data_2KGG # _entry.id 2KGG # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.323 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 2KGG RCSB RCSB101089 WWPDB D_1000101089 BMRB 16209 # _pdbx_database_related.content_type unspecified _pdbx_database_related.db_id 16209 _pdbx_database_related.db_name BMRB _pdbx_database_related.details . # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2KGG _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2009-03-11 _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code REL _pdbx_database_status.status_code_mr REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs REL _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Song, J.' 1 'Wang, Z.' 2 'Patel, D.J.' 3 # _citation.id primary _citation.title 'Haematopoietic malignancies caused by dysregulation of a chromatin-binding PHD finger.' _citation.journal_abbrev Nature _citation.journal_volume 459 _citation.page_first 847 _citation.page_last 851 _citation.year 2009 _citation.journal_id_ASTM NATUAS _citation.country UK _citation.journal_id_ISSN 0028-0836 _citation.journal_id_CSD 0006 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 19430464 _citation.pdbx_database_id_DOI 10.1038/nature08036 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Wang, G.G.' 1 ? primary 'Song, J.' 2 ? primary 'Wang, Z.' 3 ? primary 'Dormann, H.L.' 4 ? primary 'Casadio, F.' 5 ? primary 'Li, H.' 6 ? primary 'Luo, J.L.' 7 ? primary 'Patel, D.J.' 8 ? primary 'Allis, C.D.' 9 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer man 'Histone demethylase JARID1A' 5802.490 1 ? ? 'PHD-TYPE C-terminal ZINC FINGER' ? 2 non-polymer syn 'ZINC ION' 65.409 2 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'Jumonji/ARID domain-containing protein 1A, Retinoblastoma-binding protein 2, RBBP-2' # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code SVCAAQNCQRPCKDKVDWVQCDGGCDEWFHQVCVGVSPEMAENEDYICINCA _entity_poly.pdbx_seq_one_letter_code_can SVCAAQNCQRPCKDKVDWVQCDGGCDEWFHQVCVGVSPEMAENEDYICINCA _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 SER n 1 2 VAL n 1 3 CYS n 1 4 ALA n 1 5 ALA n 1 6 GLN n 1 7 ASN n 1 8 CYS n 1 9 GLN n 1 10 ARG n 1 11 PRO n 1 12 CYS n 1 13 LYS n 1 14 ASP n 1 15 LYS n 1 16 VAL n 1 17 ASP n 1 18 TRP n 1 19 VAL n 1 20 GLN n 1 21 CYS n 1 22 ASP n 1 23 GLY n 1 24 GLY n 1 25 CYS n 1 26 ASP n 1 27 GLU n 1 28 TRP n 1 29 PHE n 1 30 HIS n 1 31 GLN n 1 32 VAL n 1 33 CYS n 1 34 VAL n 1 35 GLY n 1 36 VAL n 1 37 SER n 1 38 PRO n 1 39 GLU n 1 40 MET n 1 41 ALA n 1 42 GLU n 1 43 ASN n 1 44 GLU n 1 45 ASP n 1 46 TYR n 1 47 ILE n 1 48 CYS n 1 49 ILE n 1 50 ASN n 1 51 CYS n 1 52 ALA n # _entity_src_gen.entity_id 1 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _entity_src_gen.pdbx_seq_type ? _entity_src_gen.pdbx_beg_seq_num ? _entity_src_gen.pdbx_end_seq_num ? _entity_src_gen.gene_src_common_name human _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene 'JARID1A, RBBP2, RBP2' _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain ? _entity_src_gen.gene_src_tissue ? _entity_src_gen.gene_src_tissue_fraction ? _entity_src_gen.gene_src_details ? _entity_src_gen.pdbx_gene_src_fragment ? _entity_src_gen.pdbx_gene_src_scientific_name 'Homo sapiens' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 9606 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc ? _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name ? _entity_src_gen.pdbx_host_org_scientific_name 'Escherichia coli' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 562 _entity_src_gen.host_org_genus ? _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain 'Rosetta 2(DE3)' _entity_src_gen.pdbx_host_org_variant ? _entity_src_gen.pdbx_host_org_cell_line ? _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type plasmid _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name pRSFDuet-1 _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code JAD1A_HUMAN _struct_ref.pdbx_db_accession P29375 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code VCAAQNCQRPCKDKVDWVQCDGGCDEWFHQVCVGVSPEMAENEDYICINCA _struct_ref.pdbx_align_begin 1609 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2KGG _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 2 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 52 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P29375 _struct_ref_seq.db_align_beg 1609 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 1659 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 2 _struct_ref_seq.pdbx_auth_seq_align_end 52 # _struct_ref_seq_dif.align_id 1 _struct_ref_seq_dif.pdbx_pdb_id_code 2KGG _struct_ref_seq_dif.mon_id SER _struct_ref_seq_dif.pdbx_pdb_strand_id A _struct_ref_seq_dif.seq_num 1 _struct_ref_seq_dif.pdbx_pdb_ins_code ? _struct_ref_seq_dif.pdbx_seq_db_name UNP _struct_ref_seq_dif.pdbx_seq_db_accession_code P29375 _struct_ref_seq_dif.db_mon_id ? _struct_ref_seq_dif.pdbx_seq_db_seq_num ? _struct_ref_seq_dif.details 'expression tag' _struct_ref_seq_dif.pdbx_auth_seq_num 1 _struct_ref_seq_dif.pdbx_ordinal 1 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 ZN non-polymer . 'ZINC ION' ? 'Zn 2' 65.409 # loop_ _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.type 1 1 1 1H,15N-HSQC 1 2 1 1H,13C-HSQC 1 3 1 HNCACB 1 4 1 HBHACONH 1 5 1 CBCACONH 1 6 1 '2D 1H-1H NOESY' 1 7 1 HCCHTOCSY 1 8 1 '15N-EDITED 1H,1H-NOESY' 1 9 1 '13C-EDITED 1H,1H-NOESY' 2 10 2 '15N IPAP HSQC' # loop_ _pdbx_nmr_exptl_sample_conditions.conditions_id _pdbx_nmr_exptl_sample_conditions.ionic_strength _pdbx_nmr_exptl_sample_conditions.pH _pdbx_nmr_exptl_sample_conditions.pressure _pdbx_nmr_exptl_sample_conditions.pressure_units _pdbx_nmr_exptl_sample_conditions.temperature _pdbx_nmr_exptl_sample_conditions.temperature_units 1 '20 mM Sodium Phosphate' 7.0 1 atm 293.2 K 2 '200 mM NaCl' 7.0 1 atm 298.2 K # loop_ _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.solvent_system '0.2-0.5 MM [U-100% 13C; U-100% 15N] JARID1A PHD FINGER 3, 5MM DTT, 1 MM ZINC CHLORIDE, 20 MM SODIUM PHHOSPHATE, 90% H2O/10% D2O' 1 '90% H2O/10% D2O' '0.2-0.5 MM [U-100% 15N] JARID1A PHD FINGER 3, 10 MM MOPS, 5 MM DTT, 1 MM ZINC CHLORIDE, 12 MG/ML BACTERIOPHAGE PF1, 90% H2O/10% D2O' 2 '90% H2O/10% D2O' # _pdbx_nmr_spectrometer.field_strength 800 _pdbx_nmr_spectrometer.manufacturer Bruker _pdbx_nmr_spectrometer.model DMX _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.type 'Bruker DMX' # _pdbx_nmr_refine.entry_id 2KGG _pdbx_nmr_refine.method 'simulated annealing' _pdbx_nmr_refine.details 'the structure was first calculated using CYANA and then refined using XPLOR-NIH' _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_ensemble.average_constraint_violations_per_residue ? _pdbx_nmr_ensemble.average_constraints_per_residue ? _pdbx_nmr_ensemble.average_distance_constraint_violation ? _pdbx_nmr_ensemble.average_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.conformer_selection_criteria 'structures with the lowest energy' _pdbx_nmr_ensemble.conformers_calculated_total_number 100 _pdbx_nmr_ensemble.conformers_submitted_total_number 20 _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.entry_id 2KGG _pdbx_nmr_ensemble.maximum_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation ? _pdbx_nmr_ensemble.torsion_angle_constraint_violation_method ? # _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.entry_id 2KGG _pdbx_nmr_representative.selection_criteria 'lowest energy' # loop_ _pdbx_nmr_software.authors _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.ordinal 'Schwieters, C. et al.' refinement 'X-PLOR NIH' 2.18 1 'Guntert, P. et al.' 'structure solution' CYANA 2.1 2 # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.crystals_number ? _exptl.details ? _exptl.entry_id 2KGG _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2KGG _struct.title 'Solution Structure of JARID1A C-terminal PHD finger' _struct.pdbx_descriptor 'Histone demethylase JARID1A' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2KGG _struct_keywords.pdbx_keywords 'METAL BINDING PROTEIN' _struct_keywords.text ;PHD finger, JARID1A, histone modification, leukemia, Alternative splicing, Chromatin regulator, Developmental protein, Dioxygenase, Iron, Metal-binding, Nucleus, Oxidoreductase, Phosphoprotein, Polymorphism, Transcription, Transcription regulation, Zinc, Zinc-finger, METAL BINDING PROTEIN ; # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 2 ? # _struct_conf.conf_type_id HELX_P _struct_conf.id HELX_P1 _struct_conf.pdbx_PDB_helix_id 1 _struct_conf.beg_label_comp_id SER _struct_conf.beg_label_asym_id A _struct_conf.beg_label_seq_id 37 _struct_conf.pdbx_beg_PDB_ins_code ? _struct_conf.end_label_comp_id GLU _struct_conf.end_label_asym_id A _struct_conf.end_label_seq_id 44 _struct_conf.pdbx_end_PDB_ins_code ? _struct_conf.beg_auth_comp_id SER _struct_conf.beg_auth_asym_id A _struct_conf.beg_auth_seq_id 37 _struct_conf.end_auth_comp_id GLU _struct_conf.end_auth_asym_id A _struct_conf.end_auth_seq_id 44 _struct_conf.pdbx_PDB_helix_class 1 _struct_conf.details ? _struct_conf.pdbx_PDB_helix_length 8 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc1 metalc ? ? A CYS 3 SG ? ? ? 1_555 C ZN . ZN ? ? A CYS 3 A ZN 54 1_555 ? ? ? ? ? ? ? 2.252 ? metalc2 metalc ? ? A CYS 8 SG ? ? ? 1_555 C ZN . ZN ? ? A CYS 8 A ZN 54 1_555 ? ? ? ? ? ? ? 2.299 ? metalc3 metalc ? ? A CYS 21 SG ? ? ? 1_555 B ZN . ZN ? ? A CYS 21 A ZN 53 1_555 ? ? ? ? ? ? ? 2.295 ? metalc4 metalc ? ? A CYS 25 SG ? ? ? 1_555 B ZN . ZN ? ? A CYS 25 A ZN 53 1_555 ? ? ? ? ? ? ? 2.263 ? metalc5 metalc ? ? A HIS 30 ND1 ? ? ? 1_555 C ZN . ZN ? ? A HIS 30 A ZN 54 1_555 ? ? ? ? ? ? ? 2.011 ? metalc6 metalc ? ? A CYS 33 SG ? ? ? 1_555 C ZN . ZN ? ? A CYS 33 A ZN 54 1_555 ? ? ? ? ? ? ? 2.329 ? metalc7 metalc ? ? A CYS 48 SG ? ? ? 1_555 B ZN . ZN ? ? A CYS 48 A ZN 53 1_555 ? ? ? ? ? ? ? 2.282 ? metalc8 metalc ? ? A CYS 51 SG ? ? ? 1_555 B ZN . ZN ? ? A CYS 51 A ZN 53 1_555 ? ? ? ? ? ? ? 2.280 ? # _struct_conn_type.id metalc _struct_conn_type.criteria ? _struct_conn_type.reference ? # _struct_sheet.id A _struct_sheet.type ? _struct_sheet.number_strands 2 _struct_sheet.details ? # _struct_sheet_order.sheet_id A _struct_sheet_order.range_id_1 1 _struct_sheet_order.range_id_2 2 _struct_sheet_order.offset ? _struct_sheet_order.sense anti-parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id A 1 TRP A 18 ? GLN A 20 ? TRP A 18 GLN A 20 A 2 TRP A 28 ? HIS A 30 ? TRP A 28 HIS A 30 # _pdbx_struct_sheet_hbond.sheet_id A _pdbx_struct_sheet_hbond.range_id_1 1 _pdbx_struct_sheet_hbond.range_id_2 2 _pdbx_struct_sheet_hbond.range_1_label_atom_id N _pdbx_struct_sheet_hbond.range_1_label_comp_id VAL _pdbx_struct_sheet_hbond.range_1_label_asym_id A _pdbx_struct_sheet_hbond.range_1_label_seq_id 19 _pdbx_struct_sheet_hbond.range_1_PDB_ins_code ? _pdbx_struct_sheet_hbond.range_1_auth_atom_id N _pdbx_struct_sheet_hbond.range_1_auth_comp_id VAL _pdbx_struct_sheet_hbond.range_1_auth_asym_id A _pdbx_struct_sheet_hbond.range_1_auth_seq_id 19 _pdbx_struct_sheet_hbond.range_2_label_atom_id O _pdbx_struct_sheet_hbond.range_2_label_comp_id PHE _pdbx_struct_sheet_hbond.range_2_label_asym_id A _pdbx_struct_sheet_hbond.range_2_label_seq_id 29 _pdbx_struct_sheet_hbond.range_2_PDB_ins_code ? _pdbx_struct_sheet_hbond.range_2_auth_atom_id O _pdbx_struct_sheet_hbond.range_2_auth_comp_id PHE _pdbx_struct_sheet_hbond.range_2_auth_asym_id A _pdbx_struct_sheet_hbond.range_2_auth_seq_id 29 # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software ? ? ? ? 4 'BINDING SITE FOR RESIDUE ZN A 53' AC2 Software ? ? ? ? 4 'BINDING SITE FOR RESIDUE ZN A 54' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 4 CYS A 21 ? CYS A 21 . ? 1_555 ? 2 AC1 4 CYS A 25 ? CYS A 25 . ? 1_555 ? 3 AC1 4 CYS A 48 ? CYS A 48 . ? 1_555 ? 4 AC1 4 CYS A 51 ? CYS A 51 . ? 1_555 ? 5 AC2 4 CYS A 3 ? CYS A 3 . ? 1_555 ? 6 AC2 4 CYS A 8 ? CYS A 8 . ? 1_555 ? 7 AC2 4 HIS A 30 ? HIS A 30 . ? 1_555 ? 8 AC2 4 CYS A 33 ? CYS A 33 . ? 1_555 ? # _atom_sites.entry_id 2KGG _atom_sites.fract_transf_matrix[1][1] 1.000000 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 1.000000 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 1.000000 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C H N O S ZN # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 SER 1 1 1 SER SER A . n A 1 2 VAL 2 2 2 VAL VAL A . n A 1 3 CYS 3 3 3 CYS CYS A . n A 1 4 ALA 4 4 4 ALA ALA A . n A 1 5 ALA 5 5 5 ALA ALA A . n A 1 6 GLN 6 6 6 GLN GLN A . n A 1 7 ASN 7 7 7 ASN ASN A . n A 1 8 CYS 8 8 8 CYS CYS A . n A 1 9 GLN 9 9 9 GLN GLN A . n A 1 10 ARG 10 10 10 ARG ARG A . n A 1 11 PRO 11 11 11 PRO PRO A . n A 1 12 CYS 12 12 12 CYS CYS A . n A 1 13 LYS 13 13 13 LYS LYS A . n A 1 14 ASP 14 14 14 ASP ASP A . n A 1 15 LYS 15 15 15 LYS LYS A . n A 1 16 VAL 16 16 16 VAL VAL A . n A 1 17 ASP 17 17 17 ASP ASP A . n A 1 18 TRP 18 18 18 TRP TRP A . n A 1 19 VAL 19 19 19 VAL VAL A . n A 1 20 GLN 20 20 20 GLN GLN A . n A 1 21 CYS 21 21 21 CYS CYS A . n A 1 22 ASP 22 22 22 ASP ASP A . n A 1 23 GLY 23 23 23 GLY GLY A . n A 1 24 GLY 24 24 24 GLY GLY A . n A 1 25 CYS 25 25 25 CYS CYS A . n A 1 26 ASP 26 26 26 ASP ASP A . n A 1 27 GLU 27 27 27 GLU GLU A . n A 1 28 TRP 28 28 28 TRP TRP A . n A 1 29 PHE 29 29 29 PHE PHE A . n A 1 30 HIS 30 30 30 HIS HIS A . n A 1 31 GLN 31 31 31 GLN GLN A . n A 1 32 VAL 32 32 32 VAL VAL A . n A 1 33 CYS 33 33 33 CYS CYS A . n A 1 34 VAL 34 34 34 VAL VAL A . n A 1 35 GLY 35 35 35 GLY GLY A . n A 1 36 VAL 36 36 36 VAL VAL A . n A 1 37 SER 37 37 37 SER SER A . n A 1 38 PRO 38 38 38 PRO PRO A . n A 1 39 GLU 39 39 39 GLU GLU A . n A 1 40 MET 40 40 40 MET MET A . n A 1 41 ALA 41 41 41 ALA ALA A . n A 1 42 GLU 42 42 42 GLU GLU A . n A 1 43 ASN 43 43 43 ASN ASN A . n A 1 44 GLU 44 44 44 GLU GLU A . n A 1 45 ASP 45 45 45 ASP ASP A . n A 1 46 TYR 46 46 46 TYR TYR A . n A 1 47 ILE 47 47 47 ILE ILE A . n A 1 48 CYS 48 48 48 CYS CYS A . n A 1 49 ILE 49 49 49 ILE ILE A . n A 1 50 ASN 50 50 50 ASN ASN A . n A 1 51 CYS 51 51 51 CYS CYS A . n A 1 52 ALA 52 52 52 ALA ALA A . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 ZN 1 53 53 ZN ZN A . C 2 ZN 1 54 54 ZN ZN A . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation ? _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 SG ? A CYS 3 ? A CYS 3 ? 1_555 ZN ? C ZN . ? A ZN 54 ? 1_555 SG ? A CYS 8 ? A CYS 8 ? 1_555 109.1 ? 2 SG ? A CYS 3 ? A CYS 3 ? 1_555 ZN ? C ZN . ? A ZN 54 ? 1_555 ND1 ? A HIS 30 ? A HIS 30 ? 1_555 109.7 ? 3 SG ? A CYS 8 ? A CYS 8 ? 1_555 ZN ? C ZN . ? A ZN 54 ? 1_555 ND1 ? A HIS 30 ? A HIS 30 ? 1_555 110.1 ? 4 SG ? A CYS 3 ? A CYS 3 ? 1_555 ZN ? C ZN . ? A ZN 54 ? 1_555 SG ? A CYS 33 ? A CYS 33 ? 1_555 105.4 ? 5 SG ? A CYS 8 ? A CYS 8 ? 1_555 ZN ? C ZN . ? A ZN 54 ? 1_555 SG ? A CYS 33 ? A CYS 33 ? 1_555 112.2 ? 6 ND1 ? A HIS 30 ? A HIS 30 ? 1_555 ZN ? C ZN . ? A ZN 54 ? 1_555 SG ? A CYS 33 ? A CYS 33 ? 1_555 110.2 ? 7 SG ? A CYS 21 ? A CYS 21 ? 1_555 ZN ? B ZN . ? A ZN 53 ? 1_555 SG ? A CYS 25 ? A CYS 25 ? 1_555 107.2 ? 8 SG ? A CYS 21 ? A CYS 21 ? 1_555 ZN ? B ZN . ? A ZN 53 ? 1_555 SG ? A CYS 48 ? A CYS 48 ? 1_555 110.3 ? 9 SG ? A CYS 25 ? A CYS 25 ? 1_555 ZN ? B ZN . ? A ZN 53 ? 1_555 SG ? A CYS 48 ? A CYS 48 ? 1_555 111.1 ? 10 SG ? A CYS 21 ? A CYS 21 ? 1_555 ZN ? B ZN . ? A ZN 53 ? 1_555 SG ? A CYS 51 ? A CYS 51 ? 1_555 110.5 ? 11 SG ? A CYS 25 ? A CYS 25 ? 1_555 ZN ? B ZN . ? A ZN 53 ? 1_555 SG ? A CYS 51 ? A CYS 51 ? 1_555 106.7 ? 12 SG ? A CYS 48 ? A CYS 48 ? 1_555 ZN ? B ZN . ? A ZN 53 ? 1_555 SG ? A CYS 51 ? A CYS 51 ? 1_555 111.0 ? # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2009-05-05 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2020-02-26 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' 5 3 'Structure model' Other # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' database_2 2 3 'Structure model' pdbx_database_status 3 3 'Structure model' pdbx_nmr_software 4 3 'Structure model' pdbx_struct_assembly 5 3 'Structure model' pdbx_struct_oper_list 6 3 'Structure model' struct_ref_seq_dif # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_pdbx_database_status.status_code_cs' 2 3 'Structure model' '_pdbx_nmr_software.name' 3 3 'Structure model' '_struct_ref_seq_dif.details' # loop_ _pdbx_nmr_exptl_sample.component _pdbx_nmr_exptl_sample.concentration _pdbx_nmr_exptl_sample.concentration_range _pdbx_nmr_exptl_sample.concentration_units _pdbx_nmr_exptl_sample.isotopic_labeling _pdbx_nmr_exptl_sample.solution_id 'JARID1A PHD finger 3' ? 0.2-0.5 mM '[U-100% 13C; U-100% 15N]' 1 'JARID1A PHD finger 3' ? 0.2-0.5 mM '[U-100% 15N]' 2 # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 ALA A 5 ? ? 178.34 134.24 2 2 ALA A 5 ? ? -177.55 144.15 3 2 VAL A 16 ? ? -172.28 100.31 4 3 ALA A 5 ? ? -177.22 145.96 5 3 VAL A 16 ? ? -168.76 112.50 6 4 ALA A 5 ? ? -176.68 142.85 7 4 VAL A 16 ? ? -178.14 96.17 8 4 ASP A 26 ? ? 58.68 18.50 9 5 ALA A 5 ? ? -176.58 146.49 10 6 ALA A 5 ? ? -175.37 148.79 11 6 LYS A 15 ? ? -65.55 30.07 12 7 ALA A 5 ? ? 178.73 135.34 13 7 VAL A 16 ? ? -172.31 97.00 14 8 ALA A 5 ? ? -179.98 132.02 15 8 VAL A 16 ? ? -172.02 104.79 16 8 ASP A 22 ? ? -77.58 29.10 17 9 ALA A 5 ? ? -173.81 145.52 18 9 VAL A 16 ? ? -168.66 116.30 19 9 ASP A 26 ? ? 59.54 19.77 20 10 ALA A 5 ? ? -175.60 142.03 21 10 LYS A 15 ? ? -68.19 82.95 22 10 VAL A 16 ? ? -173.10 104.52 23 11 ALA A 5 ? ? -172.32 141.66 24 11 VAL A 16 ? ? -175.79 111.35 25 12 ALA A 5 ? ? -177.08 146.38 26 13 ASP A 26 ? ? 59.92 18.48 27 14 ALA A 5 ? ? -177.64 142.26 28 15 ALA A 5 ? ? -173.78 145.30 29 15 ARG A 10 ? ? -116.69 62.88 30 15 VAL A 16 ? ? -165.61 102.04 31 16 ALA A 5 ? ? -173.25 140.91 32 16 VAL A 16 ? ? -171.56 103.79 33 17 ALA A 5 ? ? -177.03 135.56 34 18 ALA A 5 ? ? -175.25 147.19 35 18 VAL A 16 ? ? -170.43 98.29 36 18 ASP A 26 ? ? -39.73 13.96 37 19 ALA A 5 ? ? -177.88 143.80 38 19 VAL A 16 ? ? -165.07 103.85 39 20 ALA A 5 ? ? -176.65 145.70 # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 A ALA 52 ? O ? A ALA 52 O 2 2 Y 1 A ALA 52 ? O ? A ALA 52 O 3 3 Y 1 A ALA 52 ? O ? A ALA 52 O 4 4 Y 1 A ALA 52 ? O ? A ALA 52 O 5 5 Y 1 A ALA 52 ? O ? A ALA 52 O 6 6 Y 1 A ALA 52 ? O ? A ALA 52 O 7 7 Y 1 A ALA 52 ? O ? A ALA 52 O 8 8 Y 1 A ALA 52 ? O ? A ALA 52 O 9 9 Y 1 A ALA 52 ? O ? A ALA 52 O 10 10 Y 1 A ALA 52 ? O ? A ALA 52 O 11 11 Y 1 A ALA 52 ? O ? A ALA 52 O 12 12 Y 1 A ALA 52 ? O ? A ALA 52 O 13 13 Y 1 A ALA 52 ? O ? A ALA 52 O 14 14 Y 1 A ALA 52 ? O ? A ALA 52 O 15 15 Y 1 A ALA 52 ? O ? A ALA 52 O 16 16 Y 1 A ALA 52 ? O ? A ALA 52 O 17 17 Y 1 A ALA 52 ? O ? A ALA 52 O 18 18 Y 1 A ALA 52 ? O ? A ALA 52 O 19 19 Y 1 A ALA 52 ? O ? A ALA 52 O 20 20 Y 1 A ALA 52 ? O ? A ALA 52 O # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name 'ZINC ION' _pdbx_entity_nonpoly.comp_id ZN #