6R25
Structure of LSD2/NPAC-linker/nucleosome core particle complex: Class 3
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 |
| K | 0000786 | cellular_component | nucleosome |
| K | 0003682 | molecular_function | chromatin binding |
| K | 0005515 | molecular_function | protein binding |
| K | 0005634 | cellular_component | nucleus |
| K | 0005654 | cellular_component | nucleoplasm |
| K | 0005694 | cellular_component | chromosome |
| K | 0006325 | biological_process | chromatin organization |
| K | 0006338 | biological_process | chromatin remodeling |
| K | 0008270 | molecular_function | zinc ion binding |
| K | 0016491 | molecular_function | oxidoreductase activity |
| K | 0032452 | molecular_function | histone demethylase activity |
| K | 0032453 | molecular_function | histone H3K4 demethylase activity |
| K | 0042393 | molecular_function | histone binding |
| K | 0044726 | biological_process | epigenetic programing of female pronucleus |
| K | 0046872 | molecular_function | metal ion binding |
| K | 0050660 | molecular_function | flavin adenine dinucleotide binding |
| K | 0071514 | biological_process | genomic imprinting |
| K | 0071949 | molecular_function | FAD binding |
| K | 0140682 | molecular_function | FAD-dependent H3K4me/H3K4me3 demethylase activity |
| M | 0000786 | cellular_component | nucleosome |
| M | 0003677 | molecular_function | DNA binding |
| M | 0005515 | molecular_function | protein binding |
| M | 0005634 | cellular_component | nucleus |
| M | 0005654 | cellular_component | nucleoplasm |
| M | 0005694 | cellular_component | chromosome |
| M | 0030527 | molecular_function | structural constituent of chromatin |
| M | 0046982 | molecular_function | protein heterodimerization activity |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 32 |
| Details | binding site for residue FAD K 901 |
| Chain | Residue |
| K | ILE388 |
| K | GLY419 |
| K | ARG420 |
| K | ARG434 |
| K | GLY435 |
| K | ALA436 |
| K | ILE438 |
| K | VAL598 |
| K | VAL627 |
| K | PRO628 |
| K | TRP757 |
| K | GLY389 |
| K | TRP762 |
| K | ALA766 |
| K | GLY794 |
| K | GLU795 |
| K | GLN803 |
| K | THR804 |
| K | VAL805 |
| K | ALA808 |
| K | HOH1058 |
| K | HOH1062 |
| K | GLY391 |
| K | HOH1119 |
| K | HOH1125 |
| K | HOH1128 |
| K | PRO392 |
| K | ALA393 |
| K | LEU411 |
| K | GLU412 |
| K | ALA413 |
| K | LYS414 |
| site_id | AC2 |
| Number of Residues | 4 |
| Details | binding site for residue ZN K 902 |
| Chain | Residue |
| K | CYS53 |
| K | CYS58 |
| K | HIS84 |
| K | HIS90 |
| site_id | AC3 |
| Number of Residues | 4 |
| Details | binding site for residue ZN K 903 |
| Chain | Residue |
| K | CYS65 |
| K | CYS73 |
| K | CYS92 |
| K | CYS95 |
| site_id | AC4 |
| Number of Residues | 4 |
| Details | binding site for residue ZN K 904 |
| Chain | Residue |
| K | CYS142 |
| K | CYS147 |
| K | CYS169 |
| K | CYS185 |
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 |
| M | LYS14-LEU20 | |
| A | LYS14-LEU20 |
| site_id | PS00959 |
| Number of Residues | 9 |
| Details | HISTONE_H3_2 Histone H3 signature 2. PFqRLVREI |
| Chain | Residue | Details |
| M | PRO66-ILE74 | |
| A | PRO66-ILE74 |
| site_id | PS00357 |
| Number of Residues | 23 |
| Details | HISTONE_H2B Histone H2B signature. REIQTavRlLLpGELaKHAVSEG |
| Chain | Residue | Details |
| D | ARG89-GLY111 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 2 |
| Details | MOD_RES: Citrulline; alternate => ECO:0000250|UniProtKB:Q71DI3 |
| Chain | Residue | Details |
| M | ARG2 | |
| M | ARG17 | |
| D | LYS12 | |
| D | LYS17 | |
| H | LYS2 | |
| H | LYS9 | |
| H | LYS12 | |
| H | LYS17 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 1 |
| Details | MOD_RES: Phosphothreonine; by HASPIN => ECO:0000250|UniProtKB:Q71DI3 |
| Chain | Residue | Details |
| K | CYS65 | |
| K | CYS73 | |
| K | HIS84 | |
| K | HIS90 | |
| K | CYS92 | |
| K | CYS95 | |
| K | VAL598 | |
| K | GLN803 | |
| M | THR3 | |
| H | SER11 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 1 |
| Details | MOD_RES: N6-methyllysine; alternate => ECO:0000269|PubMed:12138181 |
| Chain | Residue | Details |
| H | SER109 | |
| G | LYS9 | |
| G | LYS95 | |
| M | MET4 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 1 |
| Details | MOD_RES: 5-glutamyl serotonin; alternate => ECO:0000250|UniProtKB:Q71DI3 |
| Chain | Residue | Details |
| G | LYS36 | |
| H | LYS117 | |
| M | GLN5 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphothreonine; by PKC => ECO:0000250|UniProtKB:Q71DI3 |
| Chain | Residue | Details |
| M | THR6 | |
| M | THR11 | |
| G | LYS74 | |
| G | LYS75 | |
| F | LYS8 | |
| F | LYS16 | |
| F | LYS44 | |
| F | LYS79 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 1 |
| Details | MOD_RES: Symmetric dimethylarginine; by PRMT5; alternate => ECO:0000250 |
| Chain | Residue | Details |
| M | ARG8 | |
| G | GLN104 | |
| F | LYS12 | |
| F | LYS20 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 1 |
| Details | MOD_RES: N6-methyllysine; alternate => ECO:0000305|PubMed:12138181 |
| Chain | Residue | Details |
| M | LYS9 | |
| G | LYS118 | |
| F | LYS31 | |
| F | LYS91 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 1 |
| Details | MOD_RES: Phosphoserine; alternate; by AURKB, AURKC, RPS6KA3, RPS6KA4 and RPS6KA5 => ECO:0000250|UniProtKB:Q71DI3 |
| Chain | Residue | Details |
| G | LYS15 | |
| G | LYS119 | |
| M | SER10 | |
| F | SER47 | |
| C | LYS15 | |
| C | LYS119 | |
| G | LYS13 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 1 |
| Details | MOD_RES: N6-lactoyllysine; alternate => ECO:0000250|UniProtKB:P84228 |
| Chain | Residue | Details |
| M | LYS14 | |
| B | TYR88 | |
| F | TYR51 | |
| F | TYR88 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 5 |
| Details | MOD_RES: N6-methyllysine; alternate => ECO:0000250|UniProtKB:Q71DI3 |
| Chain | Residue | Details |
| M | LYS27 | |
| M | LYS36 | |
| M | LYS64 | |
| E | LYS18 | |
| E | LYS23 | |
| E | LYS27 | |
| E | LYS36 | |
| E | LYS64 | |
| M | LYS18 | |
| M | LYS23 |
| site_id | SWS_FT_FI11 |
| Number of Residues | 1 |
| Details | MOD_RES: Citrulline => ECO:0000250|UniProtKB:Q71DI3 |
| Chain | Residue | Details |
| M | ARG26 | |
| F | LYS77 |
| site_id | SWS_FT_FI12 |
| Number of Residues | 1 |
| Details | MOD_RES: Phosphoserine; alternate; by AURKB, AURKC and RPS6KA5 => ECO:0000250|UniProtKB:Q71DI3 |
| Chain | Residue | Details |
| M | SER28 | |
| F | LYS31 |
| site_id | SWS_FT_FI13 |
| Number of Residues | 1 |
| Details | MOD_RES: N6-methyllysine => ECO:0000250|UniProtKB:P68431 |
| Chain | Residue | Details |
| M | LYS37 | |
| B | LYS91 | |
| F | LYS91 |
| site_id | SWS_FT_FI14 |
| Number of Residues | 1 |
| Details | MOD_RES: Phosphotyrosine => ECO:0000250|UniProtKB:Q71DI3 |
| Chain | Residue | Details |
| M | TYR41 | |
| E | TYR41 |
| site_id | SWS_FT_FI15 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-succinyllysine; alternate => ECO:0000250|UniProtKB:P84228 |
| Chain | Residue | Details |
| M | LYS56 | |
| M | LYS79 | |
| E | LYS56 | |
| E | LYS79 |
| site_id | SWS_FT_FI16 |
| Number of Residues | 1 |
| Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:Q71DI3 |
| Chain | Residue | Details |
| M | SER57 | |
| E | SER57 |
| site_id | SWS_FT_FI17 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:Q71DI3 |
| Chain | Residue | Details |
| E | THR80 | |
| E | THR107 | |
| M | THR80 | |
| M | THR107 |
| site_id | SWS_FT_FI18 |
| Number of Residues | 1 |
| Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:P84243 |
| Chain | Residue | Details |
| M | SER86 | |
| E | SER86 |
| site_id | SWS_FT_FI19 |
| Number of Residues | 1 |
| Details | MOD_RES: N6-glutaryllysine; alternate => ECO:0000250|UniProtKB:Q71DI3 |
| Chain | Residue | Details |
| M | LYS115 | |
| E | LYS115 |
| site_id | SWS_FT_FI20 |
| Number of Residues | 1 |
| Details | MOD_RES: N6-succinyllysine; alternate => ECO:0000250|UniProtKB:Q71DI3 |
| Chain | Residue | Details |
| M | LYS122 | |
| E | LYS122 |
| site_id | SWS_FT_FI21 |
| Number of Residues | 1 |
| Details | LIPID: S-palmitoyl cysteine => ECO:0000250|UniProtKB:Q71DI3 |
| Chain | Residue | Details |
| M | CYS110 | |
| E | CYS110 |
