3REK
2.6 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with a 146 bp Alpha-Satellite DNA (NCP146b) Derivatized with Oxaliplatin
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 | 2 |
| Details | BINDING SITE FOR RESIDUE MN A 1001 |
| Chain | Residue |
| A | ASP77 |
| H | VAL45 |
| site_id | AC2 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE MN D 1007 |
| Chain | Residue |
| D | VAL45 |
| site_id | AC3 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE SO4 D 1101 |
| Chain | Residue |
| C | ARG71 |
| D | HIS46 |
| D | PRO47 |
| D | ASP48 |
| D | THR49 |
| site_id | AC4 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE SO4 C 1102 |
| Chain | Residue |
| C | GLY46 |
| C | ALA47 |
| D | THR87 |
| D | SER88 |
| C | ALA45 |
| site_id | AC5 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE SO4 G 1103 |
| Chain | Residue |
| G | GLY44 |
| G | ALA45 |
| G | GLY46 |
| G | ALA47 |
| H | THR87 |
| H | SER88 |
| I | DC38 |
| site_id | AC6 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE PT I 74 |
| Chain | Residue |
| I | DA-72 |
| I | DT73 |
| site_id | AC7 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE PT J 73 |
| Chain | Residue |
| J | DG-3 |
| site_id | AC8 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE PT J 74 |
| Chain | Residue |
| J | DA-73 |
| site_id | AC9 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE PT J 75 |
| Chain | Residue |
| J | DG-46 |
| site_id | BC1 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE PT J 76 |
| Chain | Residue |
| J | DG7 |
| site_id | BC2 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE PT I 75 |
| Chain | Residue |
| I | DG71 |
| site_id | BC3 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE PT B 103 |
| Chain | Residue |
| B | MET84 |
| B | TYR88 |
| site_id | BC4 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE PT I 76 |
| Chain | Residue |
| I | DG-53 |
| I | DC-54 |
| site_id | BC5 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE PT I 77 |
| Chain | Residue |
| I | DG-14 |
| site_id | BC6 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE PT I 78 |
| Chain | Residue |
| I | DA-46 |
| site_id | BC7 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE PT J 77 |
| Chain | Residue |
| J | DG67 |
| J | DG68 |
| site_id | BC8 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE PT I 79 |
| Chain | Residue |
| I | DG-16 |
| site_id | BC9 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE PT F 103 |
| Chain | Residue |
| F | MET84 |
| F | TYR88 |
| site_id | CC1 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE PT I 80 |
| Chain | Residue |
| I | DG25 |
| I | PT90 |
| site_id | CC2 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE PT J 78 |
| Chain | Residue |
| J | DG-54 |
| J | DG-53 |
| site_id | CC3 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE PT I 81 |
| Chain | Residue |
| I | DT-56 |
| I | DG-55 |
| site_id | CC4 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE PT J 79 |
| Chain | Residue |
| J | DG24 |
| J | DC25 |
| site_id | CC5 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE PT J 80 |
| Chain | Residue |
| J | DG-16 |
| J | DG-17 |
| site_id | CC6 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE PT I 82 |
| Chain | Residue |
| I | DG68 |
| I | DG69 |
| site_id | CC7 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE PT J 81 |
| Chain | Residue |
| J | DG-17 |
| site_id | CC8 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE PT I 83 |
| Chain | Residue |
| I | DT33 |
| I | DG34 |
| site_id | CC9 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE PT J 82 |
| Chain | Residue |
| J | DA3 |
| J | DG4 |
| site_id | DC1 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE PT E 136 |
| Chain | Residue |
| E | MET120 |
| J | DA-2 |
| site_id | DC2 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE PT I 84 |
| Chain | Residue |
| I | DG-15 |
| site_id | DC3 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE PT J 83 |
| Chain | Residue |
| J | DG-15 |
| site_id | DC4 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE PT J 84 |
| Chain | Residue |
| J | DG70 |
| site_id | DC5 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE PT J 85 |
| Chain | Residue |
| J | DG-28 |
| site_id | DC6 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE PT A 136 |
| Chain | Residue |
| A | MET120 |
| I | DG-2 |
| site_id | DC7 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE PT I 85 |
| Chain | Residue |
| I | DG-2 |
| site_id | DC8 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE PT I 86 |
| Chain | Residue |
| I | DG21 |
| I | DA22 |
| site_id | DC9 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE PT J 86 |
| Chain | Residue |
| J | DG58 |
| J | DG59 |
| site_id | EC1 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE PT J 87 |
| Chain | Residue |
| J | DG-54 |
| J | DC-55 |
| site_id | EC2 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE PT I 87 |
| Chain | Residue |
| I | DG-27 |
| I | DT-28 |
| site_id | EC3 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE PT I 88 |
| Chain | Residue |
| I | DG5 |
| site_id | EC4 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE PT I 89 |
| Chain | Residue |
| I | DA-46 |
| I | DG-45 |
| site_id | EC5 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE PT J 88 |
| Chain | Residue |
| J | DT-39 |
| J | DG-40 |
| site_id | EC6 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE PT J 89 |
| Chain | Residue |
| J | DG-36 |
| J | DT-37 |
| site_id | EC7 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE PT I 90 |
| Chain | Residue |
| I | DG25 |
| I | PT80 |
| J | DC-25 |
| site_id | EC8 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE PT B 104 |
| Chain | Residue |
| B | MET84 |
| B | GLY101 |
| B | GLY102 |
| site_id | EC9 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE PT I 101 |
| Chain | Residue |
| I | DT-36 |
| I | DG-35 |
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 | LYS2 | |
| D | LYS9 | |
| D | LYS12 | |
| D | LYS17 | |
| H | LYS2 | |
| H | LYS9 | |
| H | LYS12 | |
| H | LYS17 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0000269|PubMed:12757711 |
| Chain | Residue | Details |
| D | SER11 | |
| H | SER11 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 2 |
| Details | CARBOHYD: O-linked (GlcNAc) serine => ECO:0000250|UniProtKB:P62807 |
| Chain | Residue | Details |
| D | SER109 | |
| H | SER109 | |
| G | LYS9 | |
| G | LYS95 |
| 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 | LYS117 | |
| G | LYS36 | |
| H | LYS117 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 4 |
| Details | MOD_RES: N6-(2-hydroxyisobutyryl)lysine => ECO:0000250|UniProtKB:P0C0S8 |
| Chain | Residue | Details |
| C | LYS74 | |
| C | LYS75 | |
| G | LYS74 | |
| G | LYS75 | |
| F | LYS8 | |
| F | LYS16 | |
| F | LYS44 | |
| F | LYS79 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 2 |
| Details | MOD_RES: N5-methylglutamine => ECO:0000250 |
| Chain | Residue | Details |
| C | GLN104 | |
| G | GLN104 | |
| F | LYS12 | |
| F | LYS20 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-glutaryllysine; alternate => ECO:0000250|UniProtKB:P0C0S8 |
| Chain | Residue | Details |
| C | LYS118 | |
| G | LYS118 | |
| F | LYS31 | |
| F | LYS91 |
| 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 | LYS13 | |
| F | SER47 | |
| C | LYS15 | |
| C | LYS119 | |
| G | LYS13 | |
| G | LYS15 | |
| G | LYS119 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphotyrosine => ECO:0000250|UniProtKB:P62805 |
| Chain | Residue | Details |
| B | TYR51 | |
| B | TYR88 | |
| F | TYR51 | |
| F | TYR88 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-glutaryllysine; alternate => ECO:0000250|UniProtKB:P62805 |
| Chain | Residue | Details |
| B | LYS59 | |
| E | LYS64 | |
| F | LYS59 | |
| A | LYS27 | |
| A | LYS36 | |
| A | LYS64 | |
| E | LYS18 | |
| E | LYS23 | |
| E | LYS27 | |
| E | LYS36 |
| site_id | SWS_FT_FI11 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-succinyllysine => ECO:0000250|UniProtKB:P62805 |
| Chain | Residue | Details |
| B | LYS77 | |
| F | LYS77 |
| 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 | LYS31 | |
| F | LYS31 |
| 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 | LYS37 | |
| B | LYS91 | |
| F | LYS91 |
| site_id | SWS_FT_FI14 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphotyrosine => ECO:0000250|UniProtKB:Q71DI3 |
| Chain | Residue | Details |
| A | TYR41 | |
| E | TYR41 |
| site_id | SWS_FT_FI15 |
| Number of Residues | 4 |
| Details | MOD_RES: N6-succinyllysine; alternate => ECO:0000250|UniProtKB:P84228 |
| Chain | Residue | Details |
| A | LYS56 | |
| A | LYS79 | |
| E | LYS56 | |
| E | LYS79 |
| site_id | SWS_FT_FI16 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:Q71DI3 |
| Chain | Residue | Details |
| A | SER57 | |
| E | SER57 |
| site_id | SWS_FT_FI17 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:Q71DI3 |
| Chain | Residue | Details |
| A | THR80 | |
| A | THR107 | |
| E | THR80 | |
| E | THR107 |
| site_id | SWS_FT_FI18 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:P84243 |
| Chain | Residue | Details |
| A | SER86 | |
| E | SER86 |
| site_id | SWS_FT_FI19 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-glutaryllysine; alternate => ECO:0000250|UniProtKB:Q71DI3 |
| Chain | Residue | Details |
| A | LYS115 | |
| E | LYS115 |
| site_id | SWS_FT_FI20 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-succinyllysine; alternate => ECO:0000250|UniProtKB:Q71DI3 |
| Chain | Residue | Details |
| A | LYS122 | |
| E | LYS122 |
| site_id | SWS_FT_FI21 |
| Number of Residues | 2 |
| Details | LIPID: S-palmitoyl cysteine => ECO:0000250|UniProtKB:Q71DI3 |
| Chain | Residue | Details |
| A | CYS110 | |
| E | CYS110 |
