4GU1
Crystal structure of LSD2
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 |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 30 |
| Details | BINDING SITE FOR RESIDUE FAD A 901 |
| Chain | Residue |
| A | ILE388 |
| A | GLY419 |
| A | ARG420 |
| A | ARG434 |
| A | GLY435 |
| A | ALA436 |
| A | GLN437 |
| A | ILE438 |
| A | PRO597 |
| A | VAL598 |
| A | THR626 |
| A | GLY389 |
| A | VAL627 |
| A | PRO628 |
| A | TRP757 |
| A | TRP762 |
| A | ALA766 |
| A | GLY794 |
| A | GLU795 |
| A | GLN803 |
| A | THR804 |
| A | VAL805 |
| A | GLY391 |
| B | LEU40 |
| A | PRO392 |
| A | ALA393 |
| A | LEU411 |
| A | GLU412 |
| A | ALA413 |
| A | LYS414 |
| site_id | AC2 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE CL A 902 |
| Chain | Residue |
| A | GLU54 |
| A | HIS84 |
| A | LYS128 |
| site_id | AC3 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE CL A 903 |
| Chain | Residue |
| A | LYS165 |
| A | LYS330 |
| site_id | AC4 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE NA A 904 |
| Chain | Residue |
| A | TYR603 |
| A | GLY605 |
| site_id | AC5 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN A 905 |
| Chain | Residue |
| A | CYS53 |
| A | CYS58 |
| A | HIS84 |
| A | HIS90 |
| site_id | AC6 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE ZN A 906 |
| Chain | Residue |
| A | CYS65 |
| A | ALA67 |
| A | CYS73 |
| A | CYS92 |
| A | CYS95 |
| site_id | AC7 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN A 907 |
| Chain | Residue |
| A | CYS142 |
| A | CYS147 |
| A | CYS169 |
| A | CYS185 |
| site_id | AC8 |
| Number of Residues | 27 |
| Details | BINDING SITE FOR RESIDUE FAD B 901 |
| Chain | Residue |
| B | ILE388 |
| B | GLY391 |
| B | PRO392 |
| B | ALA393 |
| B | LEU411 |
| B | GLU412 |
| B | ALA413 |
| B | LYS414 |
| B | GLY419 |
| B | ARG420 |
| B | ARG434 |
| B | GLY435 |
| B | ALA436 |
| B | GLN437 |
| B | ILE438 |
| B | PRO597 |
| B | VAL598 |
| B | VAL627 |
| B | PRO628 |
| B | TRP757 |
| B | TRP762 |
| B | ALA766 |
| B | GLY794 |
| B | GLU795 |
| B | GLN803 |
| B | THR804 |
| B | VAL805 |
| site_id | AC9 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE CL B 902 |
| Chain | Residue |
| B | GLU54 |
| B | HIS84 |
| B | LYS128 |
| site_id | BC1 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE CL B 903 |
| Chain | Residue |
| B | LYS165 |
| B | LYS330 |
| site_id | BC2 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE NA B 904 |
| Chain | Residue |
| B | TYR603 |
| B | GLY605 |
| site_id | BC3 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN B 905 |
| Chain | Residue |
| B | CYS53 |
| B | CYS58 |
| B | HIS84 |
| B | HIS90 |
| site_id | BC4 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE ZN B 906 |
| Chain | Residue |
| B | CYS65 |
| B | ALA67 |
| B | CYS73 |
| B | CYS92 |
| B | CYS95 |
| site_id | BC5 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN B 907 |
| Chain | Residue |
| B | CYS142 |
| B | CYS147 |
| B | CYS169 |
| B | CYS185 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 120 |
| Details | ZN_FING: CW-type => ECO:0000255|PROSITE-ProRule:PRU00454 |
| Chain | Residue | Details |
| A | ASP133-VAL193 | |
| B | ASP133-VAL193 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 20 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:23260659, ECO:0000269|PubMed:23266887, ECO:0000269|PubMed:23357850, ECO:0000269|PubMed:30970244, ECO:0007744|PDB:4FWE, ECO:0007744|PDB:4FWF, ECO:0007744|PDB:4FWJ, ECO:0007744|PDB:4GU0, ECO:0007744|PDB:4GU1, ECO:0007744|PDB:4GUR, ECO:0007744|PDB:4GUS, ECO:0007744|PDB:4GUT, ECO:0007744|PDB:4GUU, ECO:0007744|PDB:4HSU, ECO:0007744|PDB:6R1U, ECO:0007744|PDB:6R25 |
| Chain | Residue | Details |
| A | CYS53 | |
| A | GLN803 | |
| B | CYS53 | |
| B | CYS58 | |
| B | CYS65 | |
| B | CYS73 | |
| B | HIS84 | |
| B | HIS90 | |
| B | CYS92 | |
| B | CYS95 | |
| B | VAL598 | |
| A | CYS58 | |
| B | GLN803 | |
| A | CYS65 | |
| A | CYS73 | |
| A | HIS84 | |
| A | HIS90 | |
| A | CYS92 | |
| A | CYS95 | |
| A | VAL598 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 8 |
| Details | BINDING: BINDING => ECO:0000255|PROSITE-ProRule:PRU00454, ECO:0000269|PubMed:23260659, ECO:0000269|PubMed:23266887, ECO:0000269|PubMed:23357850, ECO:0000269|PubMed:30970244, ECO:0007744|PDB:4FWE, ECO:0007744|PDB:4FWF, ECO:0007744|PDB:4FWJ, ECO:0007744|PDB:4GU0, ECO:0007744|PDB:4GU1, ECO:0007744|PDB:4GUR, ECO:0007744|PDB:4GUS, ECO:0007744|PDB:4GUT, ECO:0007744|PDB:4GUU, ECO:0007744|PDB:4HSU, ECO:0007744|PDB:6R1U, ECO:0007744|PDB:6R25 |
| Chain | Residue | Details |
| A | CYS142 | |
| A | CYS147 | |
| A | CYS169 | |
| A | CYS185 | |
| B | CYS142 | |
| B | CYS147 | |
| B | CYS169 | |
| B | CYS185 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 2 |
| Details | BINDING: BINDING => ECO:0000255, ECO:0000269|PubMed:23260659, ECO:0000269|PubMed:23266887, ECO:0000269|PubMed:23357850, ECO:0000269|PubMed:30970244, ECO:0007744|PDB:4FWE, ECO:0007744|PDB:4FWF, ECO:0007744|PDB:4FWJ, ECO:0007744|PDB:4GU0, ECO:0007744|PDB:4GU1, ECO:0007744|PDB:4GUR, ECO:0007744|PDB:4GUS, ECO:0007744|PDB:4GUT, ECO:0007744|PDB:4GUU, ECO:0007744|PDB:4HSU, ECO:0007744|PDB:6R1U, ECO:0007744|PDB:6R25 |
| Chain | Residue | Details |
| A | LYS383 | |
| B | LYS383 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 2 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:23260659, ECO:0000269|PubMed:23266887, ECO:0000269|PubMed:30970244, ECO:0007744|PDB:4FWE, ECO:0007744|PDB:4FWF, ECO:0007744|PDB:4FWJ, ECO:0007744|PDB:4GU1, ECO:0007744|PDB:4GUS, ECO:0007744|PDB:4GUT, ECO:0007744|PDB:4GUU, ECO:0007744|PDB:6R1U, ECO:0007744|PDB:6R25 |
| Chain | Residue | Details |
| A | GLU795 | |
| B | GLU795 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:23186163, ECO:0007744|PubMed:24275569 |
| Chain | Residue | Details |
| A | SER247 | |
| B | SER247 |
