1M1A
LIGAND BINDING ALTERS THE STRUCTURE AND DYNAMICS OF NUCLEOSOMAL DNA
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000786 | cellular_component | nucleosome |
| A | 0003677 | molecular_function | DNA binding |
| A | 0005634 | cellular_component | nucleus |
| 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 | 0005634 | cellular_component | nucleus |
| 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 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 | 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 | PS00959 |
| Number of Residues | 9 |
| Details | HISTONE_H3_2 Histone H3 signature 2. PFqRLVREI |
| Chain | Residue | Details |
| A | PRO466-ILE474 |
| site_id | PS00046 |
| Number of Residues | 7 |
| Details | HISTONE_H2A Histone H2A signature. AGLqFPV |
| Chain | Residue | Details |
| C | ALA821-VAL827 |
| site_id | PS00357 |
| Number of Residues | 23 |
| Details | HISTONE_H2B Histone H2B signature. REIQTavRlLLpGELaKHAVSEG |
| Chain | Residue | Details |
| D | ARG1289-GLY1311 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 8 |
| Details | DNA_BIND: |
| Chain | Residue | Details |
| B | LYS16-LYS20 | |
| F | LYS216-LYS220 | |
| D | LYS1212 | |
| D | LYS1217 | |
| H | LYS1402 | |
| H | LYS1409 | |
| H | LYS1412 | |
| H | LYS1417 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:P62805 |
| Chain | Residue | Details |
| B | SER1 | |
| F | SER201 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 2 |
| Details | MOD_RES: Symmetric dimethylarginine; by PRMT5 and PRMT7; alternate => ECO:0000250|UniProtKB:P62805 |
| Chain | Residue | Details |
| B | ARG3 | |
| F | ARG203 | |
| G | LYS1009 | |
| G | LYS1095 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-lactoyllysine; alternate => ECO:0000250|UniProtKB:P62805 |
| Chain | Residue | Details |
| B | LYS5 | |
| F | LYS205 | |
| H | LYS1517 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 8 |
| Details | MOD_RES: N6-propionyllysine; alternate => ECO:0000250|UniProtKB:P62805 |
| Chain | Residue | Details |
| B | LYS8 | |
| B | LYS16 | |
| B | LYS44 | |
| B | LYS79 | |
| F | LYS208 | |
| F | LYS216 | |
| F | LYS244 | |
| F | LYS279 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 4 |
| Details | MOD_RES: N6-methyllysine; alternate => ECO:0000250|UniProtKB:P62805 |
| Chain | Residue | Details |
| B | LYS12 | |
| B | LYS20 | |
| F | LYS212 | |
| F | LYS220 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 4 |
| Details | MOD_RES: N6-succinyllysine; alternate => ECO:0000250|UniProtKB:P62805 |
| Chain | Residue | Details |
| B | LYS31 | |
| B | LYS91 | |
| F | LYS231 | |
| F | LYS291 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine; by PAK2 => ECO:0000250|UniProtKB:P62805 |
| Chain | Residue | Details |
| B | SER47 | |
| F | SER247 | |
| C | LYS815 | |
| C | LYS919 | |
| G | LYS1013 | |
| G | LYS1015 | |
| G | LYS1119 |
| 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 | TYR251 | |
| F | TYR288 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-glutaryllysine; alternate => ECO:0000250|UniProtKB:P62805 |
| Chain | Residue | Details |
| B | LYS59 | |
| F | LYS259 | |
| A | LYS436 | |
| E | LYS618 | |
| E | LYS627 | |
| E | LYS636 |
| site_id | SWS_FT_FI11 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-succinyllysine => ECO:0000250|UniProtKB:P62805 |
| Chain | Residue | Details |
| B | LYS77 | |
| F | LYS277 |
| 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 | LYS231 |
| 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 | LYS456 | |
| B | LYS91 | |
| E | LYS656 | |
| F | LYS291 |
| site_id | SWS_FT_FI14 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:P84243 |
| Chain | Residue | Details |
| A | SER457 | |
| E | SER657 |
| site_id | SWS_FT_FI15 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:P84243 |
| Chain | Residue | Details |
| A | THR480 | |
| E | THR680 |
| site_id | SWS_FT_FI16 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-glutaryllysine; alternate => ECO:0000250|UniProtKB:P84243 |
| Chain | Residue | Details |
| A | LYS515 | |
| E | LYS715 |
| site_id | SWS_FT_FI17 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-succinyllysine; alternate => ECO:0000250|UniProtKB:P84243 |
| Chain | Residue | Details |
| A | LYS522 | |
| E | LYS722 |
