6R1U

Structure of LSD2/NPAC-linker/nucleosome core particle complex: Class 2

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000786	cellular_component	nucleosome
A	0003677	molecular_function	DNA binding
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005654	cellular_component	nucleoplasm
A	0005694	cellular_component	chromosome
A	0030527	molecular_function	structural constituent of chromatin
A	0046982	molecular_function	protein heterodimerization activity
B	0000786	cellular_component	nucleosome
B	0003677	molecular_function	DNA binding
B	0005515	molecular_function	protein binding
B	0005634	cellular_component	nucleus
B	0005694	cellular_component	chromosome
B	0006334	biological_process	nucleosome assembly
B	0030527	molecular_function	structural constituent of chromatin
B	0046982	molecular_function	protein heterodimerization activity
C	0000786	cellular_component	nucleosome
C	0003677	molecular_function	DNA binding
C	0005634	cellular_component	nucleus
C	0005694	cellular_component	chromosome
C	0030527	molecular_function	structural constituent of chromatin
C	0031507	biological_process	heterochromatin formation
C	0046982	molecular_function	protein heterodimerization activity
D	0000786	cellular_component	nucleosome
D	0003677	molecular_function	DNA binding
D	0005515	molecular_function	protein binding
D	0005634	cellular_component	nucleus
D	0005694	cellular_component	chromosome
D	0030527	molecular_function	structural constituent of chromatin
D	0046982	molecular_function	protein heterodimerization activity
E	0000786	cellular_component	nucleosome
E	0003677	molecular_function	DNA binding
E	0005515	molecular_function	protein binding
E	0005634	cellular_component	nucleus
E	0005654	cellular_component	nucleoplasm
E	0005694	cellular_component	chromosome
E	0030527	molecular_function	structural constituent of chromatin
E	0046982	molecular_function	protein heterodimerization activity
F	0000786	cellular_component	nucleosome
F	0003677	molecular_function	DNA binding
F	0005515	molecular_function	protein binding
F	0005634	cellular_component	nucleus
F	0005694	cellular_component	chromosome
F	0006334	biological_process	nucleosome assembly
F	0030527	molecular_function	structural constituent of chromatin
F	0046982	molecular_function	protein heterodimerization activity
G	0000786	cellular_component	nucleosome
G	0003677	molecular_function	DNA binding
G	0005634	cellular_component	nucleus
G	0005694	cellular_component	chromosome
G	0030527	molecular_function	structural constituent of chromatin
G	0031507	biological_process	heterochromatin formation
G	0046982	molecular_function	protein heterodimerization activity
H	0000786	cellular_component	nucleosome
H	0003677	molecular_function	DNA binding
H	0005515	molecular_function	protein binding
H	0005634	cellular_component	nucleus
H	0005694	cellular_component	chromosome
H	0030527	molecular_function	structural constituent of chromatin
H	0046982	molecular_function	protein heterodimerization activity
K	0000786	cellular_component	nucleosome
K	0005515	molecular_function	protein binding
K	0005634	cellular_component	nucleus
K	0005654	cellular_component	nucleoplasm
K	0005694	cellular_component	chromosome
K	0006325	biological_process	chromatin organization
K	0008270	molecular_function	zinc ion binding
K	0016491	molecular_function	oxidoreductase activity
K	0032452	molecular_function	histone demethylase activity
K	0032453	molecular_function	histone H3K4 demethylase activity
K	0040029	biological_process	epigenetic regulation of gene expression
K	0042393	molecular_function	histone binding
K	0044726	biological_process	epigenetic programing of female pronucleus
K	0046872	molecular_function	metal ion binding
K	0050660	molecular_function	flavin adenine dinucleotide binding
K	0071514	biological_process	genomic imprinting
K	0071949	molecular_function	FAD binding
K	0140682	molecular_function	FAD-dependent H3K4me/H3K4me3 demethylase activity
M	0000786	cellular_component	nucleosome
M	0003677	molecular_function	DNA binding
M	0005515	molecular_function	protein binding
M	0005634	cellular_component	nucleus
M	0005654	cellular_component	nucleoplasm
M	0005694	cellular_component	chromosome
M	0030527	molecular_function	structural constituent of chromatin
M	0046982	molecular_function	protein heterodimerization activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	27
Details	binding site for residue FAD K 901

Chain	Residue
K	ILE388
K	GLY419
K	ARG420
K	ARG434
K	GLY435
K	ALA436
K	ILE438
K	VAL598
K	VAL627
K	PRO628
K	TRP757
K	GLY389
K	TRP762
K	ALA766
K	GLY794
K	GLU795
K	GLN803
K	THR804
K	VAL805
K	ALA808
K	GLY391
K	PRO392
K	ALA393
K	LEU411
K	GLU412
K	ALA413
K	LYS414

---

site_id	AC2
Number of Residues	4
Details	binding site for residue ZN K 902

Chain	Residue
K	CYS53
K	CYS58
K	HIS84
K	HIS90

---

site_id	AC3
Number of Residues	4
Details	binding site for residue ZN K 903

Chain	Residue
K	CYS65
K	CYS73
K	CYS92
K	CYS95

---

site_id	AC4
Number of Residues	4
Details	binding site for residue ZN K 904

Chain	Residue
K	CYS142
K	CYS147
K	CYS169
K	CYS185

---

Functional Information from PROSITE/UniProt

site_id	PS00046
Number of Residues	7
Details	HISTONE_H2A Histone H2A signature. AGLqFPV

Chain	Residue	Details
C	ALA21-VAL27

---

site_id	PS00047
Number of Residues	5
Details	HISTONE_H4 Histone H4 signature. GAKRH

Chain	Residue	Details
B	GLY14-HIS18

---

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

Chain	Residue	Details
M	LYS14-LEU20
A	LYS14-LEU20

---

site_id	PS00357
Number of Residues	23
Details	HISTONE_H2B Histone H2B signature. REIQTavRlLLpGELaKHAVSEG

Chain	Residue	Details
D	ARG89-GLY111

---

site_id	PS00959
Number of Residues	9
Details	HISTONE_H3_2 Histone H3 signature 2. PFqRLVREI

Chain	Residue	Details
M	PRO66-ILE74
A	PRO66-ILE74

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	2
Details	Modified residue: {"description":"N6-methyllysine","evidences":[{"source":"UniProtKB","id":"P68431","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	2
Details	Modified residue: {"description":"Phosphotyrosine","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	4
Details	Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P84228","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	5
Details	Modified residue: {"description":"N6-methyllysine; alternate","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	4
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI7
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"P84243","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI8
Number of Residues	2
Details	Modified residue: {"description":"N6-glutaryllysine; alternate","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI9
Number of Residues	2
Details	Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI10
Number of Residues	2
Details	Lipidation: {"description":"S-palmitoyl cysteine","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI11
Number of Residues	1
Details	Modified residue: {"description":"N6-methyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI12
Number of Residues	4
Details	Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI13
Number of Residues	4
Details	Modified residue: {"description":"N6-propionyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI14
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine; by PAK2","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI15
Number of Residues	4
Details	Modified residue: {"description":"Phosphotyrosine","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI16
Number of Residues	2
Details	Modified residue: {"description":"N6-glutaryllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI17
Number of Residues	2
Details	Modified residue: {"description":"N6-succinyllysine","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI18
Number of Residues	2
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in UFM1); alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI19
Number of Residues	4
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI20
Number of Residues	2
Details	Modified residue: {"description":"N6-(2-hydroxyisobutyryl)lysine; alternate","evidences":[{"source":"UniProtKB","id":"P0C0S8","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI21
Number of Residues	4
Details	Modified residue: {"description":"N6-(2-hydroxyisobutyryl)lysine","evidences":[{"source":"UniProtKB","id":"P0C0S8","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI22
Number of Residues	3
Details	Modified residue: {"description":"N6-succinyllysine","evidences":[{"source":"UniProtKB","id":"P0C0S8","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI23
Number of Residues	2
Details	Modified residue: {"description":"N5-methylglutamine","evidences":[{"evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI24
Number of Residues	2
Details	Modified residue: {"description":"N6-glutaryllysine; alternate","evidences":[{"source":"UniProtKB","id":"P0C0S8","evidenceCode":"ECO:0000250"}]}

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)","evidences":[{"evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI26
Number of Residues	2
Details	Glycosylation: {"description":"O-linked (GlcNAc) serine","evidences":[{"source":"UniProtKB","id":"P62807","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI27
Number of Residues	4
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"UniProtKB","id":"P0C1H4","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI28
Number of Residues	98
Details	Domain: {"description":"SWIRM","evidences":[{"source":"PROSITE-ProRule","id":"PRU00247","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI29
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_FI30
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_FI31
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_FI32
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_FI33
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_FI34
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_FI35
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_FI36
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_FI37
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_FI38
Number of Residues	1
Details	Modified residue: {"description":"Phosphothreonine; by HASPIN and VRK1","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI39
Number of Residues	2
Details	Modified residue: {"description":"Citrulline; alternate","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI40
Number of Residues	1
Details	Modified residue: {"description":"N6-methyllysine; alternate","evidences":[{"source":"PubMed","id":"12138181","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI41
Number of Residues	1
Details	Modified residue: {"description":"5-glutamyl serotonin; alternate","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI42
Number of Residues	2
Details	Modified residue: {"description":"Phosphothreonine; by PKC","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI43
Number of Residues	1
Details	Modified residue: {"description":"Symmetric dimethylarginine; by PRMT5; alternate","evidences":[{"evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI44
Number of Residues	1
Details	Modified residue: {"description":"N6-methyllysine; alternate","evidences":[{"source":"PubMed","id":"12138181","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI45
Number of Residues	1
Details	Modified residue: {"description":"Phosphoserine; alternate; by AURKB, AURKC, RPS6KA3, RPS6KA4 and RPS6KA5","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI46
Number of Residues	1
Details	Modified residue: {"description":"N6-lactoyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P84228","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI47
Number of Residues	1
Details	Modified residue: {"description":"Citrulline","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---