4GU1

Crystal structure of LSD2

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	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	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

Functional Information from PDB Data

site_id	AC1
Number of Residues	30
Details	BINDING SITE FOR RESIDUE FAD A 901

Chain	Residue
A	ILE388
A	GLY419
A	ARG420
A	ARG434
A	GLY435
A	ALA436
A	GLN437
A	ILE438
A	PRO597
A	VAL598
A	THR626
A	GLY389
A	VAL627
A	PRO628
A	TRP757
A	TRP762
A	ALA766
A	GLY794
A	GLU795
A	GLN803
A	THR804
A	VAL805
A	GLY391
B	LEU40
A	PRO392
A	ALA393
A	LEU411
A	GLU412
A	ALA413
A	LYS414

---

site_id	AC2
Number of Residues	3
Details	BINDING SITE FOR RESIDUE CL A 902

Chain	Residue
A	GLU54
A	HIS84
A	LYS128

---

site_id	AC3
Number of Residues	2
Details	BINDING SITE FOR RESIDUE CL A 903

Chain	Residue
A	LYS165
A	LYS330

---

site_id	AC4
Number of Residues	2
Details	BINDING SITE FOR RESIDUE NA A 904

Chain	Residue
A	TYR603
A	GLY605

---

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

Chain	Residue
A	CYS53
A	CYS58
A	HIS84
A	HIS90

---

site_id	AC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN A 906

Chain	Residue
A	CYS65
A	ALA67
A	CYS73
A	CYS92
A	CYS95

---

site_id	AC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN A 907

Chain	Residue
A	CYS142
A	CYS147
A	CYS169
A	CYS185

---

site_id	AC8
Number of Residues	27
Details	BINDING SITE FOR RESIDUE FAD B 901

Chain	Residue
B	ILE388
B	GLY391
B	PRO392
B	ALA393
B	LEU411
B	GLU412
B	ALA413
B	LYS414
B	GLY419
B	ARG420
B	ARG434
B	GLY435
B	ALA436
B	GLN437
B	ILE438
B	PRO597
B	VAL598
B	VAL627
B	PRO628
B	TRP757
B	TRP762
B	ALA766
B	GLY794
B	GLU795
B	GLN803
B	THR804
B	VAL805

---

site_id	AC9
Number of Residues	3
Details	BINDING SITE FOR RESIDUE CL B 902

Chain	Residue
B	GLU54
B	HIS84
B	LYS128

---

site_id	BC1
Number of Residues	2
Details	BINDING SITE FOR RESIDUE CL B 903

Chain	Residue
B	LYS165
B	LYS330

---

site_id	BC2
Number of Residues	2
Details	BINDING SITE FOR RESIDUE NA B 904

Chain	Residue
B	TYR603
B	GLY605

---

site_id	BC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN B 905

Chain	Residue
B	CYS53
B	CYS58
B	HIS84
B	HIS90

---

site_id	BC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN B 906

Chain	Residue
B	CYS65
B	ALA67
B	CYS73
B	CYS92
B	CYS95

---

site_id	BC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN B 907

Chain	Residue
B	CYS142
B	CYS147
B	CYS169
B	CYS185

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	196
Details	Domain: {"description":"SWIRM","evidences":[{"source":"PROSITE-ProRule","id":"PRU00247","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	74
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	148
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	22
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	8
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	112
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	2
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

---