4GU0
Crystal structure of LSD2 with H3
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000786 | cellular_component | nucleosome |
| A | 0003682 | molecular_function | chromatin binding |
| A | 0005515 | molecular_function | protein binding |
| A | 0005634 | cellular_component | nucleus |
| A | 0005654 | cellular_component | nucleoplasm |
| A | 0005694 | cellular_component | chromosome |
| A | 0006325 | biological_process | chromatin organization |
| A | 0006338 | biological_process | chromatin remodeling |
| A | 0008270 | molecular_function | zinc ion binding |
| A | 0016491 | molecular_function | oxidoreductase activity |
| A | 0032452 | molecular_function | histone demethylase activity |
| A | 0032453 | molecular_function | histone H3K4 demethylase activity |
| A | 0042393 | molecular_function | histone binding |
| A | 0044726 | biological_process | epigenetic programing of female pronucleus |
| A | 0046872 | molecular_function | metal ion binding |
| A | 0050660 | molecular_function | flavin adenine dinucleotide binding |
| A | 0071514 | biological_process | genomic imprinting |
| A | 0071949 | molecular_function | FAD binding |
| A | 0140682 | molecular_function | FAD-dependent H3K4me/H3K4me3 demethylase activity |
| B | 0000786 | cellular_component | nucleosome |
| B | 0003682 | molecular_function | chromatin binding |
| B | 0005515 | molecular_function | protein binding |
| B | 0005634 | cellular_component | nucleus |
| B | 0005654 | cellular_component | nucleoplasm |
| B | 0005694 | cellular_component | chromosome |
| B | 0006325 | biological_process | chromatin organization |
| B | 0006338 | biological_process | chromatin remodeling |
| B | 0008270 | molecular_function | zinc ion binding |
| B | 0016491 | molecular_function | oxidoreductase activity |
| B | 0032452 | molecular_function | histone demethylase activity |
| B | 0032453 | molecular_function | histone H3K4 demethylase activity |
| B | 0042393 | molecular_function | histone binding |
| B | 0044726 | biological_process | epigenetic programing of female pronucleus |
| B | 0046872 | molecular_function | metal ion binding |
| B | 0050660 | molecular_function | flavin adenine dinucleotide binding |
| B | 0071514 | biological_process | genomic imprinting |
| B | 0071949 | molecular_function | FAD binding |
| B | 0140682 | molecular_function | FAD-dependent H3K4me/H3K4me3 demethylase activity |
| C | 0000786 | cellular_component | nucleosome |
| C | 0003682 | molecular_function | chromatin binding |
| C | 0005515 | molecular_function | protein binding |
| C | 0005634 | cellular_component | nucleus |
| C | 0005654 | cellular_component | nucleoplasm |
| C | 0005694 | cellular_component | chromosome |
| C | 0006325 | biological_process | chromatin organization |
| C | 0006338 | biological_process | chromatin remodeling |
| C | 0008270 | molecular_function | zinc ion binding |
| C | 0016491 | molecular_function | oxidoreductase activity |
| C | 0032452 | molecular_function | histone demethylase activity |
| C | 0032453 | molecular_function | histone H3K4 demethylase activity |
| C | 0042393 | molecular_function | histone binding |
| C | 0044726 | biological_process | epigenetic programing of female pronucleus |
| C | 0046872 | molecular_function | metal ion binding |
| C | 0050660 | molecular_function | flavin adenine dinucleotide binding |
| C | 0071514 | biological_process | genomic imprinting |
| C | 0071949 | molecular_function | FAD binding |
| C | 0140682 | molecular_function | FAD-dependent H3K4me/H3K4me3 demethylase activity |
| D | 0000786 | cellular_component | nucleosome |
| D | 0003682 | molecular_function | chromatin binding |
| D | 0005515 | molecular_function | protein binding |
| D | 0005634 | cellular_component | nucleus |
| D | 0005654 | cellular_component | nucleoplasm |
| D | 0005694 | cellular_component | chromosome |
| D | 0006325 | biological_process | chromatin organization |
| D | 0006338 | biological_process | chromatin remodeling |
| D | 0008270 | molecular_function | zinc ion binding |
| D | 0016491 | molecular_function | oxidoreductase activity |
| D | 0032452 | molecular_function | histone demethylase activity |
| D | 0032453 | molecular_function | histone H3K4 demethylase activity |
| D | 0042393 | molecular_function | histone binding |
| D | 0044726 | biological_process | epigenetic programing of female pronucleus |
| D | 0046872 | molecular_function | metal ion binding |
| D | 0050660 | molecular_function | flavin adenine dinucleotide binding |
| D | 0071514 | biological_process | genomic imprinting |
| D | 0071949 | molecular_function | FAD binding |
| D | 0140682 | molecular_function | FAD-dependent H3K4me/H3K4me3 demethylase activity |
| E | 0000786 | cellular_component | nucleosome |
| E | 0003677 | molecular_function | DNA binding |
| E | 0030527 | molecular_function | structural constituent of chromatin |
| F | 0000786 | cellular_component | nucleosome |
| F | 0003677 | molecular_function | DNA binding |
| F | 0030527 | molecular_function | structural constituent of chromatin |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 28 |
| Details | BINDING SITE FOR RESIDUE FAD A 901 |
| Chain | Residue |
| A | ILE388 |
| A | ARG420 |
| A | ARG434 |
| A | GLY435 |
| A | ALA436 |
| A | GLN437 |
| A | ILE438 |
| A | PRO597 |
| A | VAL598 |
| A | VAL627 |
| A | PRO628 |
| A | GLY389 |
| A | TRP757 |
| A | TRP762 |
| A | GLY794 |
| A | GLU795 |
| A | GLN803 |
| A | THR804 |
| A | VAL805 |
| A | ALA808 |
| A | HOH1005 |
| A | PRO392 |
| A | ALA393 |
| A | LEU411 |
| A | GLU412 |
| A | ALA413 |
| A | LYS414 |
| A | GLY419 |
| site_id | AC2 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN A 902 |
| Chain | Residue |
| A | CYS53 |
| A | CYS58 |
| A | HIS84 |
| A | HIS90 |
| site_id | AC3 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN A 903 |
| Chain | Residue |
| A | CYS65 |
| A | CYS73 |
| A | CYS92 |
| A | CYS95 |
| site_id | AC4 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN A 904 |
| Chain | Residue |
| A | CYS142 |
| A | CYS147 |
| A | CYS169 |
| A | CYS185 |
| site_id | AC5 |
| Number of Residues | 27 |
| Details | BINDING SITE FOR RESIDUE FAD B 901 |
| Chain | Residue |
| B | ILE388 |
| B | GLY389 |
| B | PRO392 |
| B | ALA393 |
| B | LEU411 |
| B | GLU412 |
| B | ALA413 |
| B | LYS414 |
| B | GLY419 |
| B | ARG420 |
| B | ARG434 |
| B | GLY435 |
| B | ALA436 |
| B | ILE438 |
| B | PRO597 |
| B | VAL598 |
| B | VAL627 |
| B | PRO628 |
| B | TRP757 |
| B | TRP762 |
| B | GLY794 |
| B | GLU795 |
| B | GLN803 |
| B | THR804 |
| B | VAL805 |
| B | ALA808 |
| B | HOH1004 |
| site_id | AC6 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN B 902 |
| Chain | Residue |
| B | CYS53 |
| B | CYS58 |
| B | HIS84 |
| B | HIS90 |
| site_id | AC7 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN B 903 |
| Chain | Residue |
| B | CYS65 |
| B | CYS73 |
| B | CYS92 |
| B | CYS95 |
| site_id | AC8 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN B 904 |
| Chain | Residue |
| B | CYS142 |
| B | CYS147 |
| B | CYS169 |
| B | CYS185 |
| site_id | AC9 |
| Number of Residues | 27 |
| Details | BINDING SITE FOR RESIDUE FAD C 901 |
| Chain | Residue |
| C | GLY794 |
| C | GLU795 |
| C | GLN803 |
| C | THR804 |
| C | VAL805 |
| C | ALA808 |
| C | HOH1109 |
| C | GLY389 |
| C | GLY391 |
| C | PRO392 |
| C | ALA393 |
| C | LEU411 |
| C | GLU412 |
| C | ALA413 |
| C | LYS414 |
| C | GLY419 |
| C | ARG420 |
| C | ARG434 |
| C | GLY435 |
| C | ALA436 |
| C | GLN437 |
| C | ILE438 |
| C | PRO597 |
| C | VAL598 |
| C | VAL627 |
| C | TRP757 |
| C | TRP762 |
| site_id | BC1 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN C 902 |
| Chain | Residue |
| C | CYS53 |
| C | CYS58 |
| C | HIS84 |
| C | HIS90 |
| site_id | BC2 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN C 903 |
| Chain | Residue |
| C | CYS65 |
| C | CYS73 |
| C | CYS92 |
| C | CYS95 |
| site_id | BC3 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN C 904 |
| Chain | Residue |
| C | CYS142 |
| C | CYS147 |
| C | CYS169 |
| C | CYS185 |
| site_id | BC4 |
| Number of Residues | 29 |
| Details | BINDING SITE FOR RESIDUE FAD D 901 |
| Chain | Residue |
| D | GLY389 |
| D | ALA390 |
| D | GLY391 |
| D | PRO392 |
| D | ALA393 |
| D | LEU411 |
| D | GLU412 |
| D | ALA413 |
| D | LYS414 |
| D | GLY419 |
| D | ARG420 |
| D | ARG434 |
| D | GLY435 |
| D | ALA436 |
| D | GLN437 |
| D | ILE438 |
| D | PRO597 |
| D | VAL598 |
| D | VAL627 |
| D | PRO628 |
| D | TRP757 |
| D | TRP762 |
| D | GLY794 |
| D | GLU795 |
| D | GLN803 |
| D | THR804 |
| D | VAL805 |
| D | ALA808 |
| D | HOH1012 |
| site_id | BC5 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN D 902 |
| Chain | Residue |
| D | CYS53 |
| D | CYS58 |
| D | HIS84 |
| D | HIS90 |
| site_id | BC6 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN D 903 |
| Chain | Residue |
| D | CYS65 |
| D | CYS73 |
| D | CYS92 |
| D | CYS95 |
| site_id | BC7 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN D 904 |
| Chain | Residue |
| D | CYS142 |
| D | CYS147 |
| D | CYS169 |
| D | CYS185 |
Functional Information from PROSITE/UniProt
| site_id | PS00322 |
| Number of Residues | 7 |
| Details | HISTONE_H3_1 Histone H3 signature 1. KAPRKQL |
| Chain | Residue | Details |
| E | LYS14-LEU20 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 2 |
| Details | MOD_RES: Citrulline; alternate => ECO:0000269|PubMed:16567635 |
| Chain | Residue | Details |
| E | ARG2 | |
| F | ARG2 | |
| C | ASP133-VAL193 | |
| D | ASP133-VAL193 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphothreonine; by HASPIN and VRK1 => ECO:0000269|PubMed:15681610, ECO:0000269|PubMed:16185088, ECO:0000269|PubMed:31527692 |
| Chain | Residue | Details |
| E | THR3 | |
| A | GLN803 | |
| B | CYS53 | |
| B | CYS58 | |
| B | CYS65 | |
| B | CYS73 | |
| B | HIS84 | |
| B | HIS90 | |
| B | CYS92 | |
| B | CYS95 | |
| B | VAL598 | |
| F | THR3 | |
| B | GLN803 | |
| C | CYS53 | |
| C | CYS58 | |
| C | CYS65 | |
| C | CYS73 | |
| C | HIS84 | |
| C | HIS90 | |
| C | CYS92 | |
| C | CYS95 | |
| C | VAL598 | |
| A | CYS65 | |
| C | GLN803 | |
| D | CYS53 | |
| D | CYS58 | |
| D | CYS65 | |
| D | CYS73 | |
| D | HIS84 | |
| D | HIS90 | |
| D | CYS92 | |
| D | CYS95 | |
| D | VAL598 | |
| A | CYS73 | |
| D | GLN803 | |
| A | HIS84 | |
| A | HIS90 | |
| A | CYS92 | |
| A | CYS95 | |
| A | VAL598 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-methyllysine; alternate => ECO:0000269|PubMed:16185088, ECO:0000269|PubMed:16267050, ECO:0000269|PubMed:16457588, ECO:0000269|PubMed:17194708 |
| Chain | Residue | Details |
| E | MET4 | |
| C | CYS147 | |
| C | CYS169 | |
| C | CYS185 | |
| D | CYS142 | |
| D | CYS147 | |
| D | CYS169 | |
| D | CYS185 | |
| F | MET4 | |
| A | CYS169 | |
| A | CYS185 | |
| B | CYS142 | |
| B | CYS147 | |
| B | CYS169 | |
| B | CYS185 | |
| C | CYS142 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 2 |
| Details | MOD_RES: 5-glutamyl serotonin; alternate => ECO:0000269|PubMed:30867594 |
| Chain | Residue | Details |
| E | GLN5 | |
| F | GLN5 | |
| C | LYS383 | |
| D | LYS383 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphothreonine; by PKC => ECO:0000269|PubMed:20228790 |
| Chain | Residue | Details |
| E | THR6 | |
| F | THR6 | |
| C | GLU795 | |
| D | GLU795 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 2 |
| Details | MOD_RES: Symmetric dimethylarginine; by PRMT5; alternate => ECO:0000250|UniProtKB:P84244 |
| Chain | Residue | Details |
| E | ARG8 | |
| F | ARG8 | |
| C | SER247 | |
| D | SER247 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-methyllysine; alternate => ECO:0000269|PubMed:11242053, ECO:0000269|PubMed:16185088, ECO:0000269|PubMed:16267050, ECO:0000269|PubMed:16457588, ECO:0000269|PubMed:17194708, ECO:0000269|PubMed:7309716 |
| Chain | Residue | Details |
| E | LYS9 | |
| F | LYS9 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine; alternate; by AURKB, AURKC, RPS6KA3, RPS6KA4 and RPS6KA5 => ECO:0000269|PubMed:10464286, ECO:0000269|PubMed:11856369, ECO:0000269|PubMed:12560483, ECO:0000269|PubMed:15681610, ECO:0000269|PubMed:15851689, ECO:0000269|PubMed:16185088 |
| Chain | Residue | Details |
| E | SER10 | |
| F | SER10 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphothreonine; by PKC => ECO:0000269|PubMed:12560483, ECO:0000269|PubMed:18066052, ECO:0000269|PubMed:22901803 |
| Chain | Residue | Details |
| E | THR11 | |
| F | THR11 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-succinyllysine; alternate => ECO:0000269|PubMed:22389435 |
| Chain | Residue | Details |
| E | LYS14 | |
| F | LYS14 |
| site_id | SWS_FT_FI11 |
| Number of Residues | 2 |
| Details | MOD_RES: Citrulline; alternate => ECO:0000269|PubMed:15345777, ECO:0000269|PubMed:16497732, ECO:0000269|PubMed:16567635 |
| Chain | Residue | Details |
| E | ARG17 | |
| F | ARG17 |
| site_id | SWS_FT_FI12 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-methyllysine; alternate => ECO:0000269|PubMed:16267050, ECO:0000269|PubMed:17194708 |
| Chain | Residue | Details |
| E | LYS18 | |
| F | LYS18 |
| site_id | SWS_FT_FI13 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-methyllysine; alternate => ECO:0000269|PubMed:17194708 |
| Chain | Residue | Details |
| E | LYS23 | |
| F | LYS23 |
| site_id | SWS_FT_FI14 |
| Number of Residues | 2 |
| Details | MOD_RES: Citrulline => ECO:0000269|PubMed:16567635 |
| Chain | Residue | Details |
| E | ARG26 | |
| F | ARG26 |
| site_id | SWS_FT_FI15 |
| Number of Residues | 2 |
| Details | LIPID: N6-decanoyllysine => ECO:0000269|PubMed:35939806 |
| Chain | Residue | Details |
| E | LYS18 | |
| F | LYS18 |
