4GUT

Crystal structure of LSD2-NPAC

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

Functional Information from PDB Data

site_id	AC1
Number of Residues	36
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	VAL598
A	VAL627
A	PRO628
A	GLY389
A	ILE637
A	TRP757
A	TRP762
A	ALA766
A	GLY794
A	GLU795
A	GLN803
A	THR804
A	VAL805
A	ALA808
A	GLY391
A	GOL902
A	HOH1103
A	HOH1106
A	HOH1116
A	HOH1126
A	HOH1266
A	HOH1434
A	PRO392
A	ALA393
A	LEU411
A	GLU412
A	ALA413
A	LYS414

---

site_id	AC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL A 902

Chain	Residue
A	ALA546
A	TYR767
A	GLN803
A	THR804
A	FAD901
A	HOH1266

---

site_id	AC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL A 903

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

---

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

Chain	Residue
A	CYS53
A	CYS58
A	HIS84
A	HIS90

---

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

Chain	Residue
A	CYS65
A	CYS73
A	CYS92
A	CYS95

---

site_id	AC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN A 906

Chain	Residue
A	CYS142
A	CYS147
A	CYS169
A	CYS185

---

site_id	AC7
Number of Residues	9
Details	BINDING SITE FOR RESIDUE PGE B 301

Chain	Residue
A	TYR223
A	TYR273
A	GLN274
A	ASN276
A	GLU277
A	ARG285
A	ASP287
B	PHE217
B	HIS218

---

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

---