Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

1M1A

LIGAND BINDING ALTERS THE STRUCTURE AND DYNAMICS OF NUCLEOSOMAL DNA

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000776	cellular_component	kinetochore
A	0000786	cellular_component	nucleosome
A	0003677	molecular_function	DNA binding
A	0005634	cellular_component	nucleus
A	0005694	cellular_component	chromosome
A	0007080	biological_process	mitotic metaphase chromosome alignment
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
A	0051382	biological_process	kinetochore assembly
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	0000776	cellular_component	kinetochore
E	0000786	cellular_component	nucleosome
E	0003677	molecular_function	DNA binding
E	0005634	cellular_component	nucleus
E	0005694	cellular_component	chromosome
E	0007080	biological_process	mitotic metaphase chromosome alignment
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
E	0051382	biological_process	kinetochore assembly
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

Functional Information from PDB Data

site_id	AC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MN E 301

Chain	Residue
D	VAL1245
E	HOH55
E	HOH181
E	HOH182
E	ASP677
F	HOH99

site_id	AC2
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MN J 302

Chain	Residue
J	DG280
J	DG281

site_id	AC3
Number of Residues	1
Details	BINDING SITE FOR RESIDUE MN I 303

Chain	Residue
I	DG134

site_id	AC4
Number of Residues	1
Details	BINDING SITE FOR RESIDUE MN J 304

Chain	Residue
J	DG216

site_id	AC5
Number of Residues	1
Details	BINDING SITE FOR RESIDUE MN I 305

Chain	Residue
I	DG71

site_id	AC6
Number of Residues	1
Details	BINDING SITE FOR RESIDUE MN J 306

Chain	Residue
J	DG267

site_id	AC7
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MN J 308

Chain	Residue
J	DA245
J	DG246

site_id	AC8
Number of Residues	1
Details	BINDING SITE FOR RESIDUE MN I 309

Chain	Residue
I	DG121

site_id	AC9
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MN I 310

Chain	Residue
I	DG39
I	DG40

site_id	BC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE IMT J 1901

Chain	Residue
J	DG283
J	DG284
J	DA285
J	IMT1902
J	PYB1909
J	BAL1910

site_id	BC2
Number of Residues	7
Details	BINDING SITE FOR RESIDUE IMT J 1902

Chain	Residue
J	DG284
J	DA285
J	DT286
J	IMT1901
J	PYB1903
J	PYB1908
J	PYB1909

site_id	BC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE PYB J 1903

Chain	Residue
J	DA285
J	DT286
J	IMT1902
J	PYB1904
J	PYB1907
J	PYB1908

site_id	BC4
Number of Residues	7
Details	BINDING SITE FOR RESIDUE PYB J 1904

Chain	Residue
J	DT286
J	DA287
J	DT288
J	PYB1903
J	ABU1905
J	PYB1906
J	PYB1907

site_id	BC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ABU J 1905

Chain	Residue
I	DA7
J	DA287
J	DT288
J	PYB1904
J	PYB1906

site_id	BC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE PYB J 1906

Chain	Residue
I	DA7
I	DT8
I	DC9
J	PYB1904
J	ABU1905
J	PYB1907

site_id	BC7
Number of Residues	7
Details	BINDING SITE FOR RESIDUE PYB J 1907

Chain	Residue
I	DT8
I	DC9
I	DC10
J	PYB1903
J	PYB1904
J	PYB1906
J	PYB1908

site_id	BC8
Number of Residues	8
Details	BINDING SITE FOR RESIDUE PYB J 1908

Chain	Residue
I	DC9
I	DC10
I	DA11
J	DG284
J	IMT1902
J	PYB1903
J	PYB1907
J	PYB1909

site_id	BC9
Number of Residues	8
Details	BINDING SITE FOR RESIDUE PYB J 1909

Chain	Residue
I	DC10
I	DA11
I	DC12
J	DG283
J	IMT1901
J	IMT1902
J	PYB1908
J	BAL1910

site_id	CC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE BAL J 1910

Chain	Residue
I	DA11
J	DT282
J	DG283
J	IMT1901
J	PYB1909
J	DIB1911

site_id	CC2
Number of Residues	2
Details	BINDING SITE FOR RESIDUE DIB J 1911

Chain	Residue
J	DT282
J	BAL1910

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
C	ALA821-VAL827

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	LYS414-LEU420

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

Chain	Residue	Details
D	ARG1289-GLY1311

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

Chain	Residue	Details
A	PRO466-ILE474

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	2
Details	Modified residue: {"description":"Phosphotyrosine","evidences":[{"source":"UniProtKB","id":"P84243","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	4
Details	Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P84244","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"P84243","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	2
Details	Modified residue: {"description":"N6-methylated lysine","evidences":[{"source":"UniProtKB","id":"P84243","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	2
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"UniProtKB","id":"P84243","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	2
Details	Modified residue: {"description":"N6-glutaryllysine; alternate","evidences":[{"source":"UniProtKB","id":"P84243","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	2
Details	Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P84243","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
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_FI10
Number of Residues	5
Details	Modified residue: {"description":"N6-propionyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI11
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_FI12
Number of Residues	4
Details	Modified residue: {"description":"Phosphotyrosine","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI13
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_FI14
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_FI15
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_FI16
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_FI17
Number of Residues	4
Details	DNA binding: {}

Chain

Residue

Details

site_id	SWS_FT_FI18
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_FI19
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_FI20
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_FI21
Number of Residues	2
Details	Modified residue: {"description":"N6-succinyllysine","evidences":[{"source":"UniProtKB","id":"P0C0S8","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI22
Number of Residues	2
Details	Modified residue: {"description":"N5-methylglutamine","evidences":[{"evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI23
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_FI24
Number of Residues	5
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_FI25
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_FI26
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

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)