1KX5
X-Ray Structure of the Nucleosome Core Particle, NCP147, at 1.9 A Resolution
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 |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE MN J 3131 |
Chain | Residue |
J | DG61 |
J | HOH3221 |
J | HOH3274 |
J | HOH3430 |
J | HOH3656 |
J | HOH3694 |
site_id | AC2 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE MN E 3132 |
Chain | Residue |
E | HOH3214 |
E | HOH3225 |
F | HOH154 |
D | VAL45 |
E | ASP77 |
E | HOH3195 |
site_id | AC3 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE MN J 3133 |
Chain | Residue |
I | HOH3158 |
I | HOH3221 |
J | DG27 |
J | HOH3208 |
J | HOH3209 |
J | HOH3262 |
site_id | AC4 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE MN J 3134 |
Chain | Residue |
J | DG-3 |
J | HOH3169 |
J | HOH3195 |
J | HOH3226 |
J | HOH3307 |
J | HOH3917 |
site_id | AC5 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE MN J 3135 |
Chain | Residue |
J | DG48 |
J | HOH3201 |
J | HOH3211 |
J | HOH3316 |
J | HOH3317 |
site_id | AC6 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE MN I 3136 |
Chain | Residue |
I | HOH3212 |
I | HOH3244 |
I | HOH3261 |
I | HOH3771 |
J | HOH3175 |
J | HOH3212 |
site_id | AC7 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE MN I 3137 |
Chain | Residue |
I | DG48 |
I | HOH3193 |
I | HOH3209 |
I | HOH3251 |
I | HOH3306 |
site_id | AC8 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE MN I 3138 |
Chain | Residue |
I | DG61 |
I | HOH3152 |
I | HOH3181 |
I | HOH3201 |
I | HOH3911 |
site_id | AC9 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE MN J 3139 |
Chain | Residue |
J | DG-34 |
J | DG-35 |
J | HOH3215 |
J | HOH3238 |
J | HOH3331 |
site_id | BC1 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE MN I 3140 |
Chain | Residue |
I | DG27 |
I | HOH3243 |
I | HOH3259 |
J | HOH3931 |
site_id | BC2 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE MN I 3141 |
Chain | Residue |
I | DG5 |
I | HOH3204 |
J | HOH3152 |
J | HOH3240 |
site_id | BC3 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE MN I 3142 |
Chain | Residue |
I | DG-3 |
I | DG-2 |
I | HOH3194 |
I | HOH3333 |
site_id | BC4 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE MN I 3143 |
Chain | Residue |
I | DG-35 |
I | DG-34 |
I | HOH3217 |
I | HOH3232 |
I | HOH3319 |
J | HOH3933 |
site_id | BC5 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE MN J 3144 |
Chain | Residue |
I | HOH3396 |
I | HOH3923 |
J | DG5 |
J | HOH3230 |
J | HOH3672 |
site_id | BC6 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE CL H 3145 |
Chain | Residue |
G | GLY44 |
G | GLY46 |
G | ALA47 |
H | THR87 |
H | SER88 |
site_id | BC7 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE CL D 3146 |
Chain | Residue |
C | GLY44 |
C | GLY46 |
C | ALA47 |
D | THR87 |
D | SER88 |
site_id | BC8 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE CL A 3147 |
Chain | Residue |
A | PRO121 |
A | LYS122 |
site_id | BC9 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE CL E 3148 |
Chain | Residue |
E | PRO121 |
E | LYS122 |
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 | 8 |
Details | MOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:P0C1H4 |
Chain | Residue | Details |
D | SER3 | |
D | GLY10 | |
D | LYS13 | |
D | THR18 | |
H | SER3 | |
H | GLY10 | |
H | LYS13 | |
H | THR18 |
site_id | SWS_FT_FI2 |
Number of Residues | 2 |
Details | MOD_RES: Phosphoserine => ECO:0000269|PubMed:12757711 |
Chain | Residue | Details |
D | LYS12 | |
H | LYS12 |
site_id | SWS_FT_FI3 |
Number of Residues | 2 |
Details | CARBOHYD: O-linked (GlcNAc) serine => ECO:0000250|UniProtKB:P62807 |
Chain | Residue | Details |
D | GLU110 | |
H | GLU110 | |
G | THR10 | |
G | LEU96 |
site_id | SWS_FT_FI4 |
Number of Residues | 4 |
Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000250|UniProtKB:P0C1H4 |
Chain | Residue | Details |
D | TYR118 | |
G | GLY37 | |
H | TYR118 |
site_id | SWS_FT_FI5 |
Number of Residues | 4 |
Details | MOD_RES: N6-(2-hydroxyisobutyryl)lysine => ECO:0000250|UniProtKB:P0C0S8 |
Chain | Residue | Details |
C | LYS75 | |
E | LEU65 | |
C | THR76 | |
G | LYS75 | |
G | THR76 | |
F | GLY9 | |
F | ARG17 | |
F | ARG45 | |
F | THR80 | |
E | GLN19 |
site_id | SWS_FT_FI6 |
Number of Residues | 2 |
Details | MOD_RES: N5-methylglutamine => ECO:0000250 |
Chain | Residue | Details |
C | GLY105 | |
G | GLY105 | |
F | GLY13 | |
F | VAL21 |
site_id | SWS_FT_FI7 |
Number of Residues | 2 |
Details | MOD_RES: N6-glutaryllysine; alternate => ECO:0000250|UniProtKB:P0C0S8 |
Chain | Residue | Details |
C | LYS119 | |
G | LYS119 | |
F | PRO32 | |
F | ARG92 |
site_id | SWS_FT_FI8 |
Number of Residues | 8 |
Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000250 |
Chain | Residue | Details |
C | ALA14 | |
F | GLY48 | |
C | THR16 | |
C | THR120 | |
G | ALA14 | |
G | THR16 | |
G | THR120 |
site_id | SWS_FT_FI9 |
Number of Residues | 4 |
Details | MOD_RES: Phosphotyrosine => ECO:0000250|UniProtKB:P62805 |
Chain | Residue | Details |
B | GLU52 | |
B | ALA89 | |
F | GLU52 | |
F | ALA89 |
site_id | SWS_FT_FI10 |
Number of Residues | 2 |
Details | MOD_RES: N6-glutaryllysine; alternate => ECO:0000250|UniProtKB:P62805 |
Chain | Residue | Details |
B | VAL60 | |
F | VAL60 | |
E | ALA7 | |
E | GLY12 |
site_id | SWS_FT_FI11 |
Number of Residues | 2 |
Details | MOD_RES: N6-succinyllysine => ECO:0000250|UniProtKB:P62805 |
Chain | Residue | Details |
B | ARG78 | |
F | ARG78 |
site_id | SWS_FT_FI12 |
Number of Residues | 2 |
Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in UFM1); alternate => ECO:0000250|UniProtKB:P62805 |
Chain | Residue | Details |
B | PRO32 | |
F | PRO32 |
site_id | SWS_FT_FI13 |
Number of Residues | 4 |
Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate => ECO:0000250|UniProtKB:P62805 |
Chain | Residue | Details |
A | ALA29 | |
B | ARG92 | |
F | ARG92 |
site_id | SWS_FT_FI14 |
Number of Residues | 2 |
Details | MOD_RES: N6-methyllysine => ECO:0000250|UniProtKB:P68431 |
Chain | Residue | Details |
A | PRO38 | |
E | PRO38 |
site_id | SWS_FT_FI15 |
Number of Residues | 2 |
Details | MOD_RES: Phosphotyrosine => ECO:0000250|UniProtKB:Q71DI3 |
Chain | Residue | Details |
A | ARG42 | |
E | ARG42 |
site_id | SWS_FT_FI16 |
Number of Residues | 2 |
Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:Q71DI3 |
Chain | Residue | Details |
A | THR58 | |
E | THR58 |
site_id | SWS_FT_FI17 |
Number of Residues | 4 |
Details | MOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:Q71DI3 |
Chain | Residue | Details |
A | ASP81 | |
A | ASN108 | |
E | ASP81 | |
E | ASN108 |
site_id | SWS_FT_FI18 |
Number of Residues | 2 |
Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:P84243 |
Chain | Residue | Details |
A | SER87 | |
E | SER87 |
site_id | SWS_FT_FI19 |
Number of Residues | 2 |
Details | MOD_RES: N6-glutaryllysine; alternate => ECO:0000250|UniProtKB:Q71DI3 |
Chain | Residue | Details |
A | ARG116 | |
E | ARG116 |
site_id | SWS_FT_FI20 |
Number of Residues | 2 |
Details | MOD_RES: N6-succinyllysine; alternate => ECO:0000250|UniProtKB:Q71DI3 |
Chain | Residue | Details |
A | ASP123 | |
E | ASP123 |
site_id | SWS_FT_FI21 |
Number of Residues | 2 |
Details | LIPID: S-palmitoyl cysteine => ECO:0000250|UniProtKB:Q71DI3 |
Chain | Residue | Details |
A | ALA111 | |
E | ALA111 |