Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3LEL

Structural Insight into the Sequence-Dependence of Nucleosome Positioning

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	0031492	molecular_function	nucleosomal DNA binding
A	0031507	biological_process	heterochromatin formation
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	0031507	biological_process	heterochromatin formation
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	0002227	biological_process	innate immune response in mucosa
D	0003677	molecular_function	DNA binding
D	0005515	molecular_function	protein binding
D	0005615	cellular_component	extracellular space
D	0005634	cellular_component	nucleus
D	0005694	cellular_component	chromosome
D	0006325	biological_process	chromatin organization
D	0019731	biological_process	antibacterial humoral response
D	0030527	molecular_function	structural constituent of chromatin
D	0031507	biological_process	heterochromatin formation
D	0046982	molecular_function	protein heterodimerization activity
D	0061844	biological_process	antimicrobial humoral immune response mediated by antimicrobial peptide
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	0031492	molecular_function	nucleosomal DNA binding
E	0031507	biological_process	heterochromatin formation
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	0031507	biological_process	heterochromatin formation
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	0002227	biological_process	innate immune response in mucosa
H	0003677	molecular_function	DNA binding
H	0005515	molecular_function	protein binding
H	0005615	cellular_component	extracellular space
H	0005634	cellular_component	nucleus
H	0005694	cellular_component	chromosome
H	0006325	biological_process	chromatin organization
H	0019731	biological_process	antibacterial humoral response
H	0030527	molecular_function	structural constituent of chromatin
H	0031507	biological_process	heterochromatin formation
H	0046982	molecular_function	protein heterodimerization activity
H	0061844	biological_process	antimicrobial humoral immune response mediated by antimicrobial peptide
K	0000786	cellular_component	nucleosome
K	0003677	molecular_function	DNA binding
K	0005515	molecular_function	protein binding
K	0005634	cellular_component	nucleus
K	0005654	cellular_component	nucleoplasm
K	0005694	cellular_component	chromosome
K	0030527	molecular_function	structural constituent of chromatin
K	0031492	molecular_function	nucleosomal DNA binding
K	0031507	biological_process	heterochromatin formation
K	0046982	molecular_function	protein heterodimerization activity
L	0000786	cellular_component	nucleosome
L	0003677	molecular_function	DNA binding
L	0005515	molecular_function	protein binding
L	0005634	cellular_component	nucleus
L	0005694	cellular_component	chromosome
L	0006334	biological_process	nucleosome assembly
L	0030527	molecular_function	structural constituent of chromatin
L	0031507	biological_process	heterochromatin formation
L	0046982	molecular_function	protein heterodimerization activity
M	0000786	cellular_component	nucleosome
M	0003677	molecular_function	DNA binding
M	0005634	cellular_component	nucleus
M	0005694	cellular_component	chromosome
M	0030527	molecular_function	structural constituent of chromatin
M	0031507	biological_process	heterochromatin formation
M	0046982	molecular_function	protein heterodimerization activity
N	0000786	cellular_component	nucleosome
N	0002227	biological_process	innate immune response in mucosa
N	0003677	molecular_function	DNA binding
N	0005515	molecular_function	protein binding
N	0005615	cellular_component	extracellular space
N	0005634	cellular_component	nucleus
N	0005694	cellular_component	chromosome
N	0006325	biological_process	chromatin organization
N	0019731	biological_process	antibacterial humoral response
N	0030527	molecular_function	structural constituent of chromatin
N	0031507	biological_process	heterochromatin formation
N	0046982	molecular_function	protein heterodimerization activity
N	0061844	biological_process	antimicrobial humoral immune response mediated by antimicrobial peptide
O	0000786	cellular_component	nucleosome
O	0003677	molecular_function	DNA binding
O	0005515	molecular_function	protein binding
O	0005634	cellular_component	nucleus
O	0005654	cellular_component	nucleoplasm
O	0005694	cellular_component	chromosome
O	0030527	molecular_function	structural constituent of chromatin
O	0031492	molecular_function	nucleosomal DNA binding
O	0031507	biological_process	heterochromatin formation
O	0046982	molecular_function	protein heterodimerization activity
P	0000786	cellular_component	nucleosome
P	0003677	molecular_function	DNA binding
P	0005515	molecular_function	protein binding
P	0005634	cellular_component	nucleus
P	0005694	cellular_component	chromosome
P	0006334	biological_process	nucleosome assembly
P	0030527	molecular_function	structural constituent of chromatin
P	0031507	biological_process	heterochromatin formation
P	0046982	molecular_function	protein heterodimerization activity
Q	0000786	cellular_component	nucleosome
Q	0003677	molecular_function	DNA binding
Q	0005634	cellular_component	nucleus
Q	0005694	cellular_component	chromosome
Q	0030527	molecular_function	structural constituent of chromatin
Q	0031507	biological_process	heterochromatin formation
Q	0046982	molecular_function	protein heterodimerization activity
R	0000786	cellular_component	nucleosome
R	0002227	biological_process	innate immune response in mucosa
R	0003677	molecular_function	DNA binding
R	0005515	molecular_function	protein binding
R	0005615	cellular_component	extracellular space
R	0005634	cellular_component	nucleus
R	0005694	cellular_component	chromosome
R	0006325	biological_process	chromatin organization
R	0019731	biological_process	antibacterial humoral response
R	0030527	molecular_function	structural constituent of chromatin
R	0031507	biological_process	heterochromatin formation
R	0046982	molecular_function	protein heterodimerization activity
R	0061844	biological_process	antimicrobial humoral immune response mediated by antimicrobial peptide

Functional Information from PDB Data

site_id	AC1
Number of Residues	1
Details	BINDING SITE FOR RESIDUE MN N 3132

Chain	Residue
N	GLU102

site_id	AC2
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MN O 3152

Chain	Residue
D	VAL45
O	ASP77

site_id	AC3
Number of Residues	1
Details	BINDING SITE FOR RESIDUE MN T 3134

Chain	Residue
T	DG61

site_id	AC4
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MN J 3135

Chain	Residue
J	DG27
S	DT67

site_id	AC5
Number of Residues	1
Details	BINDING SITE FOR RESIDUE MN I 3136

Chain	Residue
I	DG27

site_id	AC6
Number of Residues	1
Details	BINDING SITE FOR RESIDUE MN J 3137

Chain	Residue
J	DG61

site_id	AC7
Number of Residues	1
Details	BINDING SITE FOR RESIDUE MN J 3138

Chain	Residue
J	DG48

site_id	AC8
Number of Residues	1
Details	BINDING SITE FOR RESIDUE MN T 3139

Chain	Residue
T	DG64

site_id	AC9
Number of Residues	1
Details	BINDING SITE FOR RESIDUE MN G 3140

Chain	Residue
G	GLU91

site_id	BC1
Number of Residues	1
Details	BINDING SITE FOR RESIDUE MN I 3142

Chain	Residue
I	DG61

site_id	BC2
Number of Residues	1
Details	BINDING SITE FOR RESIDUE MN T 3143

Chain	Residue
T	DG27

site_id	BC3
Number of Residues	1
Details	BINDING SITE FOR RESIDUE MN I 3144

Chain	Residue
I	DG-2

site_id	BC4
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MN T 3145

Chain	Residue
T	DT67
T	DA68

site_id	BC5
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MN S 3146

Chain	Residue
S	DG64
S	DG65

site_id	BC6
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MN T 3147

Chain	Residue
T	DA-3
T	DG-2

site_id	BC7
Number of Residues	1
Details	BINDING SITE FOR RESIDUE MN J 3148

Chain	Residue
J	DG64

site_id	BC8
Number of Residues	1
Details	BINDING SITE FOR RESIDUE MN J 3149

Chain	Residue
J	DG-2

site_id	BC9
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MN I 3150

Chain	Residue
I	DG-35
I	DG-34

site_id	CC1
Number of Residues	1
Details	BINDING SITE FOR RESIDUE MN S 3151

Chain	Residue
S	DG-2

site_id	CC2
Number of Residues	1
Details	BINDING SITE FOR RESIDUE MN S 3153

Chain	Residue
S	DG61

site_id	CC3
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MN T 3154

Chain	Residue
T	DG-56
T	DA-57

site_id	CC4
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MN S 3155

Chain	Residue
S	DT47
S	DG48

site_id	CC5
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MN T 3156

Chain	Residue
T	DG-34
T	DG-35

site_id	CC6
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MN S 3157

Chain	Residue
S	DA26
S	DG27

site_id	CC7
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MN S 3158

Chain	Residue
S	DG-35
S	DG-34

site_id	CC8
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MN T 3159

Chain	Residue
T	DG48
T	DG49

site_id	CC9
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MN I 3160

Chain	Residue
I	DT63
I	DG64
I	DG65

site_id	DC1
Number of Residues	1
Details	BINDING SITE FOR RESIDUE MN I 3161

Chain	Residue
I	DG48

site_id	DC2
Number of Residues	1
Details	BINDING SITE FOR RESIDUE MN T 3162

Chain	Residue
T	DT5

site_id	DC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MN J 3164

Chain	Residue
J	DG64
J	DG65
J	DA66

site_id	DC4
Number of Residues	1
Details	BINDING SITE FOR RESIDUE MN J 3165

Chain	Residue
J	DT5

site_id	DC5
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MN J 3166

Chain	Residue
I	DT4
J	DA-3

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	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
A	PRO66-ILE74

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	4
Details	Modified residue: {"description":"Phosphotyrosine","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	8
Details	Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P84228","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	4
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	4
Details	Modified residue: {"description":"N6-methyllysine; alternate","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	8
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	4
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"P84243","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	4
Details	Modified residue: {"description":"N6-glutaryllysine; alternate","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	4
Details	Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	4
Details	Lipidation: {"description":"S-palmitoyl cysteine","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI10
Number of Residues	1
Details	Modified residue: {"description":"N6-methyllysine","evidences":[{"source":"UniProtKB","id":"P68431","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI11
Number of Residues	8
Details	Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI12
Number of Residues	9
Details	Modified residue: {"description":"N6-propionyllysine; 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":"Phosphoserine; by PAK2","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI14
Number of Residues	8
Details	Modified residue: {"description":"Phosphotyrosine","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI15
Number of Residues	4
Details	Modified residue: {"description":"N6-glutaryllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI16
Number of Residues	4
Details	Modified residue: {"description":"N6-succinyllysine","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI17
Number of Residues	4
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_FI18
Number of Residues	8
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_FI19
Number of Residues	2
Details	Modified residue: {"description":"N6-methyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI20
Number of Residues	4
Details	DNA binding: {}

Chain

Residue

Details

site_id	SWS_FT_FI21
Number of Residues	4
Details	Glycosylation: {"description":"O-linked (GlcNAc) serine","evidences":[{"source":"UniProtKB","id":"P62807","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI22
Number of Residues	8
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

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