data_4UP0 # _entry.id 4UP0 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.279 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 4UP0 PDBE EBI-60877 WWPDB D_1290060877 # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 4UP0 _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.SG_entry . _pdbx_database_status.recvd_initial_deposition_date 2014-06-11 _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Miller, T.C.R.' 1 'Fiedler, M.' 2 'Rutherford, T.J.' 3 'Birchall, K.' 4 'Chugh, J.' 5 'Bienz, M.' 6 # _citation.id primary _citation.title 'Competitive Binding of a Benzimidazole to the Histone-Binding Pocket of the Pygo Phd Finger.' _citation.journal_abbrev 'Acs Chem.Biol.' _citation.journal_volume 9 _citation.page_first 2864 _citation.page_last ? _citation.year 2014 _citation.journal_id_ASTM ? _citation.country US _citation.journal_id_ISSN 1554-8929 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 25323450 _citation.pdbx_database_id_DOI 10.1021/CB500585S # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Miller, T.C.R.' 1 primary 'Rutherford, T.J.' 2 primary 'Birchall, K.' 3 primary 'Chugh, J.' 4 primary 'Fiedler, M.' 5 primary 'Bienz, M.' 6 # _cell.entry_id 4UP0 _cell.length_a 53.910 _cell.length_b 53.910 _cell.length_c 57.940 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4UP0 _symmetry.space_group_name_H-M 'P 41 21 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 # 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 'PYGOPUS HOMOLOG 2, B-CELL CLL/LYMPHOMA 9-LIKE PROTEIN' 10537.676 1 ? ? 'PHD FINGER, HD1,RESIDUES 327-387,235-263' ? 2 polymer syn 'HISTONE H3.1' 1633.872 1 ? ? 'RESIDUES 2-16' 'DIMETHYLATED LYSINE 4 - K4ME2' 3 non-polymer syn 'ZINC ION' 65.409 2 ? ? ? ? 4 water nat water 18.015 94 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'PYGO2, B9L, B-CELL LYMPHOMA 9-LIKE PROTEIN, BCL9-LIKE PROTEIN, PROTEIN BCL9-2' # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 'polypeptide(L)' no no ;GVYPCGACRSEVNDDQDAILCEASCQKWFHRECTGMTESAYGLLTTEASAVWACDLCLKTKEGSGSGSGSVYVFTTHLAN TAAEAVLQGRADSILAYHQ ; ;GVYPCGACRSEVNDDQDAILCEASCQKWFHRECTGMTESAYGLLTTEASAVWACDLCLKTKEGSGSGSGSVYVFTTHLAN TAAEAVLQGRADSILAYHQ ; A ? 2 'polypeptide(L)' no yes 'ART(MLY)QTAR(ALY)STGGKA' ARTKQTARKSTGGKA F ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 GLY n 1 2 VAL n 1 3 TYR n 1 4 PRO n 1 5 CYS n 1 6 GLY n 1 7 ALA n 1 8 CYS n 1 9 ARG n 1 10 SER n 1 11 GLU n 1 12 VAL n 1 13 ASN n 1 14 ASP n 1 15 ASP n 1 16 GLN n 1 17 ASP n 1 18 ALA n 1 19 ILE n 1 20 LEU n 1 21 CYS n 1 22 GLU n 1 23 ALA n 1 24 SER n 1 25 CYS n 1 26 GLN n 1 27 LYS n 1 28 TRP n 1 29 PHE n 1 30 HIS n 1 31 ARG n 1 32 GLU n 1 33 CYS n 1 34 THR n 1 35 GLY n 1 36 MET n 1 37 THR n 1 38 GLU n 1 39 SER n 1 40 ALA n 1 41 TYR n 1 42 GLY n 1 43 LEU n 1 44 LEU n 1 45 THR n 1 46 THR n 1 47 GLU n 1 48 ALA n 1 49 SER n 1 50 ALA n 1 51 VAL n 1 52 TRP n 1 53 ALA n 1 54 CYS n 1 55 ASP n 1 56 LEU n 1 57 CYS n 1 58 LEU n 1 59 LYS n 1 60 THR n 1 61 LYS n 1 62 GLU n 1 63 GLY n 1 64 SER n 1 65 GLY n 1 66 SER n 1 67 GLY n 1 68 SER n 1 69 GLY n 1 70 SER n 1 71 VAL n 1 72 TYR n 1 73 VAL n 1 74 PHE n 1 75 THR n 1 76 THR n 1 77 HIS n 1 78 LEU n 1 79 ALA n 1 80 ASN n 1 81 THR n 1 82 ALA n 1 83 ALA n 1 84 GLU n 1 85 ALA n 1 86 VAL n 1 87 LEU n 1 88 GLN n 1 89 GLY n 1 90 ARG n 1 91 ALA n 1 92 ASP n 1 93 SER n 1 94 ILE n 1 95 LEU n 1 96 ALA n 1 97 TYR n 1 98 HIS n 1 99 GLN n 2 1 ALA n 2 2 ARG n 2 3 THR n 2 4 MLY n 2 5 GLN n 2 6 THR n 2 7 ALA n 2 8 ARG n 2 9 ALY n 2 10 SER n 2 11 THR n 2 12 GLY n 2 13 GLY n 2 14 LYS n 2 15 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 ? _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 469008 _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 'BL21(DE3)' _entity_src_gen.pdbx_host_org_variant 'CODONPLUS RIL' _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 PETM11 _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _pdbx_entity_src_syn.entity_id 2 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific 'HOMO SAPIENS' _pdbx_entity_src_syn.organism_common_name HUMAN _pdbx_entity_src_syn.ncbi_taxonomy_id 9606 _pdbx_entity_src_syn.details ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform 1 UNP PYGO2_HUMAN 1 ? ? Q9BRQ0 ? 2 UNP BCL9L_HUMAN 1 ? ? Q86UU0 ? 3 UNP H31_HUMAN 2 ? ? P68431 ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 4UP0 A 2 ? 62 ? Q9BRQ0 327 ? 387 ? 327 387 2 2 4UP0 A 71 ? 99 ? Q86UU0 235 ? 263 ? 1235 1263 3 3 4UP0 F 1 ? 15 ? P68431 2 ? 16 ? 1 15 # loop_ _struct_ref_seq_dif.align_id _struct_ref_seq_dif.pdbx_pdb_id_code _struct_ref_seq_dif.mon_id _struct_ref_seq_dif.pdbx_pdb_strand_id _struct_ref_seq_dif.seq_num _struct_ref_seq_dif.pdbx_pdb_ins_code _struct_ref_seq_dif.pdbx_seq_db_name _struct_ref_seq_dif.pdbx_seq_db_accession_code _struct_ref_seq_dif.db_mon_id _struct_ref_seq_dif.pdbx_seq_db_seq_num _struct_ref_seq_dif.details _struct_ref_seq_dif.pdbx_auth_seq_num _struct_ref_seq_dif.pdbx_ordinal 1 4UP0 GLY A 63 ? UNP Q9BRQ0 ? ? linker 388 1 1 4UP0 SER A 64 ? UNP Q9BRQ0 ? ? linker 389 2 1 4UP0 GLY A 65 ? UNP Q9BRQ0 ? ? linker 390 3 1 4UP0 SER A 66 ? UNP Q9BRQ0 ? ? linker 391 4 1 4UP0 GLY A 67 ? UNP Q9BRQ0 ? ? linker 392 5 1 4UP0 SER A 68 ? UNP Q9BRQ0 ? ? linker 393 6 1 4UP0 GLY A 69 ? UNP Q9BRQ0 ? ? linker 394 7 1 4UP0 SER A 70 ? UNP Q9BRQ0 ? ? linker 395 8 # 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 ALY 'L-peptide linking' n 'N(6)-ACETYLLYSINE' ? 'C8 H16 N2 O3' 188.224 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 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? '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 MLY 'L-peptide linking' n N-DIMETHYL-LYSINE ? 'C8 H18 N2 O2' 174.241 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 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 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 # _exptl.entry_id 4UP0 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.16 _exptl_crystal.density_percent_sol 43.1 _exptl_crystal.description NONE # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method ? _exptl_crystal_grow.temp ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH ? _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details '1 M SODIUM CITRATE, 0.1 M TRIS PH 7, 0.2 M NACL' # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector PIXEL _diffrn_detector.type 'DECTRIS PILATUS 6M' _diffrn_detector.pdbx_collection_date 2011-01-29 _diffrn_detector.details MIRRORS # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.976219 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ESRF BEAMLINE ID29' _diffrn_source.pdbx_synchrotron_site ESRF _diffrn_source.pdbx_synchrotron_beamline ID29 _diffrn_source.pdbx_wavelength 0.976219 _diffrn_source.pdbx_wavelength_list ? # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 4UP0 _reflns.observed_criterion_sigma_I 2.4 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 39.47 _reflns.d_resolution_high 1.28 _reflns.number_obs 22695 _reflns.number_all ? _reflns.percent_possible_obs 99.9 _reflns.pdbx_Rmerge_I_obs 0.09 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 13.00 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 11.6 # _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_ordinal 1 _reflns_shell.d_res_high 1.28 _reflns_shell.d_res_low 1.30 _reflns_shell.percent_possible_all 99.6 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 2.40 _reflns_shell.pdbx_redundancy 12.3 # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 4UP0 _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 21476 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F . _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 39.47 _refine.ls_d_res_high 1.28 _refine.ls_percent_reflns_obs 99.79 _refine.ls_R_factor_obs 0.13946 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.13797 _refine.ls_R_factor_R_free 0.16611 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.1 _refine.ls_number_reflns_R_free 1157 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.977 _refine.correlation_coeff_Fo_to_Fc_free 0.971 _refine.B_iso_mean 21.159 _refine.aniso_B[1][1] 0.07 _refine.aniso_B[2][2] 0.07 _refine.aniso_B[3][3] -0.14 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details MASK _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.20 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ;HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.CHAIN A RESIDUES 383-387 AND 8AA GSGSGSGS LINKER ARE DISORDERED CHAIN A RESIDUE 1263 IS DISORDERED. CHAIN F RESIDUES 7-15 ARE DISORDERED ; _refine.pdbx_starting_model 'PDB ENTRY 2XB1' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.042 _refine.pdbx_overall_ESU_R_Free 0.041 _refine.overall_SU_ML 0.024 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 1.222 _refine.overall_SU_R_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 692 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 2 _refine_hist.number_atoms_solvent 94 _refine_hist.number_atoms_total 788 _refine_hist.d_res_high 1.28 _refine_hist.d_res_low 39.47 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 0.020 0.019 ? 703 'X-RAY DIFFRACTION' ? r_bond_other_d ? ? ? ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.955 1.927 ? 954 'X-RAY DIFFRACTION' ? r_angle_other_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 5.655 5.000 ? 88 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 36.505 24.063 ? 32 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 11.258 15.000 ? 102 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 21.112 15.000 ? 4 'X-RAY DIFFRACTION' ? r_chiral_restr 0.133 0.200 ? 111 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.013 0.020 ? 528 'X-RAY DIFFRACTION' ? r_gen_planes_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_scbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_scbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_scangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_scangle_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_long_range_B_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_long_range_B_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_rigid_bond_restr 8.079 3.000 ? 702 'X-RAY DIFFRACTION' ? r_sphericity_free 32.703 5.000 ? 33 'X-RAY DIFFRACTION' ? r_sphericity_bonded 19.139 5.000 ? 756 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.279 _refine_ls_shell.d_res_low 1.312 _refine_ls_shell.number_reflns_R_work 1403 _refine_ls_shell.R_factor_R_work 0.255 _refine_ls_shell.percent_reflns_obs 99.40 _refine_ls_shell.R_factor_R_free 0.299 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 83 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? # _struct.entry_id 4UP0 _struct.title 'Ternary crystal structure of the Pygo2 PHD finger in complex with the B9L HD1 domain and a H3K4me2 peptide' _struct.pdbx_descriptor 'PYGOPUS HOMOLOG 2, B-CELL CLL/LYMPHOMA 9-LIKE PROTEIN, HISTONE H3.1' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4UP0 _struct_keywords.pdbx_keywords TRANSCRIPTION _struct_keywords.text 'TRANSCRIPTION, WNT SIGNALLING, PHD FINGER, BCL9L, HD1 DOMAIN' # 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 3 ? D N N 3 ? E N N 4 ? F N N 4 ? # _struct_biol.id 1 # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 1 GLU A 32 ? THR A 34 ? GLU A 357 THR A 359 5 ? 3 HELX_P HELX_P2 2 THR A 37 ? GLU A 47 ? THR A 362 GLU A 372 1 ? 11 HELX_P HELX_P3 3 THR A 75 ? GLN A 88 ? THR A 1239 GLN A 1252 1 ? 14 HELX_P HELX_P4 4 SER A 93 ? HIS A 98 ? SER A 1257 HIS A 1262 5 ? 6 # _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 ? ? C ZN . ZN ? ? ? 1_555 A CYS 5 SG ? ? A ZN 1383 A CYS 330 1_555 ? ? ? ? ? ? ? 2.344 ? metalc2 metalc ? ? C ZN . ZN ? ? ? 1_555 A CYS 8 SG ? ? A ZN 1383 A CYS 333 1_555 ? ? ? ? ? ? ? 2.310 ? metalc3 metalc ? ? C ZN . ZN ? ? ? 1_555 A HIS 30 ND1 ? ? A ZN 1383 A HIS 355 1_555 ? ? ? ? ? ? ? 2.096 ? metalc4 metalc ? ? C ZN . ZN ? ? ? 1_555 A CYS 33 SG ? ? A ZN 1383 A CYS 358 1_555 ? ? ? ? ? ? ? 2.295 ? metalc5 metalc ? ? D ZN . ZN ? ? ? 1_555 A CYS 57 SG ? ? A ZN 1384 A CYS 382 1_555 ? ? ? ? ? ? ? 2.332 ? metalc6 metalc ? ? D ZN . ZN ? ? ? 1_555 A CYS 54 SG ? ? A ZN 1384 A CYS 379 1_555 ? ? ? ? ? ? ? 2.325 ? metalc7 metalc ? ? D ZN . ZN ? ? ? 1_555 A CYS 21 SG ? ? A ZN 1384 A CYS 346 1_555 ? ? ? ? ? ? ? 2.354 ? metalc8 metalc ? ? D ZN . ZN ? ? ? 1_555 A CYS 25 SG ? ? A ZN 1384 A CYS 350 1_555 ? ? ? ? ? ? ? 2.318 ? covale1 covale ? ? B THR 3 C ? ? ? 1_555 B MLY 4 N ? ? F THR 3 F MLY 4 1_555 ? ? ? ? ? ? ? 1.320 ? covale2 covale ? ? B MLY 4 C ? ? ? 1_555 B GLN 5 N ? ? F MLY 4 F GLN 5 1_555 ? ? ? ? ? ? ? 1.323 ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? covale ? ? # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details AA ? 2 ? AB ? 2 ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense AA 1 2 ? anti-parallel AB 1 2 ? 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 AA 1 ALA A 18 ? LEU A 20 ? ALA A 343 LEU A 345 AA 2 TRP A 28 ? HIS A 30 ? TRP A 353 HIS A 355 AB 1 ALA A 50 ? TRP A 52 ? ALA A 375 TRP A 377 AB 2 TYR A 72 ? PHE A 74 ? TYR A 1236 PHE A 1238 # loop_ _pdbx_struct_sheet_hbond.sheet_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_1_PDB_ins_code _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_2_PDB_ins_code _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id AA 1 2 N ILE A 19 ? N ILE A 344 O PHE A 29 ? O PHE A 354 AB 1 2 N VAL A 51 ? N VAL A 376 O TYR A 72 ? O TYR A 1236 # 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 1383' AC2 Software ? ? ? ? 4 'BINDING SITE FOR RESIDUE ZN A 1384' # 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 5 ? CYS A 330 . ? 1_555 ? 2 AC1 4 CYS A 8 ? CYS A 333 . ? 1_555 ? 3 AC1 4 HIS A 30 ? HIS A 355 . ? 1_555 ? 4 AC1 4 CYS A 33 ? CYS A 358 . ? 1_555 ? 5 AC2 4 CYS A 21 ? CYS A 346 . ? 1_555 ? 6 AC2 4 CYS A 25 ? CYS A 350 . ? 1_555 ? 7 AC2 4 CYS A 54 ? CYS A 379 . ? 1_555 ? 8 AC2 4 CYS A 57 ? CYS A 382 . ? 1_555 ? # _database_PDB_matrix.entry_id 4UP0 _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _atom_sites.entry_id 4UP0 _atom_sites.fract_transf_matrix[1][1] 0.018549 _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] 0.018549 _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] 0.017259 _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 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 GLY 1 326 326 GLY GLY A . n A 1 2 VAL 2 327 327 VAL VAL A . n A 1 3 TYR 3 328 328 TYR TYR A . n A 1 4 PRO 4 329 329 PRO PRO A . n A 1 5 CYS 5 330 330 CYS CYS A . n A 1 6 GLY 6 331 331 GLY GLY A . n A 1 7 ALA 7 332 332 ALA ALA A . n A 1 8 CYS 8 333 333 CYS CYS A . n A 1 9 ARG 9 334 334 ARG ARG A . n A 1 10 SER 10 335 335 SER SER A . n A 1 11 GLU 11 336 336 GLU GLU A . n A 1 12 VAL 12 337 337 VAL VAL A . n A 1 13 ASN 13 338 338 ASN ASN A . n A 1 14 ASP 14 339 339 ASP ASP A . n A 1 15 ASP 15 340 340 ASP ASP A . n A 1 16 GLN 16 341 341 GLN GLN A . n A 1 17 ASP 17 342 342 ASP ASP A . n A 1 18 ALA 18 343 343 ALA ALA A . n A 1 19 ILE 19 344 344 ILE ILE A . n A 1 20 LEU 20 345 345 LEU LEU A . n A 1 21 CYS 21 346 346 CYS CYS A . n A 1 22 GLU 22 347 347 GLU GLU A . n A 1 23 ALA 23 348 348 ALA ALA A . n A 1 24 SER 24 349 349 SER SER A . n A 1 25 CYS 25 350 350 CYS CYS A . n A 1 26 GLN 26 351 351 GLN GLN A . n A 1 27 LYS 27 352 352 LYS LYS A . n A 1 28 TRP 28 353 353 TRP TRP A . n A 1 29 PHE 29 354 354 PHE PHE A . n A 1 30 HIS 30 355 355 HIS HIS A . n A 1 31 ARG 31 356 356 ARG ARG A . n A 1 32 GLU 32 357 357 GLU GLU A . n A 1 33 CYS 33 358 358 CYS CYS A . n A 1 34 THR 34 359 359 THR THR A . n A 1 35 GLY 35 360 360 GLY GLY A . n A 1 36 MET 36 361 361 MET MET A . n A 1 37 THR 37 362 362 THR THR A . n A 1 38 GLU 38 363 363 GLU GLU A . n A 1 39 SER 39 364 364 SER SER A . n A 1 40 ALA 40 365 365 ALA ALA A . n A 1 41 TYR 41 366 366 TYR TYR A . n A 1 42 GLY 42 367 367 GLY GLY A . n A 1 43 LEU 43 368 368 LEU LEU A . n A 1 44 LEU 44 369 369 LEU LEU A . n A 1 45 THR 45 370 370 THR THR A . n A 1 46 THR 46 371 371 THR THR A . n A 1 47 GLU 47 372 372 GLU GLU A . n A 1 48 ALA 48 373 373 ALA ALA A . n A 1 49 SER 49 374 374 SER SER A . n A 1 50 ALA 50 375 375 ALA ALA A . n A 1 51 VAL 51 376 376 VAL VAL A . n A 1 52 TRP 52 377 377 TRP TRP A . n A 1 53 ALA 53 378 378 ALA ALA A . n A 1 54 CYS 54 379 379 CYS CYS A . n A 1 55 ASP 55 380 380 ASP ASP A . n A 1 56 LEU 56 381 381 LEU LEU A . n A 1 57 CYS 57 382 382 CYS CYS A . n A 1 58 LEU 58 383 ? ? ? A . n A 1 59 LYS 59 384 ? ? ? A . n A 1 60 THR 60 385 ? ? ? A . n A 1 61 LYS 61 386 ? ? ? A . n A 1 62 GLU 62 387 ? ? ? A . n A 1 63 GLY 63 388 ? ? ? A . n A 1 64 SER 64 389 ? ? ? A . n A 1 65 GLY 65 390 ? ? ? A . n A 1 66 SER 66 391 ? ? ? A . n A 1 67 GLY 67 392 ? ? ? A . n A 1 68 SER 68 393 ? ? ? A . n A 1 69 GLY 69 394 ? ? ? A . n A 1 70 SER 70 395 ? ? ? A . n A 1 71 VAL 71 1235 1235 VAL VAL A . n A 1 72 TYR 72 1236 1236 TYR TYR A . n A 1 73 VAL 73 1237 1237 VAL VAL A . n A 1 74 PHE 74 1238 1238 PHE PHE A . n A 1 75 THR 75 1239 1239 THR THR A . n A 1 76 THR 76 1240 1240 THR THR A . n A 1 77 HIS 77 1241 1241 HIS HIS A . n A 1 78 LEU 78 1242 1242 LEU LEU A . n A 1 79 ALA 79 1243 1243 ALA ALA A . n A 1 80 ASN 80 1244 1244 ASN ASN A . n A 1 81 THR 81 1245 1245 THR THR A . n A 1 82 ALA 82 1246 1246 ALA ALA A . n A 1 83 ALA 83 1247 1247 ALA ALA A . n A 1 84 GLU 84 1248 1248 GLU GLU A . n A 1 85 ALA 85 1249 1249 ALA ALA A . n A 1 86 VAL 86 1250 1250 VAL VAL A . n A 1 87 LEU 87 1251 1251 LEU LEU A . n A 1 88 GLN 88 1252 1252 GLN GLN A . n A 1 89 GLY 89 1253 1253 GLY GLY A . n A 1 90 ARG 90 1254 1254 ARG ARG A . n A 1 91 ALA 91 1255 1255 ALA ALA A . n A 1 92 ASP 92 1256 1256 ASP ASP A . n A 1 93 SER 93 1257 1257 SER SER A . n A 1 94 ILE 94 1258 1258 ILE ILE A . n A 1 95 LEU 95 1259 1259 LEU LEU A . n A 1 96 ALA 96 1260 1260 ALA ALA A . n A 1 97 TYR 97 1261 1261 TYR TYR A . n A 1 98 HIS 98 1262 1262 HIS HIS A . n A 1 99 GLN 99 1263 ? ? ? A . n B 2 1 ALA 1 1 1 ALA ALA F . n B 2 2 ARG 2 2 2 ARG ARG F . n B 2 3 THR 3 3 3 THR THR F . n B 2 4 MLY 4 4 4 MLY MLY F . n B 2 5 GLN 5 5 5 GLN GLN F . n B 2 6 THR 6 6 6 THR THR F . n B 2 7 ALA 7 7 ? ? ? F . n B 2 8 ARG 8 8 ? ? ? F . n B 2 9 ALY 9 9 ? ? ? F . n B 2 10 SER 10 10 ? ? ? F . n B 2 11 THR 11 11 ? ? ? F . n B 2 12 GLY 12 12 ? ? ? F . n B 2 13 GLY 13 13 ? ? ? F . n B 2 14 LYS 14 14 ? ? ? F . n B 2 15 ALA 15 15 ? ? ? F . 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 C 3 ZN 1 1383 1383 ZN ZN A . D 3 ZN 1 1384 1384 ZN ZN A . E 4 HOH 1 2001 2001 HOH HOH A . E 4 HOH 2 2002 2002 HOH HOH A . E 4 HOH 3 2003 2003 HOH HOH A . E 4 HOH 4 2004 2004 HOH HOH A . E 4 HOH 5 2005 2005 HOH HOH A . E 4 HOH 6 2006 2006 HOH HOH A . E 4 HOH 7 2007 2007 HOH HOH A . E 4 HOH 8 2008 2008 HOH HOH A . E 4 HOH 9 2009 2009 HOH HOH A . E 4 HOH 10 2010 2010 HOH HOH A . E 4 HOH 11 2011 2011 HOH HOH A . E 4 HOH 12 2012 2012 HOH HOH A . E 4 HOH 13 2013 2013 HOH HOH A . E 4 HOH 14 2014 2014 HOH HOH A . E 4 HOH 15 2015 2015 HOH HOH A . E 4 HOH 16 2016 2016 HOH HOH A . E 4 HOH 17 2017 2017 HOH HOH A . E 4 HOH 18 2018 2018 HOH HOH A . E 4 HOH 19 2019 2019 HOH HOH A . E 4 HOH 20 2020 2020 HOH HOH A . E 4 HOH 21 2021 2021 HOH HOH A . E 4 HOH 22 2022 2022 HOH HOH A . E 4 HOH 23 2023 2023 HOH HOH A . E 4 HOH 24 2024 2024 HOH HOH A . E 4 HOH 25 2025 2025 HOH HOH A . E 4 HOH 26 2026 2026 HOH HOH A . E 4 HOH 27 2027 2027 HOH HOH A . E 4 HOH 28 2028 2028 HOH HOH A . E 4 HOH 29 2029 2029 HOH HOH A . E 4 HOH 30 2030 2030 HOH HOH A . E 4 HOH 31 2031 2031 HOH HOH A . E 4 HOH 32 2032 2032 HOH HOH A . E 4 HOH 33 2033 2033 HOH HOH A . E 4 HOH 34 2034 2034 HOH HOH A . E 4 HOH 35 2035 2035 HOH HOH A . E 4 HOH 36 2036 2036 HOH HOH A . E 4 HOH 37 2037 2037 HOH HOH A . E 4 HOH 38 2038 2038 HOH HOH A . E 4 HOH 39 2039 2039 HOH HOH A . E 4 HOH 40 2040 2040 HOH HOH A . E 4 HOH 41 2041 2041 HOH HOH A . E 4 HOH 42 2042 2042 HOH HOH A . E 4 HOH 43 2043 2043 HOH HOH A . E 4 HOH 44 2044 2044 HOH HOH A . E 4 HOH 45 2045 2045 HOH HOH A . E 4 HOH 46 2046 2046 HOH HOH A . E 4 HOH 47 2047 2047 HOH HOH A . E 4 HOH 48 2048 2048 HOH HOH A . E 4 HOH 49 2049 2049 HOH HOH A . E 4 HOH 50 2050 2050 HOH HOH A . E 4 HOH 51 2051 2051 HOH HOH A . E 4 HOH 52 2052 2052 HOH HOH A . E 4 HOH 53 2053 2053 HOH HOH A . E 4 HOH 54 2054 2054 HOH HOH A . E 4 HOH 55 2056 2056 HOH HOH A . E 4 HOH 56 2057 2057 HOH HOH A . E 4 HOH 57 2058 2058 HOH HOH A . E 4 HOH 58 2059 2059 HOH HOH A . E 4 HOH 59 2060 2060 HOH HOH A . E 4 HOH 60 2061 2061 HOH HOH A . E 4 HOH 61 2062 2062 HOH HOH A . E 4 HOH 62 2063 2063 HOH HOH A . E 4 HOH 63 2064 2064 HOH HOH A . E 4 HOH 64 2065 2065 HOH HOH A . E 4 HOH 65 2066 2066 HOH HOH A . E 4 HOH 66 2067 2067 HOH HOH A . E 4 HOH 67 2068 2068 HOH HOH A . E 4 HOH 68 2069 2069 HOH HOH A . E 4 HOH 69 2070 2070 HOH HOH A . E 4 HOH 70 2071 2071 HOH HOH A . E 4 HOH 71 2072 2072 HOH HOH A . E 4 HOH 72 2073 2073 HOH HOH A . E 4 HOH 73 2074 2074 HOH HOH A . E 4 HOH 74 2075 2075 HOH HOH A . E 4 HOH 75 2076 2076 HOH HOH A . E 4 HOH 76 2077 2077 HOH HOH A . E 4 HOH 77 2078 2078 HOH HOH A . E 4 HOH 78 2079 2079 HOH HOH A . E 4 HOH 79 2080 2080 HOH HOH A . E 4 HOH 80 2081 2081 HOH HOH A . E 4 HOH 81 2082 2082 HOH HOH A . E 4 HOH 82 2083 2083 HOH HOH A . E 4 HOH 83 2084 2084 HOH HOH A . E 4 HOH 84 2085 2085 HOH HOH A . E 4 HOH 85 2086 2086 HOH HOH A . F 4 HOH 1 2001 2001 HOH HOH F . F 4 HOH 2 2002 2002 HOH HOH F . F 4 HOH 3 2003 2003 HOH HOH F . F 4 HOH 4 2004 2004 HOH HOH F . F 4 HOH 5 2005 2005 HOH HOH F . F 4 HOH 6 2006 2006 HOH HOH F . F 4 HOH 7 2007 2007 HOH HOH F . F 4 HOH 8 2008 2008 HOH HOH F . F 4 HOH 9 2009 2009 HOH HOH F . # _pdbx_struct_mod_residue.id 1 _pdbx_struct_mod_residue.label_asym_id B _pdbx_struct_mod_residue.label_comp_id MLY _pdbx_struct_mod_residue.label_seq_id 4 _pdbx_struct_mod_residue.auth_asym_id F _pdbx_struct_mod_residue.auth_comp_id MLY _pdbx_struct_mod_residue.auth_seq_id 4 _pdbx_struct_mod_residue.PDB_ins_code ? _pdbx_struct_mod_residue.parent_comp_id LYS _pdbx_struct_mod_residue.details N-DIMETHYL-LYSINE # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 2070 ? 1 MORE -16.5 ? 1 'SSA (A^2)' 5210 ? # _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 x,y,z _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 5 ? A CYS 330 ? 1_555 ZN ? C ZN . ? A ZN 1383 ? 1_555 SG ? A CYS 8 ? A CYS 333 ? 1_555 109.1 ? 2 SG ? A CYS 5 ? A CYS 330 ? 1_555 ZN ? C ZN . ? A ZN 1383 ? 1_555 ND1 ? A HIS 30 ? A HIS 355 ? 1_555 100.6 ? 3 SG ? A CYS 8 ? A CYS 333 ? 1_555 ZN ? C ZN . ? A ZN 1383 ? 1_555 ND1 ? A HIS 30 ? A HIS 355 ? 1_555 103.6 ? 4 SG ? A CYS 5 ? A CYS 330 ? 1_555 ZN ? C ZN . ? A ZN 1383 ? 1_555 SG ? A CYS 33 ? A CYS 358 ? 1_555 118.6 ? 5 SG ? A CYS 8 ? A CYS 333 ? 1_555 ZN ? C ZN . ? A ZN 1383 ? 1_555 SG ? A CYS 33 ? A CYS 358 ? 1_555 110.8 ? 6 ND1 ? A HIS 30 ? A HIS 355 ? 1_555 ZN ? C ZN . ? A ZN 1383 ? 1_555 SG ? A CYS 33 ? A CYS 358 ? 1_555 112.7 ? 7 SG ? A CYS 57 ? A CYS 382 ? 1_555 ZN ? D ZN . ? A ZN 1384 ? 1_555 SG ? A CYS 54 ? A CYS 379 ? 1_555 102.0 ? 8 SG ? A CYS 57 ? A CYS 382 ? 1_555 ZN ? D ZN . ? A ZN 1384 ? 1_555 SG ? A CYS 21 ? A CYS 346 ? 1_555 114.4 ? 9 SG ? A CYS 54 ? A CYS 379 ? 1_555 ZN ? D ZN . ? A ZN 1384 ? 1_555 SG ? A CYS 21 ? A CYS 346 ? 1_555 114.0 ? 10 SG ? A CYS 57 ? A CYS 382 ? 1_555 ZN ? D ZN . ? A ZN 1384 ? 1_555 SG ? A CYS 25 ? A CYS 350 ? 1_555 105.1 ? 11 SG ? A CYS 54 ? A CYS 379 ? 1_555 ZN ? D ZN . ? A ZN 1384 ? 1_555 SG ? A CYS 25 ? A CYS 350 ? 1_555 115.3 ? 12 SG ? A CYS 21 ? A CYS 346 ? 1_555 ZN ? D ZN . ? A ZN 1384 ? 1_555 SG ? A CYS 25 ? A CYS 350 ? 1_555 106.0 ? # 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 2014-11-05 2 'Structure model' 1 1 2015-01-14 # _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_group.ordinal 1 _pdbx_audit_revision_group.revision_ordinal 2 _pdbx_audit_revision_group.data_content_type 'Structure model' _pdbx_audit_revision_group.group 'Database references' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal REFMAC refinement 5.7.0002 ? 1 MOSFLM 'data reduction' . ? 2 Aimless 'data scaling' . ? 3 PHASER phasing . ? 4 # _pdbx_entry_details.entry_id 4UP0 _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ;GLYCINE (REMNANT OF TEV CLEAVAGE SITE), PYGO2 PHD FINGER ( AAS 327-387), ARTIFICIAL LINKER (8AA LINKER-GSGSGSGS), B9L HD1 DOMAIN (AAS 235-263) OF ISOFORM 2 OF Q86UU0 ; # _pdbx_validate_rmsd_angle.id 1 _pdbx_validate_rmsd_angle.PDB_model_num 1 _pdbx_validate_rmsd_angle.auth_atom_id_1 NE _pdbx_validate_rmsd_angle.auth_asym_id_1 A _pdbx_validate_rmsd_angle.auth_comp_id_1 ARG _pdbx_validate_rmsd_angle.auth_seq_id_1 334 _pdbx_validate_rmsd_angle.PDB_ins_code_1 ? _pdbx_validate_rmsd_angle.label_alt_id_1 ? _pdbx_validate_rmsd_angle.auth_atom_id_2 CZ _pdbx_validate_rmsd_angle.auth_asym_id_2 A _pdbx_validate_rmsd_angle.auth_comp_id_2 ARG _pdbx_validate_rmsd_angle.auth_seq_id_2 334 _pdbx_validate_rmsd_angle.PDB_ins_code_2 ? _pdbx_validate_rmsd_angle.label_alt_id_2 ? _pdbx_validate_rmsd_angle.auth_atom_id_3 NH2 _pdbx_validate_rmsd_angle.auth_asym_id_3 A _pdbx_validate_rmsd_angle.auth_comp_id_3 ARG _pdbx_validate_rmsd_angle.auth_seq_id_3 334 _pdbx_validate_rmsd_angle.PDB_ins_code_3 ? _pdbx_validate_rmsd_angle.label_alt_id_3 ? _pdbx_validate_rmsd_angle.angle_value 116.66 _pdbx_validate_rmsd_angle.angle_target_value 120.30 _pdbx_validate_rmsd_angle.angle_deviation -3.64 _pdbx_validate_rmsd_angle.angle_standard_deviation 0.50 _pdbx_validate_rmsd_angle.linker_flag N # _pdbx_validate_torsion.id 1 _pdbx_validate_torsion.PDB_model_num 1 _pdbx_validate_torsion.auth_comp_id SER _pdbx_validate_torsion.auth_asym_id A _pdbx_validate_torsion.auth_seq_id 349 _pdbx_validate_torsion.PDB_ins_code ? _pdbx_validate_torsion.label_alt_id ? _pdbx_validate_torsion.phi -156.36 _pdbx_validate_torsion.psi -75.29 # _pdbx_distant_solvent_atoms.id 1 _pdbx_distant_solvent_atoms.PDB_model_num 1 _pdbx_distant_solvent_atoms.auth_atom_id O _pdbx_distant_solvent_atoms.label_alt_id ? _pdbx_distant_solvent_atoms.auth_asym_id A _pdbx_distant_solvent_atoms.auth_comp_id HOH _pdbx_distant_solvent_atoms.auth_seq_id 2012 _pdbx_distant_solvent_atoms.PDB_ins_code ? _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance 6.00 _pdbx_distant_solvent_atoms.neighbor_ligand_distance . # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 A LEU 383 ? A LEU 58 2 1 Y 1 A LYS 384 ? A LYS 59 3 1 Y 1 A THR 385 ? A THR 60 4 1 Y 1 A LYS 386 ? A LYS 61 5 1 Y 1 A GLU 387 ? A GLU 62 6 1 Y 1 A GLY 388 ? A GLY 63 7 1 Y 1 A SER 389 ? A SER 64 8 1 Y 1 A GLY 390 ? A GLY 65 9 1 Y 1 A SER 391 ? A SER 66 10 1 Y 1 A GLY 392 ? A GLY 67 11 1 Y 1 A SER 393 ? A SER 68 12 1 Y 1 A GLY 394 ? A GLY 69 13 1 Y 1 A SER 395 ? A SER 70 14 1 Y 1 A GLN 1263 ? A GLN 99 15 1 Y 1 F ALA 7 ? B ALA 7 16 1 Y 1 F ARG 8 ? B ARG 8 17 1 Y 1 F ALY 9 ? B ALY 9 18 1 Y 1 F SER 10 ? B SER 10 19 1 Y 1 F THR 11 ? B THR 11 20 1 Y 1 F GLY 12 ? B GLY 12 21 1 Y 1 F GLY 13 ? B GLY 13 22 1 Y 1 F LYS 14 ? B LYS 14 23 1 Y 1 F ALA 15 ? B ALA 15 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 3 'ZINC ION' ZN 4 water HOH #