3SMR
Crystal structure of human WD repeat domain 5 with compound
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000122 | biological_process | negative regulation of transcription by RNA polymerase II |
| A | 0000123 | cellular_component | histone acetyltransferase complex |
| A | 0005515 | molecular_function | protein binding |
| A | 0005634 | cellular_component | nucleus |
| A | 0005654 | cellular_component | nucleoplasm |
| A | 0006325 | biological_process | chromatin organization |
| A | 0006355 | biological_process | regulation of DNA-templated transcription |
| A | 0006357 | biological_process | regulation of transcription by RNA polymerase II |
| A | 0035097 | cellular_component | histone methyltransferase complex |
| A | 0042393 | molecular_function | histone binding |
| A | 0042800 | molecular_function | histone H3K4 methyltransferase activity |
| A | 0044545 | cellular_component | NSL complex |
| A | 0044665 | cellular_component | MLL1/2 complex |
| A | 0044666 | cellular_component | MLL3/4 complex |
| A | 0045815 | biological_process | transcription initiation-coupled chromatin remodeling |
| A | 0045893 | biological_process | positive regulation of DNA-templated transcription |
| A | 0045995 | biological_process | regulation of embryonic development |
| A | 0048188 | cellular_component | Set1C/COMPASS complex |
| A | 0051302 | biological_process | regulation of cell division |
| A | 0051726 | biological_process | regulation of cell cycle |
| A | 0071339 | cellular_component | MLL1 complex |
| A | 0072686 | cellular_component | mitotic spindle |
| A | 0090043 | biological_process | regulation of tubulin deacetylation |
| A | 0140004 | molecular_function | histone H3Q5ser reader activity |
| A | 0140109 | molecular_function | histone H3K4me1 reader activity |
| A | 0140672 | cellular_component | ATAC complex |
| B | 0000122 | biological_process | negative regulation of transcription by RNA polymerase II |
| B | 0000123 | cellular_component | histone acetyltransferase complex |
| B | 0005515 | molecular_function | protein binding |
| B | 0005634 | cellular_component | nucleus |
| B | 0005654 | cellular_component | nucleoplasm |
| B | 0006325 | biological_process | chromatin organization |
| B | 0006355 | biological_process | regulation of DNA-templated transcription |
| B | 0006357 | biological_process | regulation of transcription by RNA polymerase II |
| B | 0035097 | cellular_component | histone methyltransferase complex |
| B | 0042393 | molecular_function | histone binding |
| B | 0042800 | molecular_function | histone H3K4 methyltransferase activity |
| B | 0044545 | cellular_component | NSL complex |
| B | 0044665 | cellular_component | MLL1/2 complex |
| B | 0044666 | cellular_component | MLL3/4 complex |
| B | 0045815 | biological_process | transcription initiation-coupled chromatin remodeling |
| B | 0045893 | biological_process | positive regulation of DNA-templated transcription |
| B | 0045995 | biological_process | regulation of embryonic development |
| B | 0048188 | cellular_component | Set1C/COMPASS complex |
| B | 0051302 | biological_process | regulation of cell division |
| B | 0051726 | biological_process | regulation of cell cycle |
| B | 0071339 | cellular_component | MLL1 complex |
| B | 0072686 | cellular_component | mitotic spindle |
| B | 0090043 | biological_process | regulation of tubulin deacetylation |
| B | 0140004 | molecular_function | histone H3Q5ser reader activity |
| B | 0140109 | molecular_function | histone H3K4me1 reader activity |
| B | 0140672 | cellular_component | ATAC complex |
| C | 0000122 | biological_process | negative regulation of transcription by RNA polymerase II |
| C | 0000123 | cellular_component | histone acetyltransferase complex |
| C | 0005515 | molecular_function | protein binding |
| C | 0005634 | cellular_component | nucleus |
| C | 0005654 | cellular_component | nucleoplasm |
| C | 0006325 | biological_process | chromatin organization |
| C | 0006355 | biological_process | regulation of DNA-templated transcription |
| C | 0006357 | biological_process | regulation of transcription by RNA polymerase II |
| C | 0035097 | cellular_component | histone methyltransferase complex |
| C | 0042393 | molecular_function | histone binding |
| C | 0042800 | molecular_function | histone H3K4 methyltransferase activity |
| C | 0044545 | cellular_component | NSL complex |
| C | 0044665 | cellular_component | MLL1/2 complex |
| C | 0044666 | cellular_component | MLL3/4 complex |
| C | 0045815 | biological_process | transcription initiation-coupled chromatin remodeling |
| C | 0045893 | biological_process | positive regulation of DNA-templated transcription |
| C | 0045995 | biological_process | regulation of embryonic development |
| C | 0048188 | cellular_component | Set1C/COMPASS complex |
| C | 0051302 | biological_process | regulation of cell division |
| C | 0051726 | biological_process | regulation of cell cycle |
| C | 0071339 | cellular_component | MLL1 complex |
| C | 0072686 | cellular_component | mitotic spindle |
| C | 0090043 | biological_process | regulation of tubulin deacetylation |
| C | 0140004 | molecular_function | histone H3Q5ser reader activity |
| C | 0140109 | molecular_function | histone H3K4me1 reader activity |
| C | 0140672 | cellular_component | ATAC complex |
| D | 0000122 | biological_process | negative regulation of transcription by RNA polymerase II |
| D | 0000123 | cellular_component | histone acetyltransferase complex |
| D | 0005515 | molecular_function | protein binding |
| D | 0005634 | cellular_component | nucleus |
| D | 0005654 | cellular_component | nucleoplasm |
| D | 0006325 | biological_process | chromatin organization |
| D | 0006355 | biological_process | regulation of DNA-templated transcription |
| D | 0006357 | biological_process | regulation of transcription by RNA polymerase II |
| D | 0035097 | cellular_component | histone methyltransferase complex |
| D | 0042393 | molecular_function | histone binding |
| D | 0042800 | molecular_function | histone H3K4 methyltransferase activity |
| D | 0044545 | cellular_component | NSL complex |
| D | 0044665 | cellular_component | MLL1/2 complex |
| D | 0044666 | cellular_component | MLL3/4 complex |
| D | 0045815 | biological_process | transcription initiation-coupled chromatin remodeling |
| D | 0045893 | biological_process | positive regulation of DNA-templated transcription |
| D | 0045995 | biological_process | regulation of embryonic development |
| D | 0048188 | cellular_component | Set1C/COMPASS complex |
| D | 0051302 | biological_process | regulation of cell division |
| D | 0051726 | biological_process | regulation of cell cycle |
| D | 0071339 | cellular_component | MLL1 complex |
| D | 0072686 | cellular_component | mitotic spindle |
| D | 0090043 | biological_process | regulation of tubulin deacetylation |
| D | 0140004 | molecular_function | histone H3Q5ser reader activity |
| D | 0140109 | molecular_function | histone H3K4me1 reader activity |
| D | 0140672 | cellular_component | ATAC complex |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE NP7 A 1000 |
| Chain | Residue |
| A | SER49 |
| A | CYS261 |
| A | HOH576 |
| A | HOH647 |
| A | SER50 |
| A | ILE90 |
| A | SER91 |
| A | ASP92 |
| A | PHE133 |
| A | PRO173 |
| A | SER175 |
| A | TYR191 |
| site_id | AC2 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EDO A 2002 |
| Chain | Residue |
| A | PRO55 |
| A | TRP95 |
| A | SER96 |
| A | SER97 |
| A | PHE137 |
| A | EDO2003 |
| site_id | AC3 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EDO A 2003 |
| Chain | Residue |
| A | ASN136 |
| A | HIS178 |
| A | LYS221 |
| A | HOH522 |
| A | HOH616 |
| A | EDO2002 |
| site_id | AC4 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO A 2004 |
| Chain | Residue |
| A | LEU164 |
| A | LYS165 |
| A | THR200 |
| A | ALA201 |
| site_id | AC5 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO A 2013 |
| Chain | Residue |
| A | LYS165 |
| A | ALA201 |
| A | SER202 |
| B | HIS44 |
| B | HOH560 |
| site_id | AC6 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE EDO A 2014 |
| Chain | Residue |
| A | TRP241 |
| A | HOH581 |
| site_id | AC7 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO A 2015 |
| Chain | Residue |
| A | TYR260 |
| A | ASP302 |
| A | LEU321 |
| A | GLU322 |
| site_id | AC8 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE EDO A 2018 |
| Chain | Residue |
| A | ASP199 |
| A | SER202 |
| A | LEU206 |
| B | THR301 |
| B | ASP324 |
| B | THR326 |
| B | LYS328 |
| site_id | AC9 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE EDO A 2020 |
| Chain | Residue |
| A | LYS250 |
| A | GLN289 |
| site_id | BC1 |
| Number of Residues | 15 |
| Details | BINDING SITE FOR RESIDUE NP7 B 1000 |
| Chain | Residue |
| B | SER49 |
| B | SER50 |
| B | ILE90 |
| B | SER91 |
| B | ASP92 |
| B | ASP107 |
| B | PHE133 |
| B | SER175 |
| B | TYR191 |
| B | CYS261 |
| B | ILE305 |
| B | HOH517 |
| B | HOH540 |
| B | HOH611 |
| B | HOH692 |
| site_id | BC2 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO B 2000 |
| Chain | Residue |
| B | TYR228 |
| B | LYS250 |
| B | GLN289 |
| site_id | BC3 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO B 2001 |
| Chain | Residue |
| B | ASP98 |
| B | ASN100 |
| C | LYS38 |
| site_id | BC4 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO B 2005 |
| Chain | Residue |
| B | TRP95 |
| B | SER97 |
| B | PHE137 |
| B | ASN138 |
| B | EDO2022 |
| site_id | BC5 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO B 2006 |
| Chain | Residue |
| B | LYS165 |
| B | THR200 |
| B | ALA201 |
| site_id | BC6 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO B 2007 |
| Chain | Residue |
| B | VAL31 |
| B | GLY271 |
| B | LYS272 |
| B | TRP273 |
| B | ASN287 |
| site_id | BC7 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO B 2022 |
| Chain | Residue |
| B | SER97 |
| B | HOH593 |
| B | EDO2005 |
| C | ASP76 |
| site_id | BC8 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE NP7 C 1000 |
| Chain | Residue |
| C | SER49 |
| C | SER50 |
| C | ILE90 |
| C | SER91 |
| C | ASP92 |
| C | PHE133 |
| C | PRO173 |
| C | SER175 |
| C | TYR191 |
| C | CYS261 |
| C | ILE305 |
| C | HOH660 |
| site_id | BC9 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO C 2008 |
| Chain | Residue |
| C | GLY271 |
| C | LYS272 |
| C | ASN287 |
| C | VAL31 |
| site_id | CC1 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO C 2009 |
| Chain | Residue |
| C | TYR260 |
| C | ASP302 |
| C | GLU322 |
| site_id | CC2 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EDO C 2010 |
| Chain | Residue |
| C | THR40 |
| C | THR301 |
| C | ASP324 |
| C | THR326 |
| C | LYS328 |
| D | LEU206 |
| site_id | CC3 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO C 2017 |
| Chain | Residue |
| C | PHE39 |
| C | ALA74 |
| C | TYR75 |
| C | LEU329 |
| site_id | CC4 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO C 2021 |
| Chain | Residue |
| C | TYR228 |
| C | LYS250 |
| C | GLN289 |
| C | HOH595 |
| site_id | CC5 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE NP7 D 1000 |
| Chain | Residue |
| D | SER49 |
| D | SER50 |
| D | ILE90 |
| D | SER91 |
| D | ASP92 |
| D | PHE133 |
| D | SER175 |
| D | TYR191 |
| D | CYS261 |
| D | ILE305 |
| D | HOH596 |
| D | HOH636 |
| D | HOH680 |
| site_id | CC6 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO D 2011 |
| Chain | Residue |
| D | LYS165 |
| D | THR200 |
| D | ALA201 |
| site_id | CC7 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO D 2012 |
| Chain | Residue |
| D | TYR228 |
| D | LYS250 |
| D | GLN289 |
| D | HOH602 |
| site_id | CC8 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO D 2016 |
| Chain | Residue |
| D | PHE39 |
| D | ALA74 |
| D | TYR75 |
| D | ILE315 |
| D | LEU329 |
| site_id | CC9 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EDO D 2019 |
| Chain | Residue |
| C | LEU206 |
| D | THR40 |
| D | THR301 |
| D | ASP324 |
| D | THR326 |
| D | LYS328 |
Functional Information from PROSITE/UniProt
| site_id | PS00678 |
| Number of Residues | 15 |
| Details | WD_REPEATS_1 Trp-Asp (WD) repeats signature. LVSAsdDkTLKIWDV |
| Chain | Residue | Details |
| A | LEU102-VAL116 | |
| A | ILE144-VAL158 | |
| A | ILE186-THR200 | |
| A | ILE274-LEU288 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 156 |
| Details | Repeat: {"description":"WD 1"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 164 |
| Details | Repeat: {"description":"WD 2"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 160 |
| Details | Repeat: {"description":"WD 3"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 156 |
| Details | Repeat: {"description":"WD 4"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 160 |
| Details | Repeat: {"description":"WD 6"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI6 |
| Number of Residues | 136 |
| Details | Repeat: {"description":"WD 7"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI7 |
| Number of Residues | 16 |
| Details | Site: {"description":"Important for interaction with histone H3"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI8 |
| Number of Residues | 4 |
| Details | Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI9 |
| Number of Residues | 8 |
| Details | Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)","evidences":[{"source":"PubMed","id":"28112733","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI10 |
| Number of Residues | 82 |
| Details | Repeat: {"description":"WD 5"} |
| Chain | Residue | Details |
