Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6VYP

Crystal structure of the LSD1/CoREST histone demethylase bound to its nucleosome substrate

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	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	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	0005634	cellular_component	nucleus
K	0006355	biological_process	regulation of DNA-templated transcription
K	0016491	molecular_function	oxidoreductase activity
K	0050660	molecular_function	flavin adenine dinucleotide binding
M	0005634	cellular_component	nucleus
M	0006355	biological_process	regulation of DNA-templated transcription
M	0016491	molecular_function	oxidoreductase activity
M	0050660	molecular_function	flavin adenine dinucleotide binding
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	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	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	0005634	cellular_component	nucleus
k	0006355	biological_process	regulation of DNA-templated transcription
k	0016491	molecular_function	oxidoreductase activity
k	0050660	molecular_function	flavin adenine dinucleotide binding
m	0005634	cellular_component	nucleus
m	0006355	biological_process	regulation of DNA-templated transcription
m	0016491	molecular_function	oxidoreductase activity
m	0050660	molecular_function	flavin adenine dinucleotide binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	28
Details	binding site for residue FAD M 900

Chain	Residue
E	MET4
M	GLY315
M	ARG316
M	VAL317
M	GLY330
M	ALA331
M	VAL333
M	VAL590
M	THR624
M	LEU625
M	PRO626
M	GLY285
M	LEU659
M	TRP756
M	SER760
M	TYR761
M	GLY800
M	GLU801
M	THR810
M	VAL811
M	ALA814
M	GLY287
M	VAL288
M	SER289
M	GLU308
M	ALA309
M	ARG310
M	GLY314

site_id	AC2
Number of Residues	31
Details	binding site for Di-peptide FAD K 900 and ARG K 310

Chain	Residue
K	GLY285
K	GLY287
K	VAL288
K	SER289
K	LEU307
K	GLU308
K	ALA309
K	ASP311
K	ARG312
K	GLY314
K	GLY315
K	ARG316
K	GLY330
K	ALA331
K	MET332
K	VAL333
K	VAL334
K	LEU586
K	ASN587
K	THR624
K	LEU625
K	ASP754
K	TRP756
K	SER760
K	TYR761
K	GLY800
K	GLU801
K	ALA809
K	THR810
K	VAL811
K	ALA814

site_id	AC3
Number of Residues	29
Details	binding site for Di-peptide FAD K 900 and GLY K 315

Chain	Residue
K	GLY285
K	GLY287
K	VAL288
K	SER289
K	LEU307
K	GLU308
K	ALA309
K	ARG310
K	ARG312
K	VAL313
K	GLY314
K	ARG316
K	VAL317
K	GLY330
K	ALA331
K	MET332
K	VAL333
K	VAL334
K	THR624
K	LEU625
K	TRP756
K	SER760
K	TYR761
K	GLY800
K	GLU801
K	ALA809
K	THR810
K	VAL811
K	ALA814

site_id	AC4
Number of Residues	29
Details	binding site for Di-peptide FAD K 900 and GLY K 330

Chain	Residue
K	ASP328
K	LEU329
K	ALA331
K	MET332
K	VAL333
K	VAL334
K	THR624
K	LEU625
K	TRP751
K	TRP756
K	SER760
K	TYR761
K	GLY800
K	GLU801
K	ALA809
K	THR810
K	VAL811
K	ALA814
K	GLY285
K	GLY287
K	VAL288
K	SER289
K	LEU307
K	GLU308
K	ALA309
K	ARG310
K	GLY314
K	GLY315
K	ARG316

site_id	AC5
Number of Residues	28
Details	binding site for Di-peptide FAD K 900 and VAL K 333

Chain	Residue
K	GLY285
K	GLY287
K	VAL288
K	SER289
K	LEU307
K	GLU308
K	ALA309
K	ARG310
K	GLY314
K	GLY315
K	ARG316
K	GLY330
K	ALA331
K	MET332
K	VAL334
K	LEU565
K	THR566
K	THR624
K	LEU625
K	TRP756
K	SER760
K	TYR761
K	GLY800
K	GLU801
K	ALA809
K	THR810
K	VAL811
K	ALA814

site_id	AC6
Number of Residues	29
Details	binding site for Di-peptide FAD k 900 and ALA k 331

Chain	Residue
k	GLY285
k	SER286
k	GLY287
k	VAL288
k	SER289
k	GLU308
k	ALA309
k	ARG310
k	GLY314
k	GLY315
k	ARG316
k	GLY330
k	MET332
k	VAL333
k	VAL590
k	THR624
k	LEU625
k	PRO626
k	VAL629
k	LEU659
k	TRP756
k	SER760
k	TYR761
k	GLY800
k	GLU801
k	THR810
k	VAL811
k	HIS812
k	ALA814

site_id	AC7
Number of Residues	31
Details	binding site for Di-peptide FAD k 900 and VAL k 811

Chain	Residue
k	GLY285
k	SER286
k	GLY287
k	VAL288
k	SER289
k	GLU308
k	ALA309
k	ARG310
k	GLY314
k	GLY315
k	ARG316
k	ALA331
k	MET332
k	VAL333
k	TYR571
k	VAL590
k	THR624
k	LEU625
k	PRO626
k	VAL629
k	LEU659
k	TRP756
k	SER760
k	TYR761
k	GLY800
k	GLU801
k	THR810
k	HIS812
k	GLY813
k	ALA814
k	LEU815

site_id	AC8
Number of Residues	34
Details	binding site for Di-peptide FAD k 900 and HIS k 812

Chain	Residue
k	GLY285
k	SER286
k	GLY287
k	VAL288
k	SER289
k	GLU308
k	ALA309
k	ARG310
k	GLY314
k	GLY315
k	ARG316
k	ALA331
k	MET332
k	VAL333
k	THR335
k	ASN340
k	MET342
k	VAL590
k	THR624
k	LEU625
k	PRO626
k	VAL629
k	LEU659
k	TRP756
k	SER760
k	TYR761
k	GLY800
k	GLU801
k	THR810
k	VAL811
k	GLY813
k	ALA814
k	LEU815
k	LEU816

site_id	AC9
Number of Residues	33
Details	binding site for Di-peptide FAD k 900 and ALA k 814

Chain	Residue
k	GLY285
k	SER286
k	GLY287
k	VAL288
k	SER289
k	GLU308
k	ALA309
k	ARG310
k	GLY314
k	GLY315
k	ARG316
k	ALA331
k	MET332
k	VAL333
k	VAL590
k	THR624
k	LEU625
k	PRO626
k	VAL629
k	LEU659
k	TRP756
k	SER760
k	TYR761
k	GLY800
k	GLU801
k	THR810
k	VAL811
k	HIS812
k	GLY813
k	LEU815
k	LEU816
k	SER817
k	GLY818

site_id	AD1
Number of Residues	29
Details	binding site for Di-peptide FAD m 900 and GLY m 330

Chain	Residue
m	GLY285
m	SER286
m	GLY287
m	VAL288
m	SER289
m	GLU308
m	ALA309
m	ARG310
m	GLY314
m	GLY315
m	ARG316
m	VAL317
m	ALA318
m	ASP328
m	LEU329
m	ALA331
m	VAL333
m	VAL590
m	THR624
m	LEU625
m	PRO626
m	LYS661
m	TRP751
m	TRP756
m	GLY800
m	GLU801
m	THR810
m	VAL811
m	ALA814

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
A	LYS14-LEU20

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

Chain	Residue	Details
A	PRO66-ILE74

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

Chain	Residue	Details
D	ARG89-GLY111

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	8
Details	MOD_RES: Citrulline; alternate => ECO:0000250\|UniProtKB:Q71DI3

Chain	Residue	Details
K	ARG310
K	ARG316
K	MET332
K	GLU801
K	THR810
k	SER289
k	GLU308
k	ARG310
k	ARG316
k	MET332
k	GLU801
k	THR810
A	ARG2
A	ARG17
E	ARG2
E	ARG17
a	ARG2
a	ARG17
e	ARG2
e	ARG17
m	GLU308
m	ARG310
m	ARG316
m	MET332
m	GLU801
m	THR810
K	SER289
K	GLU308

site_id	SWS_FT_FI2
Number of Residues	4
Details	MOD_RES: Phosphothreonine; by HASPIN => ECO:0000250\|UniProtKB:Q71DI3

Chain	Residue	Details
A	THR3
E	THR3
a	THR3
e	THR3

site_id	SWS_FT_FI3
Number of Residues	4
Details	MOD_RES: N6-methyllysine; alternate => ECO:0000269\|PubMed:12138181

Chain	Residue	Details
A	MET4
E	MET4
a	MET4
e	MET4
c	LYS9
c	LYS95
g	LYS9
g	LYS95

site_id	SWS_FT_FI4
Number of Residues	4
Details	MOD_RES: 5-glutamyl serotonin; alternate => ECO:0000250\|UniProtKB:Q71DI3

Chain	Residue	Details
K	LYS469
k	LYS469
A	GLN5
E	GLN5
a	GLN5
e	GLN5
K	LYS442
k	LYS442

site_id	SWS_FT_FI5
Number of Residues	8
Details	MOD_RES: Phosphothreonine; by PKC => ECO:0000250\|UniProtKB:Q71DI3

Chain	Residue	Details
A	THR6
A	THR11
E	THR6
E	THR11
a	THR6
a	THR11
e	THR6
e	THR11
b	LYS8
b	LYS16
b	LYS44
b	LYS79
f	LYS8
f	LYS16
f	LYS44
f	LYS79

site_id	SWS_FT_FI6
Number of Residues	4
Details	MOD_RES: Symmetric dimethylarginine; by PRMT5; alternate => ECO:0000250

Chain	Residue	Details
A	ARG8
E	ARG8
a	ARG8
e	ARG8
b	LYS12
b	LYS20
f	LYS12
f	LYS20

site_id	SWS_FT_FI7
Number of Residues	4
Details	MOD_RES: N6-methyllysine; alternate => ECO:0000305\|PubMed:12138181

Chain	Residue	Details
A	LYS9
E	LYS9
a	LYS9
e	LYS9
b	LYS31
b	LYS91
f	LYS31
f	LYS91

site_id	SWS_FT_FI8
Number of Residues	4
Details	MOD_RES: Phosphoserine; alternate; by AURKB, AURKC, RPS6KA3, RPS6KA4 and RPS6KA5 => ECO:0000250\|UniProtKB:Q71DI3

Chain	Residue	Details
g	LYS13
g	LYS15
g	LYS119
A	SER10
E	SER10
a	SER10
e	SER10
G	LYS13
G	LYS15
G	LYS119
c	LYS13
c	LYS15
c	LYS119

site_id	SWS_FT_FI9
Number of Residues	4
Details	MOD_RES: N6-lactoyllysine; alternate => ECO:0000250\|UniProtKB:P84228

Chain	Residue	Details
A	LYS14
E	LYS14
a	LYS14
e	LYS14
b	TYR51
b	TYR88
f	TYR51
f	TYR88

site_id	SWS_FT_FI10
Number of Residues	20
Details	MOD_RES: N6-methyllysine; alternate => ECO:0000250\|UniProtKB:Q71DI3

Chain	Residue	Details
E	LYS64
a	LYS18
a	LYS23
a	LYS27
a	LYS36
a	LYS64
e	LYS18
e	LYS23
e	LYS27
e	LYS36
e	LYS64
A	LYS64
E	LYS18
E	LYS23
E	LYS27
E	LYS36
A	LYS18
A	LYS23
A	LYS27
A	LYS36

site_id	SWS_FT_FI11
Number of Residues	4
Details	MOD_RES: Citrulline => ECO:0000250\|UniProtKB:Q71DI3

Chain	Residue	Details
A	ARG26
E	ARG26
a	ARG26
e	ARG26

site_id	SWS_FT_FI12
Number of Residues	4
Details	MOD_RES: Phosphoserine; alternate; by AURKB, AURKC and RPS6KA5 => ECO:0000250\|UniProtKB:Q71DI3

Chain	Residue	Details
A	SER28
E	SER28
a	SER28
e	SER28

site_id	SWS_FT_FI13
Number of Residues	4
Details	MOD_RES: N6-methyllysine => ECO:0000250\|UniProtKB:P68431

Chain	Residue	Details
b	LYS91
f	LYS91
A	LYS37
E	LYS37
a	LYS37
e	LYS37

site_id	SWS_FT_FI14
Number of Residues	4
Details	MOD_RES: Phosphotyrosine => ECO:0000250\|UniProtKB:Q71DI3

Chain	Residue	Details
A	TYR41
E	TYR41
a	TYR41
e	TYR41

site_id	SWS_FT_FI15
Number of Residues	8
Details	MOD_RES: N6-succinyllysine; alternate => ECO:0000250\|UniProtKB:P84228

Chain	Residue	Details
a	LYS56
a	LYS79
e	LYS56
e	LYS79
A	LYS56
A	LYS79
E	LYS56
E	LYS79

site_id	SWS_FT_FI16
Number of Residues	4
Details	MOD_RES: Phosphoserine => ECO:0000250\|UniProtKB:Q71DI3

Chain	Residue	Details
A	SER57
E	SER57
a	SER57
e	SER57

site_id	SWS_FT_FI17
Number of Residues	8
Details	MOD_RES: Phosphothreonine => ECO:0000250\|UniProtKB:Q71DI3

Chain	Residue	Details
a	THR80
a	THR107
e	THR80
e	THR107
A	THR80
A	THR107
E	THR80
E	THR107

site_id	SWS_FT_FI18
Number of Residues	4
Details	MOD_RES: Phosphoserine => ECO:0000250\|UniProtKB:P84243

Chain	Residue	Details
A	SER86
E	SER86
a	SER86
e	SER86

site_id	SWS_FT_FI19
Number of Residues	4
Details	MOD_RES: N6-glutaryllysine; alternate => ECO:0000250\|UniProtKB:Q71DI3

Chain	Residue	Details
A	LYS115
E	LYS115
a	LYS115
e	LYS115

site_id	SWS_FT_FI20
Number of Residues	4
Details	MOD_RES: N6-succinyllysine; alternate => ECO:0000250\|UniProtKB:Q71DI3

Chain	Residue	Details
A	LYS122
E	LYS122
a	LYS122
e	LYS122

site_id	SWS_FT_FI21
Number of Residues	4
Details	LIPID: S-palmitoyl cysteine => ECO:0000250\|UniProtKB:Q71DI3

Chain	Residue	Details
A	CYS110
E	CYS110
a	CYS110
e	CYS110

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