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1KX5

X-Ray Structure of the Nucleosome Core Particle, NCP147, at 1.9 A Resolution

Functional Information from GO Data
ChainGOidnamespacecontents
A0000786cellular_componentnucleosome
A0003677molecular_functionDNA binding
A0005515molecular_functionprotein binding
A0005634cellular_componentnucleus
A0005654cellular_componentnucleoplasm
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
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
E0005515molecular_functionprotein binding
E0005634cellular_componentnucleus
E0005654cellular_componentnucleoplasm
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
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 J 3131
ChainResidue
JDG61
JHOH3221
JHOH3274
JHOH3430
JHOH3656
JHOH3694

site_idAC2
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MN E 3132
ChainResidue
EHOH3214
EHOH3225
FHOH154
DVAL45
EASP77
EHOH3195

site_idAC3
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MN J 3133
ChainResidue
IHOH3158
IHOH3221
JDG27
JHOH3208
JHOH3209
JHOH3262

site_idAC4
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MN J 3134
ChainResidue
JDG-3
JHOH3169
JHOH3195
JHOH3226
JHOH3307
JHOH3917

site_idAC5
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MN J 3135
ChainResidue
JDG48
JHOH3201
JHOH3211
JHOH3316
JHOH3317

site_idAC6
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MN I 3136
ChainResidue
IHOH3212
IHOH3244
IHOH3261
IHOH3771
JHOH3175
JHOH3212

site_idAC7
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MN I 3137
ChainResidue
IDG48
IHOH3193
IHOH3209
IHOH3251
IHOH3306

site_idAC8
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MN I 3138
ChainResidue
IDG61
IHOH3152
IHOH3181
IHOH3201
IHOH3911

site_idAC9
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MN J 3139
ChainResidue
JDG-34
JDG-35
JHOH3215
JHOH3238
JHOH3331

site_idBC1
Number of Residues4
DetailsBINDING SITE FOR RESIDUE MN I 3140
ChainResidue
IDG27
IHOH3243
IHOH3259
JHOH3931

site_idBC2
Number of Residues4
DetailsBINDING SITE FOR RESIDUE MN I 3141
ChainResidue
IDG5
IHOH3204
JHOH3152
JHOH3240

site_idBC3
Number of Residues4
DetailsBINDING SITE FOR RESIDUE MN I 3142
ChainResidue
IDG-3
IDG-2
IHOH3194
IHOH3333

site_idBC4
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MN I 3143
ChainResidue
IDG-35
IDG-34
IHOH3217
IHOH3232
IHOH3319
JHOH3933

site_idBC5
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MN J 3144
ChainResidue
IHOH3396
IHOH3923
JDG5
JHOH3230
JHOH3672

site_idBC6
Number of Residues5
DetailsBINDING SITE FOR RESIDUE CL H 3145
ChainResidue
GGLY44
GGLY46
GALA47
HTHR87
HSER88

site_idBC7
Number of Residues5
DetailsBINDING SITE FOR RESIDUE CL D 3146
ChainResidue
CGLY44
CGLY46
CALA47
DTHR87
DSER88

site_idBC8
Number of Residues2
DetailsBINDING SITE FOR RESIDUE CL A 3147
ChainResidue
APRO121
ALYS122

site_idBC9
Number of Residues2
DetailsBINDING SITE FOR RESIDUE CL E 3148
ChainResidue
EPRO121
ELYS122

Functional Information from PROSITE/UniProt
site_idPS00046
Number of Residues7
DetailsHISTONE_H2A Histone H2A signature. AGLqFPV
ChainResidueDetails
CALA21-VAL27

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
ALYS14-LEU20

site_idPS00357
Number of Residues23
DetailsHISTONE_H2B Histone H2B signature. REIQTavRlLLpGELaKHAVSEG
ChainResidueDetails
DARG89-GLY111

site_idPS00959
Number of Residues9
DetailsHISTONE_H3_2 Histone H3 signature 2. PFqRLVREI
ChainResidueDetails
APRO66-ILE74

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues8
DetailsMOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:P0C1H4
ChainResidueDetails
DSER3
DGLY10
DLYS13
DTHR18
HSER3
HGLY10
HLYS13
HTHR18

site_idSWS_FT_FI2
Number of Residues2
DetailsMOD_RES: Phosphoserine => ECO:0000269|PubMed:12757711
ChainResidueDetails
DLYS12
HLYS12

site_idSWS_FT_FI3
Number of Residues2
DetailsCARBOHYD: O-linked (GlcNAc) serine => ECO:0000250|UniProtKB:P62807
ChainResidueDetails
DGLU110
HGLU110
GTHR10
GLEU96

site_idSWS_FT_FI4
Number of Residues4
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000250|UniProtKB:P0C1H4
ChainResidueDetails
DTYR118
GGLY37
HTYR118

site_idSWS_FT_FI5
Number of Residues4
DetailsMOD_RES: N6-(2-hydroxyisobutyryl)lysine => ECO:0000250|UniProtKB:P0C0S8
ChainResidueDetails
CLYS75
ELEU65
CTHR76
GLYS75
GTHR76
FGLY9
FARG17
FARG45
FTHR80
EGLN19

site_idSWS_FT_FI6
Number of Residues2
DetailsMOD_RES: N5-methylglutamine => ECO:0000250
ChainResidueDetails
CGLY105
GGLY105
FGLY13
FVAL21

site_idSWS_FT_FI7
Number of Residues2
DetailsMOD_RES: N6-glutaryllysine; alternate => ECO:0000250|UniProtKB:P0C0S8
ChainResidueDetails
CLYS119
GLYS119
FPRO32
FARG92

site_idSWS_FT_FI8
Number of Residues8
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000250
ChainResidueDetails
CALA14
FGLY48
CTHR16
CTHR120
GALA14
GTHR16
GTHR120

site_idSWS_FT_FI9
Number of Residues4
DetailsMOD_RES: Phosphotyrosine => ECO:0000250|UniProtKB:P62805
ChainResidueDetails
BGLU52
BALA89
FGLU52
FALA89

site_idSWS_FT_FI10
Number of Residues2
DetailsMOD_RES: N6-glutaryllysine; alternate => ECO:0000250|UniProtKB:P62805
ChainResidueDetails
BVAL60
FVAL60
EALA7
EGLY12

site_idSWS_FT_FI11
Number of Residues2
DetailsMOD_RES: N6-succinyllysine => ECO:0000250|UniProtKB:P62805
ChainResidueDetails
BARG78
FARG78

site_idSWS_FT_FI12
Number of Residues2
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in UFM1); alternate => ECO:0000250|UniProtKB:P62805
ChainResidueDetails
BPRO32
FPRO32

site_idSWS_FT_FI13
Number of Residues4
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate => ECO:0000250|UniProtKB:P62805
ChainResidueDetails
AALA29
BARG92
FARG92

site_idSWS_FT_FI14
Number of Residues2
DetailsMOD_RES: N6-methyllysine => ECO:0000250|UniProtKB:P68431
ChainResidueDetails
APRO38
EPRO38

site_idSWS_FT_FI15
Number of Residues2
DetailsMOD_RES: Phosphotyrosine => ECO:0000250|UniProtKB:Q71DI3
ChainResidueDetails
AARG42
EARG42

site_idSWS_FT_FI16
Number of Residues2
DetailsMOD_RES: Phosphoserine => ECO:0000250|UniProtKB:Q71DI3
ChainResidueDetails
ATHR58
ETHR58

site_idSWS_FT_FI17
Number of Residues4
DetailsMOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:Q71DI3
ChainResidueDetails
AASP81
AASN108
EASP81
EASN108

site_idSWS_FT_FI18
Number of Residues2
DetailsMOD_RES: Phosphoserine => ECO:0000250|UniProtKB:P84243
ChainResidueDetails
ASER87
ESER87

site_idSWS_FT_FI19
Number of Residues2
DetailsMOD_RES: N6-glutaryllysine; alternate => ECO:0000250|UniProtKB:Q71DI3
ChainResidueDetails
AARG116
EARG116

site_idSWS_FT_FI20
Number of Residues2
DetailsMOD_RES: N6-succinyllysine; alternate => ECO:0000250|UniProtKB:Q71DI3
ChainResidueDetails
AASP123
EASP123

site_idSWS_FT_FI21
Number of Residues2
DetailsLIPID: S-palmitoyl cysteine => ECO:0000250|UniProtKB:Q71DI3
ChainResidueDetails
AALA111
EALA111

225158

PDB entries from 2024-09-18

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