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1M19

LIGAND BINDING ALTERS THE STRUCTURE AND DYNAMICS OF NUCLEOSOMAL DNA

Functional Information from GO Data
ChainGOidnamespacecontents
A0000786cellular_componentnucleosome
A0003677molecular_functionDNA binding
A0005634cellular_componentnucleus
A0005694cellular_componentchromosome
A0030527molecular_functionstructural constituent of chromatin
A0046982molecular_functionprotein heterodimerization activity
B0000786cellular_componentnucleosome
B0003677molecular_functionDNA binding
B0005515molecular_functionprotein binding
B0005634cellular_componentnucleus
B0005694cellular_componentchromosome
B0006334biological_processnucleosome assembly
B0030527molecular_functionstructural constituent of chromatin
B0046982molecular_functionprotein heterodimerization activity
C0000786cellular_componentnucleosome
C0003677molecular_functionDNA binding
C0005634cellular_componentnucleus
C0005694cellular_componentchromosome
C0030527molecular_functionstructural constituent of chromatin
C0031507biological_processheterochromatin formation
C0046982molecular_functionprotein heterodimerization activity
D0000786cellular_componentnucleosome
D0003677molecular_functionDNA binding
D0005515molecular_functionprotein binding
D0005634cellular_componentnucleus
D0005694cellular_componentchromosome
D0030527molecular_functionstructural constituent of chromatin
D0046982molecular_functionprotein heterodimerization activity
E0000786cellular_componentnucleosome
E0003677molecular_functionDNA binding
E0005634cellular_componentnucleus
E0005694cellular_componentchromosome
E0030527molecular_functionstructural constituent of chromatin
E0046982molecular_functionprotein heterodimerization activity
F0000786cellular_componentnucleosome
F0003677molecular_functionDNA binding
F0005515molecular_functionprotein binding
F0005634cellular_componentnucleus
F0005694cellular_componentchromosome
F0006334biological_processnucleosome assembly
F0030527molecular_functionstructural constituent of chromatin
F0046982molecular_functionprotein heterodimerization activity
G0000786cellular_componentnucleosome
G0003677molecular_functionDNA binding
G0005634cellular_componentnucleus
G0005694cellular_componentchromosome
G0030527molecular_functionstructural constituent of chromatin
G0031507biological_processheterochromatin formation
G0046982molecular_functionprotein heterodimerization activity
H0000786cellular_componentnucleosome
H0003677molecular_functionDNA binding
H0005515molecular_functionprotein binding
H0005634cellular_componentnucleus
H0005694cellular_componentchromosome
H0030527molecular_functionstructural constituent of chromatin
H0046982molecular_functionprotein heterodimerization activity
Functional Information from PDB Data
site_idAC1
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MN E 736
ChainResidue
DVAL1245
EASP677
EHOH750
EHOH780
EHOH781
FHOH341

site_idAC2
Number of Residues1
DetailsBINDING SITE FOR RESIDUE MN J 702
ChainResidue
JDG280

site_idAC3
Number of Residues2
DetailsBINDING SITE FOR RESIDUE MN I 703
ChainResidue
IDG134
IHOH2093

site_idAC4
Number of Residues1
DetailsBINDING SITE FOR RESIDUE MN J 704
ChainResidue
JDG217

site_idAC5
Number of Residues2
DetailsBINDING SITE FOR RESIDUE MN I 705
ChainResidue
IDG70
IHOH2098

site_idAC6
Number of Residues2
DetailsBINDING SITE FOR RESIDUE MN J 706
ChainResidue
JDG267
JHOH2051

site_idAC7
Number of Residues1
DetailsBINDING SITE FOR RESIDUE MN I 707
ChainResidue
JHOH2064

site_idAC8
Number of Residues2
DetailsBINDING SITE FOR RESIDUE MN J 708
ChainResidue
JDG246
JHOH2046

site_idAC9
Number of Residues2
DetailsBINDING SITE FOR RESIDUE MN I 709
ChainResidue
IDG138
IHOH2034

site_idBC1
Number of Residues2
DetailsBINDING SITE FOR RESIDUE MN I 710
ChainResidue
IDT38
IDG39

site_idBC2
Number of Residues2
DetailsBINDING SITE FOR RESIDUE MN I 711
ChainResidue
IDT120
IDG121

site_idBC3
Number of Residues6
DetailsBINDING SITE FOR RESIDUE IMT J 1901
ChainResidue
IDG31
IDT32
JPYB1902
JPYB1908
JPYB1909
JBAL1910

site_idBC4
Number of Residues7
DetailsBINDING SITE FOR RESIDUE PYB J 1902
ChainResidue
IDT32
IDG33
JIMT1901
JPYB1903
JPYB1907
JPYB1908
JPYB1909

site_idBC5
Number of Residues6
DetailsBINDING SITE FOR RESIDUE PYB J 1903
ChainResidue
IDG33
IDT34
JPYB1902
JPYB1904
JPYB1906
JPYB1907

site_idBC6
Number of Residues5
DetailsBINDING SITE FOR RESIDUE PYB J 1904
ChainResidue
IDA35
IDT36
JPYB1903
JABU1905
JPYB1906

site_idBC7
Number of Residues4
DetailsBINDING SITE FOR RESIDUE ABU J 1905
ChainResidue
JDA259
JDC260
JPYB1904
JPYB1906

site_idBC8
Number of Residues7
DetailsBINDING SITE FOR RESIDUE PYB J 1906
ChainResidue
JDA259
JDC260
JDA261
JPYB1903
JPYB1904
JABU1905
JPYB1907

site_idBC9
Number of Residues8
DetailsBINDING SITE FOR RESIDUE PYB J 1907
ChainResidue
IDG33
JDC260
JDA261
JDC262
JPYB1902
JPYB1903
JPYB1906
JPYB1908

site_idCC1
Number of Residues7
DetailsBINDING SITE FOR RESIDUE PYB J 1908
ChainResidue
JDA261
JDC262
JDT263
JIMT1901
JPYB1902
JPYB1907
JPYB1909

site_idCC2
Number of Residues7
DetailsBINDING SITE FOR RESIDUE PYB J 1909
ChainResidue
JDC262
JDT263
JDT264
JIMT1901
JPYB1902
JPYB1908
JBAL1910

site_idCC3
Number of Residues3
DetailsBINDING SITE FOR RESIDUE BAL J 1910
ChainResidue
JIMT1901
JPYB1909
JDIB1911

site_idCC4
Number of Residues4
DetailsBINDING SITE FOR RESIDUE DIB J 1911
ChainResidue
CALA814
JDT265
JDT266
JBAL1910

site_idCC5
Number of Residues4
DetailsBINDING SITE FOR RESIDUE IMT J 1921
ChainResidue
JDT250
JPYB1922
JPYB1929
JBAL1930

site_idCC6
Number of Residues7
DetailsBINDING SITE FOR RESIDUE PYB J 1922
ChainResidue
JDT250
JDT251
JDT252
JIMT1921
JPYB1923
JPYB1928
JPYB1929

site_idCC7
Number of Residues7
DetailsBINDING SITE FOR RESIDUE PYB J 1923
ChainResidue
JDT252
JDC253
JPYB1922
JPYB1924
JPYB1927
JPYB1928
JDT251

site_idCC8
Number of Residues6
DetailsBINDING SITE FOR RESIDUE PYB J 1924
ChainResidue
JDT252
JDC253
JDC254
JPYB1923
JABU1925
JPYB1926

site_idCC9
Number of Residues2
DetailsBINDING SITE FOR RESIDUE ABU J 1925
ChainResidue
JPYB1924
JPYB1926

site_idDC1
Number of Residues4
DetailsBINDING SITE FOR RESIDUE PYB J 1926
ChainResidue
IDA42
JPYB1924
JABU1925
JPYB1927

site_idDC2
Number of Residues4
DetailsBINDING SITE FOR RESIDUE PYB J 1927
ChainResidue
IDA43
JPYB1923
JPYB1926
JPYB1928

site_idDC3
Number of Residues7
DetailsBINDING SITE FOR RESIDUE PYB J 1928
ChainResidue
IDA43
IDC44
IDT45
JPYB1922
JPYB1923
JPYB1927
JPYB1929

site_idDC4
Number of Residues8
DetailsBINDING SITE FOR RESIDUE PYB J 1929
ChainResidue
IDC44
IDT45
IDG46
JDG249
JIMT1921
JPYB1922
JPYB1928
JBAL1930

site_idDC5
Number of Residues7
DetailsBINDING SITE FOR RESIDUE BAL J 1930
ChainResidue
IDT45
IDC47
JDA248
JDG249
JIMT1921
JPYB1929
JDIB1931

site_idDC6
Number of Residues3
DetailsBINDING SITE FOR RESIDUE DIB J 1931
ChainResidue
IDC47
IDT48
JBAL1930

site_idDC7
Number of Residues5
DetailsBINDING SITE FOR RESIDUE IMT I 1961
ChainResidue
IDA72
IDA73
IPYB1962
IPYB1969
IBAL1970

site_idDC8
Number of Residues7
DetailsBINDING SITE FOR RESIDUE PYB I 1962
ChainResidue
IDA72
IDA73
IIMT1961
IPYB1963
IPYB1967
IPYB1968
IPYB1969

site_idDC9
Number of Residues8
DetailsBINDING SITE FOR RESIDUE PYB I 1963
ChainResidue
IDA73
IDT74
IDT75
IPYB1962
IPYB1964
IPYB1966
IPYB1967
IPYB1968

site_idEC1
Number of Residues7
DetailsBINDING SITE FOR RESIDUE PYB I 1964
ChainResidue
IDT74
IDT75
IDC76
IPYB1963
IABU1965
IPYB1966
IPYB1967

site_idEC2
Number of Residues4
DetailsBINDING SITE FOR RESIDUE ABU I 1965
ChainResidue
IDT75
IPYB1964
IPYB1966
JDA219

site_idEC3
Number of Residues6
DetailsBINDING SITE FOR RESIDUE PYB I 1966
ChainResidue
IPYB1963
IPYB1964
IABU1965
IPYB1967
JDA219
JDT220

site_idEC4
Number of Residues7
DetailsBINDING SITE FOR RESIDUE PYB I 1967
ChainResidue
IPYB1962
IPYB1963
IPYB1964
IPYB1966
IPYB1968
JDT220
JDT221

site_idEC5
Number of Residues7
DetailsBINDING SITE FOR RESIDUE PYB I 1968
ChainResidue
IPYB1962
IPYB1963
IPYB1967
IPYB1969
JDT221
JDC222
JDC223

site_idEC6
Number of Residues8
DetailsBINDING SITE FOR RESIDUE PYB I 1969
ChainResidue
IDG71
IIMT1961
IPYB1962
IPYB1968
IBAL1970
JDC222
JDC223
JDG224

site_idEC7
Number of Residues6
DetailsBINDING SITE FOR RESIDUE BAL I 1970
ChainResidue
IDG70
IIMT1961
IPYB1969
IDIB1971
JDG224
JDC225

site_idEC8
Number of Residues5
DetailsBINDING SITE FOR RESIDUE DIB I 1971
ChainResidue
IDG70
IDG71
IBAL1970
JDG224
JDT226

site_idEC9
Number of Residues3
DetailsBINDING SITE FOR RESIDUE IMT J 2001
ChainResidue
IDT104
JPYB2002
JPYB2009

site_idFC1
Number of Residues6
DetailsBINDING SITE FOR RESIDUE PYB J 2002
ChainResidue
IDT104
IDT105
JIMT2001
JPYB2003
JPYB2008
JPYB2009

site_idFC2
Number of Residues6
DetailsBINDING SITE FOR RESIDUE PYB J 2003
ChainResidue
IDT105
IDT106
JPYB2002
JPYB2004
JPYB2007
JPYB2008

site_idFC3
Number of Residues7
DetailsBINDING SITE FOR RESIDUE PYB J 2004
ChainResidue
IDT106
IDC107
IDC108
JPYB2003
JABU2005
JPYB2006
JPYB2007

site_idFC4
Number of Residues3
DetailsBINDING SITE FOR RESIDUE ABU J 2005
ChainResidue
JDA187
JPYB2004
JPYB2006

site_idFC5
Number of Residues5
DetailsBINDING SITE FOR RESIDUE PYB J 2006
ChainResidue
JDA188
JDA189
JPYB2004
JABU2005
JPYB2007

site_idFC6
Number of Residues7
DetailsBINDING SITE FOR RESIDUE PYB J 2007
ChainResidue
JDA188
JDA189
JDC190
JPYB2003
JPYB2004
JPYB2006
JPYB2008

site_idFC7
Number of Residues7
DetailsBINDING SITE FOR RESIDUE PYB J 2008
ChainResidue
JDA189
JDC190
JDT191
JPYB2002
JPYB2003
JPYB2007
JPYB2009

site_idFC8
Number of Residues8
DetailsBINDING SITE FOR RESIDUE PYB J 2009
ChainResidue
IDG103
JDC190
JDT191
JDG192
JIMT2001
JPYB2002
JPYB2008
JBAL2010

site_idFC9
Number of Residues4
DetailsBINDING SITE FOR RESIDUE BAL J 2010
ChainResidue
JDG192
JDC193
JPYB2009
JDIB2011

site_idGC1
Number of Residues4
DetailsBINDING SITE FOR RESIDUE DIB J 2011
ChainResidue
IDA102
JDG192
JDT194
JBAL2010

site_idGC2
Number of Residues6
DetailsBINDING SITE FOR RESIDUE IMT I 2021
ChainResidue
IPYB2022
IPYB2028
IPYB2029
IBAL2030
JDT178
JDG179

site_idGC3
Number of Residues7
DetailsBINDING SITE FOR RESIDUE PYB I 2022
ChainResidue
IIMT2021
IPYB2023
IPYB2027
IPYB2028
IPYB2029
JDG179
JDT180

site_idGC4
Number of Residues7
DetailsBINDING SITE FOR RESIDUE PYB I 2023
ChainResidue
IPYB2022
IPYB2024
IPYB2027
IPYB2028
JDT180
JDA181
JDT182

site_idGC5
Number of Residues6
DetailsBINDING SITE FOR RESIDUE PYB I 2024
ChainResidue
IPYB2023
IABU2025
IPYB2026
IPYB2027
JDT182
JDT183

site_idGC6
Number of Residues5
DetailsBINDING SITE FOR RESIDUE ABU I 2025
ChainResidue
IDT112
IPYB2024
IPYB2026
JDT182
JDT183

site_idGC7
Number of Residues5
DetailsBINDING SITE FOR RESIDUE PYB I 2026
ChainResidue
IDT112
IDA113
IPYB2024
IABU2025
IPYB2027

site_idGC8
Number of Residues7
DetailsBINDING SITE FOR RESIDUE PYB I 2027
ChainResidue
IDA113
IDC114
IPYB2022
IPYB2023
IPYB2024
IPYB2026
IPYB2028

site_idGC9
Number of Residues7
DetailsBINDING SITE FOR RESIDUE PYB I 2028
ChainResidue
IDC114
IDA115
IIMT2021
IPYB2022
IPYB2023
IPYB2027
IPYB2029

site_idHC1
Number of Residues7
DetailsBINDING SITE FOR RESIDUE PYB I 2029
ChainResidue
IDA115
IDC116
IDT117
IIMT2021
IPYB2022
IPYB2028
IBAL2030

site_idHC2
Number of Residues8
DetailsBINDING SITE FOR RESIDUE BAL I 2030
ChainResidue
IDA115
IDC116
IDT117
IIMT2021
IPYB2029
IDIB2031
JDG177
JDT178

site_idHC3
Number of Residues5
DetailsBINDING SITE FOR RESIDUE DIB I 2031
ChainResidue
IDT117
IDT118
IBAL2030
JDG177
JDT178

Functional Information from PROSITE/UniProt
site_idPS00046
Number of Residues7
DetailsHISTONE_H2A Histone H2A signature. AGLqFPV
ChainResidueDetails
CALA821-VAL827

site_idPS00047
Number of Residues5
DetailsHISTONE_H4 Histone H4 signature. GAKRH
ChainResidueDetails
BGLY14-HIS18

site_idPS00322
Number of Residues7
DetailsHISTONE_H3_1 Histone H3 signature 1. KAPRKQL
ChainResidueDetails
ALYS414-LEU420

site_idPS00357
Number of Residues23
DetailsHISTONE_H2B Histone H2B signature. REIQTavRlLLpGELaKHAVSEG
ChainResidueDetails
DARG1289-GLY1311

site_idPS00959
Number of Residues9
DetailsHISTONE_H3_2 Histone H3 signature 2. PFqRLVREI
ChainResidueDetails
APRO466-ILE474

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues1
DetailsModified residue: {"description":"N6-methylated lysine; alternate","evidences":[{"source":"UniProtKB","id":"P84243","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI2
Number of Residues2
DetailsModified residue: {"description":"Phosphotyrosine","evidences":[{"source":"UniProtKB","id":"P84243","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI3
Number of Residues4
DetailsModified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P84244","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI4
Number of Residues2
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"P84243","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI5
Number of Residues2
DetailsModified residue: {"description":"N6-methylated lysine","evidences":[{"source":"UniProtKB","id":"P84243","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI6
Number of Residues2
DetailsModified residue: {"description":"Phosphothreonine","evidences":[{"source":"UniProtKB","id":"P84243","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI7
Number of Residues2
DetailsModified residue: {"description":"N6-glutaryllysine; alternate","evidences":[{"source":"UniProtKB","id":"P84243","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI8
Number of Residues2
DetailsModified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P84243","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI10
Number of Residues4
DetailsModified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI11
Number of Residues4
DetailsModified residue: {"description":"N6-propionyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI12
Number of Residues2
DetailsModified residue: {"description":"Phosphoserine; by PAK2","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI13
Number of Residues4
DetailsModified residue: {"description":"Phosphotyrosine","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI14
Number of Residues2
DetailsModified residue: {"description":"N6-glutaryllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI15
Number of Residues2
DetailsModified residue: {"description":"N6-succinyllysine","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI16
Number of Residues2
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in UFM1); alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI17
Number of Residues4
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI18
Number of Residues1
DetailsModified residue: {"description":"N6-methyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI19
Number of Residues2
DetailsModified residue: {"description":"N6-(2-hydroxyisobutyryl)lysine; alternate","evidences":[{"source":"UniProtKB","id":"P0C0S8","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI20
Number of Residues4
DetailsModified residue: {"description":"N6-(2-hydroxyisobutyryl)lysine","evidences":[{"source":"UniProtKB","id":"P0C0S8","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI21
Number of Residues2
DetailsModified residue: {"description":"N6-succinyllysine","evidences":[{"source":"UniProtKB","id":"P0C0S8","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI22
Number of Residues2
DetailsModified residue: {"description":"N5-methylglutamine","evidences":[{"evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI23
Number of Residues2
DetailsModified residue: {"description":"N6-glutaryllysine; alternate","evidences":[{"source":"UniProtKB","id":"P0C0S8","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI24
Number of Residues6
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI25
Number of Residues2
DetailsGlycosylation: {"description":"O-linked (GlcNAc) serine","evidences":[{"source":"UniProtKB","id":"P62807","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI26
Number of Residues4
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"UniProtKB","id":"P0C1H4","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

243911

PDB entries from 2025-10-29

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