding
B	0050660	molecular_function	flavin adenine dinucleotide binding
B	0071514	biological_process	genomic imprinting
B	0071949	molecular_function	FAD binding
B	0140682	molecular_function	FAD-dependent H3K4me/H3K4me3 demethylase activity
C	0000786	cellular_component	nucleosome
C	0005515	molecular_function	protein binding
C	0005634	cellular_component	nucleus
C	0005654	cellular_component	nucleoplasm
C	0005694	cellular_component	chromosome
C	0006325	biological_process	chromatin organization
C	0006351	biological_process	DNA-templated transcription
C	0008270	molecular_function	zinc ion binding
C	0016491	molecular_function	oxidoreductase activity
C	0032452	molecular_function	histone demethylase activity
C	0032453	molecular_function	histone H3K4 demethylase activity
C	0040029	biological_process	epigenetic regulation of gene expression
C	0042393	molecular_function	histone binding
C	0046872	molecular_function	metal ion binding
C	0050660	molecular_function	flavin adenine dinucleotide binding
C	0071514	biological_process	genomic imprinting
C	0071949	molecular_function	FAD binding
C	0140682	molecular_function	FAD-dependent H3K4me/H3K4me3 demethylase activity
D	0000786	cellular_component	nucleosome
D	0005515	molecular_function	protein binding
D	0005634	cellular_component	nucleus
D	0005654	cellular_component	nucleoplasm
D	0005694	cellular_component	chromosome
D	0006325	biological_process	chromatin organization
D	0006351	biological_process	DNA-templated transcription
D	0008270	molecular_function	zinc ion binding
D	0016491	molecular_function	oxidoreductase activity
D	0032452	molecular_function	histone demethylase activity
D	0032453	molecular_function	histone H3K4 demethylase activity
D	0040029	biological_process	epigenetic regulation of gene expression
D	0042393	molecular_function	histone binding
D	0046872	molecular_function	metal ion binding
D	0050660	molecular_function	flavin adenine dinucleotide binding
D	0071514	biological_process	genomic imprinting
D	0071949	molecular_function	FAD binding
D	0140682	molecular_function	FAD-dependent H3K4me/H3K4me3 demethylase activity
E	0000786	cellular_component	nucleosome
E	0003677	molecular_function	DNA binding
E	0030527	molecular_function	structural constituent of chromatin
F	0000786	cellular_component	nucleosome
F	0003677	molecular_function	DNA binding
F	0030527	molecular_function	structural constituent of chromatin

Functional Information from PDB Data

site_id	AC1
Number of Residues	28
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	PRO597
A	VAL598
A	VAL627
A	PRO628
A	GLY389
A	TRP757
A	TRP762
A	GLY794
A	GLU795
A	GLN803
A	THR804
A	VAL805
A	ALA808
A	HOH1005
A	PRO392
A	ALA393
A	LEU411
A	GLU412
A	ALA413
A	LYS414
A	GLY419

---

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

Chain	Residue
A	CYS53
A	CYS58
A	HIS84
A	HIS90

---

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

Chain	Residue
A	CYS65
A	CYS73
A	CYS92
A	CYS95

---

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

Chain	Residue
A	CYS142
A	CYS147
A	CYS169
A	CYS185

---

site_id	AC5
Number of Residues	27
Details	BINDING SITE FOR RESIDUE FAD B 901

Chain	Residue
B	ILE388
B	GLY389
B	PRO392
B	ALA393
B	LEU411
B	GLU412
B	ALA413
B	LYS414
B	GLY419
B	ARG420
B	ARG434
B	GLY435
B	ALA436
B	ILE438
B	PRO597
B	VAL598
B	VAL627
B	PRO628
B	TRP757
B	TRP762
B	GLY794
B	GLU795
B	GLN803
B	THR804
B	VAL805
B	ALA808
B	HOH1004

---

site_id	AC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN B 902

Chain	Residue
B	CYS53
B	CYS58
B	HIS84
B	HIS90

---

site_id	AC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN B 903

Chain	Residue
B	CYS65
B	CYS73
B	CYS92
B	CYS95

---

site_id	AC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN B 904

Chain	Residue
B	CYS142
B	CYS147
B	CYS169
B	CYS185

---

site_id	AC9
Number of Residues	27
Details	BINDING SITE FOR RESIDUE FAD C 901

Chain	Residue
C	GLY794
C	GLU795
C	GLN803
C	THR804
C	VAL805
C	ALA808
C	HOH1109
C	GLY389
C	GLY391
C	PRO392
C	ALA393
C	LEU411
C	GLU412
C	ALA413
C	LYS414
C	GLY419
C	ARG420
C	ARG434
C	GLY435
C	ALA436
C	GLN437
C	ILE438
C	PRO597
C	VAL598
C	VAL627
C	TRP757
C	TRP762

---

site_id	BC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN C 902

Chain	Residue
C	CYS53
C	CYS58
C	HIS84
C	HIS90

---

site_id	BC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN C 903

Chain	Residue
C	CYS65
C	CYS73
C	CYS92
C	CYS95

---

site_id	BC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN C 904

Chain	Residue
C	CYS142
C	CYS147
C	CYS169
C	CYS185

---

site_id	BC4
Number of Residues	29
Details	BINDING SITE FOR RESIDUE FAD D 901

Chain	Residue
D	GLY389
D	ALA390
D	GLY391
D	PRO392
D	ALA393
D	LEU411
D	GLU412
D	ALA413
D	LYS414
D	GLY419
D	ARG420
D	ARG434
D	GLY435
D	ALA436
D	GLN437
D	ILE438
D	PRO597
D	VAL598
D	VAL627
D	PRO628
D	TRP757
D	TRP762
D	GLY794
D	GLU795
D	GLN803
D	THR804
D	VAL805
D	ALA808
D	HOH1012

---

site_id	BC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN D 902

Chain	Residue
D	CYS53
D	CYS58
D	HIS84
D	HIS90

---

site_id	BC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN D 903

Chain	Residue
D	CYS65
D	CYS73
D	CYS92
D	CYS95

---

site_id	BC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN D 904

Chain	Residue
D	CYS142
D	CYS147
D	CYS169
D	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
E	LYS14-LEU20

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	392
Details	Domain: {"description":"SWIRM","evidences":[{"source":"PROSITE-ProRule","id":"PRU00247","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	120
Details	Zinc finger: {"description":"CW-type","evidences":[{"source":"PROSITE-ProRule","id":"PRU00454","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	148
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_FI4
Number of Residues	296
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_FI5
Number of Residues	44
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_FI6
Number of Residues	16
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_FI7
Number of Residues	224
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_FI8
Number of Residues	4
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_FI9
Number of Residues	2
Details	Modified residue: {"description":"Citrulline; alternate","evidences":[{"source":"PubMed","id":"16567635","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI10
Number of Residues	2
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_FI11
Number of Residues	2
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_FI12
Number of Residues	2
Details	Modified residue: {"description":"5-glutamyl serotonin; alternate","evidences":[{"source":"PubMed","id":"30867594","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI13
Number of Residues	2
Details	Modified residue: {"description":"Phosphothreonine; by PKC","evidences":[{"source":"PubMed","id":"20228790","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI14
Number of Residues	2
Details	Modified residue: {"description":"Symmetric dimethylarginine; by PRMT5; alternate","evidences":[{"source":"UniProtKB","id":"P84244","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI15
Number of Residues	2
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_FI16
Number of Residues	2
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_FI17
Number of Residues	2
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_FI18
Number of Residues	2
Details	Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"PubMed","id":"22389435","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI19
Number of Residues	2
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_FI20
Number of Residues	2
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_FI21
Number of Residues	2
Details	Modified residue: {"description":"N6-methyllysine; alternate","evidences":[{"source":"PubMed","id":"17194708","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI22
Number of Residues	2
Details	Modified residue: {"description":"Citrulline","evidences":[{"source":"PubMed","id":"16567635","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI23
Number of Residues	2
Details	Lipidation: {"description":"N6-decanoyllysine","evidences":[{"source":"PubMed","id":"35939806","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI24
Number of Residues	2
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate","evidences":[{"source":"PubMed","id":"27595565","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI25
Number of Residues	6
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate","evidences":[{"source":"PubMed","id":"27595565","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"29053958","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---