data_5FQ2 # _entry.id 5FQ2 # _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 5FQ2 PDBE EBI-65708 WWPDB D_1290065708 # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 5FQ2 _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.SG_entry . _pdbx_database_status.recvd_initial_deposition_date 2015-12-04 _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 _audit_author.identifier_ORCID 'Liu, B.' 1 ? 'Castano, L.' 2 ? 'Lois, M.' 3 ? 'Reverter, D.' 4 ? # _citation.id primary _citation.title 'Crystal Structure of Human Sumo E1 Ufd Domain in Complex with Ubc9.' _citation.journal_abbrev 'To be Published' _citation.journal_volume ? _citation.page_first ? _citation.page_last ? _citation.year ? _citation.journal_id_ASTM ? _citation.country ? _citation.journal_id_ISSN ? _citation.journal_id_CSD 0353 _citation.book_publisher ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_DOI ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Liu, B.' 1 primary 'Castano, L.' 2 primary 'Lois, M.' 3 primary 'Reverter, D.' 4 # _cell.entry_id 5FQ2 _cell.length_a 129.614 _cell.length_b 129.614 _cell.length_c 66.578 _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 5FQ2 _symmetry.space_group_name_H-M 'P 43 21 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 # 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 'SUMO-CONJUGATING ENZYME UBC9' 18340.139 1 6.3.2.- ? ? 'LYSINE METHYLATION AT LYS110' 2 polymer man 'SUMO-ACTIVATING ENZYME SUBUNIT 2' 11746.217 1 6.3.2.- ? 'UBIQUITIN FOLD DOMAIN, UNP RESIDUES 446-547' 'LYSINE METHYLATION AT LYS505' 3 water nat water 18.015 38 ? ? ? ? # loop_ _entity_name_com.entity_id _entity_name_com.name 1 ;SUMO-PROTEIN LIGASE, UBIQUITIN CARRIER PROTEIN 9, UBIQUITIN CARRIER PROTEIN I, UBIQUITIN-CONJUGATING ENZYME E2 I, UBIQUITIN- PROTEIN LIGASE I, P18, SUMO E2-CONJUGATING ENZYME ; 2 ;ANTHRACYCLINE-ASSOCIATED RESISTANCE ARX, UBIQUITIN-LIKE 1-ACTIVATING ENZYME E1B, UBIQUITIN-LIKE MODIFIER-ACTIVATING ENZYME 2, SUMO E1 ACTIVATING ENZYME ; # 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 yes ;GSHMSGIALSRLAQERKAWRKDHPFGFVAVPTKNPDGTMNLMNWECAIPGKKGTPWEGGLFKLRMLFKDDYPSSPPKCKF EPPLFHPNVYPSGTVCLSILEEDKDWRPAITI(LDH)QILLGIQELLNEPNIQDPAQAEAYTIYCQNRVEYEKRVRAQAK KFAPS ; ;GSHMSGIALSRLAQERKAWRKDHPFGFVAVPTKNPDGTMNLMNWECAIPGKKGTPWEGGLFKLRMLFKDDYPSSPPKCKF EPPLFHPNVYPSGTVCLSILEEDKDWRPAITIKQILLGIQELLNEPNIQDPAQAEAYTIYCQNRVEYEKRVRAQAKKFAP S ; A ? 2 'polypeptide(L)' no yes ;GSHSKPEVTVRLNVHKVTVLTLQDKIVKEKFAMVAPDVQIEDGKGTILISSEEGETEANNHK(MLZ)LSEFGIRNGSRLQ ADDFLQDYTLLINILHSEDLGKDVEFEVV ; ;GSHSKPEVTVRLNVHKVTVLTLQDKIVKEKFAMVAPDVQIEDGKGTILISSEEGETEANNHKKLSEFGIRNGSRLQADDF LQDYTLLINILHSEDLGKDVEFEVV ; B ? # 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 SER n 1 3 HIS n 1 4 MET n 1 5 SER n 1 6 GLY n 1 7 ILE n 1 8 ALA n 1 9 LEU n 1 10 SER n 1 11 ARG n 1 12 LEU n 1 13 ALA n 1 14 GLN n 1 15 GLU n 1 16 ARG n 1 17 LYS n 1 18 ALA n 1 19 TRP n 1 20 ARG n 1 21 LYS n 1 22 ASP n 1 23 HIS n 1 24 PRO n 1 25 PHE n 1 26 GLY n 1 27 PHE n 1 28 VAL n 1 29 ALA n 1 30 VAL n 1 31 PRO n 1 32 THR n 1 33 LYS n 1 34 ASN n 1 35 PRO n 1 36 ASP n 1 37 GLY n 1 38 THR n 1 39 MET n 1 40 ASN n 1 41 LEU n 1 42 MET n 1 43 ASN n 1 44 TRP n 1 45 GLU n 1 46 CYS n 1 47 ALA n 1 48 ILE n 1 49 PRO n 1 50 GLY n 1 51 LYS n 1 52 LYS n 1 53 GLY n 1 54 THR n 1 55 PRO n 1 56 TRP n 1 57 GLU n 1 58 GLY n 1 59 GLY n 1 60 LEU n 1 61 PHE n 1 62 LYS n 1 63 LEU n 1 64 ARG n 1 65 MET n 1 66 LEU n 1 67 PHE n 1 68 LYS n 1 69 ASP n 1 70 ASP n 1 71 TYR n 1 72 PRO n 1 73 SER n 1 74 SER n 1 75 PRO n 1 76 PRO n 1 77 LYS n 1 78 CYS n 1 79 LYS n 1 80 PHE n 1 81 GLU n 1 82 PRO n 1 83 PRO n 1 84 LEU n 1 85 PHE n 1 86 HIS n 1 87 PRO n 1 88 ASN n 1 89 VAL n 1 90 TYR n 1 91 PRO n 1 92 SER n 1 93 GLY n 1 94 THR n 1 95 VAL n 1 96 CYS n 1 97 LEU n 1 98 SER n 1 99 ILE n 1 100 LEU n 1 101 GLU n 1 102 GLU n 1 103 ASP n 1 104 LYS n 1 105 ASP n 1 106 TRP n 1 107 ARG n 1 108 PRO n 1 109 ALA n 1 110 ILE n 1 111 THR n 1 112 ILE n 1 113 LDH n 1 114 GLN n 1 115 ILE n 1 116 LEU n 1 117 LEU n 1 118 GLY n 1 119 ILE n 1 120 GLN n 1 121 GLU n 1 122 LEU n 1 123 LEU n 1 124 ASN n 1 125 GLU n 1 126 PRO n 1 127 ASN n 1 128 ILE n 1 129 GLN n 1 130 ASP n 1 131 PRO n 1 132 ALA n 1 133 GLN n 1 134 ALA n 1 135 GLU n 1 136 ALA n 1 137 TYR n 1 138 THR n 1 139 ILE n 1 140 TYR n 1 141 CYS n 1 142 GLN n 1 143 ASN n 1 144 ARG n 1 145 VAL n 1 146 GLU n 1 147 TYR n 1 148 GLU n 1 149 LYS n 1 150 ARG n 1 151 VAL n 1 152 ARG n 1 153 ALA n 1 154 GLN n 1 155 ALA n 1 156 LYS n 1 157 LYS n 1 158 PHE n 1 159 ALA n 1 160 PRO n 1 161 SER n 2 1 GLY n 2 2 SER n 2 3 HIS n 2 4 SER n 2 5 LYS n 2 6 PRO n 2 7 GLU n 2 8 VAL n 2 9 THR n 2 10 VAL n 2 11 ARG n 2 12 LEU n 2 13 ASN n 2 14 VAL n 2 15 HIS n 2 16 LYS n 2 17 VAL n 2 18 THR n 2 19 VAL n 2 20 LEU n 2 21 THR n 2 22 LEU n 2 23 GLN n 2 24 ASP n 2 25 LYS n 2 26 ILE n 2 27 VAL n 2 28 LYS n 2 29 GLU n 2 30 LYS n 2 31 PHE n 2 32 ALA n 2 33 MET n 2 34 VAL n 2 35 ALA n 2 36 PRO n 2 37 ASP n 2 38 VAL n 2 39 GLN n 2 40 ILE n 2 41 GLU n 2 42 ASP n 2 43 GLY n 2 44 LYS n 2 45 GLY n 2 46 THR n 2 47 ILE n 2 48 LEU n 2 49 ILE n 2 50 SER n 2 51 SER n 2 52 GLU n 2 53 GLU n 2 54 GLY n 2 55 GLU n 2 56 THR n 2 57 GLU n 2 58 ALA n 2 59 ASN n 2 60 ASN n 2 61 HIS n 2 62 LYS n 2 63 MLZ n 2 64 LEU n 2 65 SER n 2 66 GLU n 2 67 PHE n 2 68 GLY n 2 69 ILE n 2 70 ARG n 2 71 ASN n 2 72 GLY n 2 73 SER n 2 74 ARG n 2 75 LEU n 2 76 GLN n 2 77 ALA n 2 78 ASP n 2 79 ASP n 2 80 PHE n 2 81 LEU n 2 82 GLN n 2 83 ASP n 2 84 TYR n 2 85 THR n 2 86 LEU n 2 87 LEU n 2 88 ILE n 2 89 ASN n 2 90 ILE n 2 91 LEU n 2 92 HIS n 2 93 SER n 2 94 GLU n 2 95 ASP n 2 96 LEU n 2 97 GLY n 2 98 LYS n 2 99 ASP n 2 100 VAL n 2 101 GLU n 2 102 PHE n 2 103 GLU n 2 104 VAL n 2 105 VAL n # loop_ _entity_src_gen.entity_id _entity_src_gen.pdbx_src_id _entity_src_gen.pdbx_alt_source_flag _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 _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 _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id _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 _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id _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 _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 _entity_src_gen.pdbx_host_org_vector _entity_src_gen.host_org_details _entity_src_gen.expression_system_id _entity_src_gen.plasmid_name _entity_src_gen.plasmid_details _entity_src_gen.pdbx_description 1 1 sample ? ? ? HUMAN ? ? ? ? ? ? ? ? 'HOMO SAPIENS' 9606 ? ? ? ? ? ? ? ? 'ESCHERICHIA COLI' 511693 ? ? ? ? ? ? BL21 ? ? ? ? ? ? ? PLASMID PET28 ? ? ? ? ? 2 1 sample ? ? ? HUMAN ? ? ? ? ? ? ? ? 'HOMO SAPIENS' 9606 ? ? ? ? ? ? ? ? 'ESCHERICHIA COLI' 511693 ? ? ? ? ? ? BL21 ? ? ? ? ? ? ? PLASMID PET28 ? ? ? ? ? # 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 UBC9_HUMAN 1 ? ? P63279 ? 2 UNP SAE2_HUMAN 2 ? ? Q9UBT2 ? # 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 5FQ2 A 4 ? 161 ? P63279 1 ? 158 ? 1 158 2 2 5FQ2 B 4 ? 105 ? Q9UBT2 446 ? 547 ? 446 547 # 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 5FQ2 GLY A 1 ? UNP P63279 ? ? 'expression tag' -2 1 1 5FQ2 SER A 2 ? UNP P63279 ? ? 'expression tag' -1 2 1 5FQ2 HIS A 3 ? UNP P63279 ? ? 'expression tag' 0 3 2 5FQ2 GLY B 1 ? UNP Q9UBT2 ? ? 'expression tag' 443 4 2 5FQ2 SER B 2 ? UNP Q9UBT2 ? ? 'expression tag' 444 5 2 5FQ2 HIS B 3 ? UNP Q9UBT2 ? ? 'expression tag' 445 6 # 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 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LDH 'L-peptide linking' n N~6~-ETHYL-L-LYSINE ? 'C8 H18 N2 O2' 174.241 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 MLZ 'L-peptide linking' n N-METHYL-LYSINE ? 'C7 H16 N2 O2' 160.214 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 # _exptl.entry_id 5FQ2 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 4.65 _exptl_crystal.density_percent_sol 75.53 _exptl_crystal.description NONE # _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 ? _diffrn_detector.details ? # _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 0.9794 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ALBA BEAMLINE XALOC' _diffrn_source.pdbx_synchrotron_site ALBA _diffrn_source.pdbx_synchrotron_beamline XALOC _diffrn_source.pdbx_wavelength 0.9794 _diffrn_source.pdbx_wavelength_list ? # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 5FQ2 _reflns.observed_criterion_sigma_I 2.0 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 46.44 _reflns.d_resolution_high 2.20 _reflns.number_obs 29309 _reflns.number_all ? _reflns.percent_possible_obs 99.8 _reflns.pdbx_Rmerge_I_obs 0.04 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 26.40 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 10.9 # _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_ordinal 1 _reflns_shell.d_res_high 2.20 _reflns_shell.d_res_low 2.32 _reflns_shell.percent_possible_all 98.4 _reflns_shell.Rmerge_I_obs 0.60 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 4.30 _reflns_shell.pdbx_redundancy 11 # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 5FQ2 _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 29254 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.33 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 46.439 _refine.ls_d_res_high 2.201 _refine.ls_percent_reflns_obs 99.75 _refine.ls_R_factor_obs 0.2303 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.2293 _refine.ls_R_factor_R_free 0.2489 _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 1488 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.11 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.90 _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model NONE _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ML _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML 0.22 _refine.pdbx_overall_phase_error 24.82 _refine.overall_SU_B ? _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 2062 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 38 _refine_hist.number_atoms_total 2100 _refine_hist.d_res_high 2.201 _refine_hist.d_res_low 46.439 # 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 f_bond_d 0.008 ? ? 2108 'X-RAY DIFFRACTION' ? f_angle_d 1.114 ? ? 2853 'X-RAY DIFFRACTION' ? f_dihedral_angle_d 14.191 ? ? 808 'X-RAY DIFFRACTION' ? f_chiral_restr 0.048 ? ? 312 'X-RAY DIFFRACTION' ? f_plane_restr 0.005 ? ? 373 'X-RAY DIFFRACTION' ? # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_R_work _refine_ls_shell.R_factor_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.R_factor_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_all _refine_ls_shell.R_factor_all 'X-RAY DIFFRACTION' . 2.2009 2.2720 2408 0.2633 97.00 0.3149 . . 145 . . 'X-RAY DIFFRACTION' . 2.2720 2.3532 2479 0.2583 100.00 0.2703 . . 127 . . 'X-RAY DIFFRACTION' . 2.3532 2.4474 2479 0.2554 100.00 0.3334 . . 140 . . 'X-RAY DIFFRACTION' . 2.4474 2.5588 2494 0.2431 100.00 0.2482 . . 139 . . 'X-RAY DIFFRACTION' . 2.5588 2.6937 2506 0.2604 100.00 0.2986 . . 129 . . 'X-RAY DIFFRACTION' . 2.6937 2.8624 2502 0.2600 100.00 0.2630 . . 132 . . 'X-RAY DIFFRACTION' . 2.8624 3.0834 2508 0.2558 100.00 0.2553 . . 141 . . 'X-RAY DIFFRACTION' . 3.0834 3.3936 2530 0.2524 100.00 0.2841 . . 135 . . 'X-RAY DIFFRACTION' . 3.3936 3.8844 2529 0.2244 100.00 0.2485 . . 144 . . 'X-RAY DIFFRACTION' . 3.8844 4.8931 2592 0.1981 100.00 0.2188 . . 126 . . 'X-RAY DIFFRACTION' . 4.8931 46.4493 2739 0.2228 100.00 0.2317 . . 130 . . # _struct.entry_id 5FQ2 _struct.title 'Crystal structure of human SUMO E1 UFD domain in complex with Ubc9 in a P422 space group.' _struct.pdbx_descriptor 'SUMO-CONJUGATING ENZYME UBC9 (E.C.6.3.2.-), SUMO-ACTIVATING ENZYME SUBUNIT 2 (E.C.6.3.2.-)' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 5FQ2 _struct_keywords.pdbx_keywords LIGASE _struct_keywords.text 'LIGASE, ACTIVATING ENZYME, CONJUGATING ENZYME, SUMO' # 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 ? # 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 SER A 5 ? ASP A 22 ? SER A 2 ASP A 19 1 ? 18 HELX_P HELX_P2 2 LEU A 97 ? GLU A 101 ? LEU A 94 GLU A 98 5 ? 5 HELX_P HELX_P3 3 THR A 111 ? GLU A 125 ? THR A 108 GLU A 122 1 ? 15 HELX_P HELX_P4 4 GLN A 133 ? ASN A 143 ? GLN A 130 ASN A 140 1 ? 11 HELX_P HELX_P5 5 ASN A 143 ? PHE A 158 ? ASN A 140 PHE A 155 1 ? 16 HELX_P HELX_P6 6 THR B 18 ? LYS B 25 ? THR B 460 LYS B 467 1 ? 8 HELX_P HELX_P7 7 ILE B 26 ? PHE B 31 ? ILE B 468 PHE B 473 1 ? 6 HELX_P HELX_P8 8 THR B 56 ? ASN B 60 ? THR B 498 ASN B 502 5 ? 5 HELX_P HELX_P9 9 LEU B 64 ? GLY B 68 ? LEU B 506 GLY B 510 5 ? 5 # _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 covale1 covale ? ? A ILE 112 C ? ? ? 1_555 A LDH 113 N ? ? A ILE 109 A LDH 110 1_555 ? ? ? ? ? ? ? 1.324 ? covale2 covale ? ? A LDH 113 C ? ? ? 1_555 A GLN 114 N ? ? A LDH 110 A GLN 111 1_555 ? ? ? ? ? ? ? 1.333 ? covale3 covale ? ? B LYS 62 C ? ? ? 1_555 B MLZ 63 N ? ? B LYS 504 B MLZ 505 1_555 ? ? ? ? ? ? ? 1.337 ? covale4 covale ? ? B MLZ 63 C ? ? ? 1_555 B LEU 64 N ? ? B MLZ 505 B LEU 506 1_555 ? ? ? ? ? ? ? 1.333 ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _struct_mon_prot_cis.pdbx_id _struct_mon_prot_cis.label_comp_id _struct_mon_prot_cis.label_seq_id _struct_mon_prot_cis.label_asym_id _struct_mon_prot_cis.label_alt_id _struct_mon_prot_cis.pdbx_PDB_ins_code _struct_mon_prot_cis.auth_comp_id _struct_mon_prot_cis.auth_seq_id _struct_mon_prot_cis.auth_asym_id _struct_mon_prot_cis.pdbx_label_comp_id_2 _struct_mon_prot_cis.pdbx_label_seq_id_2 _struct_mon_prot_cis.pdbx_label_asym_id_2 _struct_mon_prot_cis.pdbx_PDB_ins_code_2 _struct_mon_prot_cis.pdbx_auth_comp_id_2 _struct_mon_prot_cis.pdbx_auth_seq_id_2 _struct_mon_prot_cis.pdbx_auth_asym_id_2 _struct_mon_prot_cis.pdbx_PDB_model_num _struct_mon_prot_cis.pdbx_omega_angle 1 TYR 71 A . ? TYR 68 A PRO 72 A ? PRO 69 A 1 7.21 2 GLU 81 A . ? GLU 78 A PRO 82 A ? PRO 79 A 1 1.10 3 GLU 53 B . ? GLU 495 B GLY 54 B ? GLY 496 B 1 -6.08 # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details AA ? 2 ? AB ? 9 ? AC ? 4 ? # 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 ? anti-parallel AB 2 3 ? parallel AB 3 4 ? anti-parallel AB 4 5 ? anti-parallel AB 5 6 ? anti-parallel AB 6 7 ? anti-parallel AB 7 8 ? parallel AB 8 9 ? anti-parallel AC 1 2 ? anti-parallel AC 2 3 ? parallel AC 3 4 ? 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 AA 1 VAL A 28 ? LYS A 33 ? VAL A 25 LYS A 30 AA 2 MET A 39 ? PRO A 49 ? MET A 36 PRO A 46 AB 1 LYS A 77 ? PHE A 80 ? LYS A 74 PHE A 77 AB 2 LEU A 60 ? LEU A 66 ? LEU A 57 LEU A 63 AB 3 MET A 39 ? PRO A 49 ? MET A 36 PRO A 46 AB 4 THR B 46 ? ILE B 49 ? THR B 488 ILE B 491 AB 5 PRO B 36 ? ILE B 40 ? PRO B 478 ILE B 482 AB 6 ARG B 74 ? ASP B 79 ? ARG B 516 ASP B 521 AB 7 THR B 85 ? HIS B 92 ? THR B 527 HIS B 534 AB 8 GLU B 7 ? LEU B 12 ? GLU B 449 LEU B 454 AB 9 PHE B 102 ? VAL B 104 ? PHE B 544 VAL B 546 AC 1 LYS A 77 ? PHE A 80 ? LYS A 74 PHE A 77 AC 2 LEU A 60 ? LEU A 66 ? LEU A 57 LEU A 63 AC 3 MET A 39 ? PRO A 49 ? MET A 36 PRO A 46 AC 4 VAL A 28 ? LYS A 33 ? VAL A 25 LYS A 30 # 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 O THR A 32 ? O THR A 29 N ASN A 40 ? N ASN A 37 AB 1 2 N LYS A 79 ? N LYS A 76 O ARG A 64 ? O ARG A 61 AB 2 3 N MET A 65 ? N MET A 62 O TRP A 44 ? O TRP A 41 AB 3 4 N MET A 39 ? N MET A 36 O ILE B 47 ? O ILE B 489 AB 4 5 N LEU B 48 ? N LEU B 490 O VAL B 38 ? O VAL B 480 AB 5 6 N GLN B 39 ? N GLN B 481 O GLN B 76 ? O GLN B 518 AB 6 7 N ALA B 77 ? N ALA B 519 O LEU B 86 ? O LEU B 528 AB 7 8 N ASN B 89 ? N ASN B 531 O VAL B 8 ? O VAL B 450 AB 8 9 N ARG B 11 ? N ARG B 453 O GLU B 103 ? O GLU B 545 AC 1 2 N LYS A 79 ? N LYS A 76 O ARG A 64 ? O ARG A 61 AC 2 3 N MET A 65 ? N MET A 62 O TRP A 44 ? O TRP A 41 AC 3 4 N ALA A 47 ? N ALA A 44 O VAL A 28 ? O VAL A 25 # _database_PDB_matrix.entry_id 5FQ2 _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 5FQ2 _atom_sites.fract_transf_matrix[1][1] 0.007715 _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] 0.007715 _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] 0.015020 _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 # 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 -2 ? ? ? A . n A 1 2 SER 2 -1 ? ? ? A . n A 1 3 HIS 3 0 ? ? ? A . n A 1 4 MET 4 1 ? ? ? A . n A 1 5 SER 5 2 2 SER SER A . n A 1 6 GLY 6 3 3 GLY GLY A . n A 1 7 ILE 7 4 4 ILE ILE A . n A 1 8 ALA 8 5 5 ALA ALA A . n A 1 9 LEU 9 6 6 LEU LEU A . n A 1 10 SER 10 7 7 SER SER A . n A 1 11 ARG 11 8 8 ARG ARG A . n A 1 12 LEU 12 9 9 LEU LEU A . n A 1 13 ALA 13 10 10 ALA ALA A . n A 1 14 GLN 14 11 11 GLN GLN A . n A 1 15 GLU 15 12 12 GLU GLU A . n A 1 16 ARG 16 13 13 ARG ARG A . n A 1 17 LYS 17 14 14 LYS LYS A . n A 1 18 ALA 18 15 15 ALA ALA A . n A 1 19 TRP 19 16 16 TRP TRP A . n A 1 20 ARG 20 17 17 ARG ARG A . n A 1 21 LYS 21 18 18 LYS LYS A . n A 1 22 ASP 22 19 19 ASP ASP A . n A 1 23 HIS 23 20 20 HIS HIS A . n A 1 24 PRO 24 21 21 PRO PRO A . n A 1 25 PHE 25 22 22 PHE PHE A . n A 1 26 GLY 26 23 23 GLY GLY A . n A 1 27 PHE 27 24 24 PHE PHE A . n A 1 28 VAL 28 25 25 VAL VAL A . n A 1 29 ALA 29 26 26 ALA ALA A . n A 1 30 VAL 30 27 27 VAL VAL A . n A 1 31 PRO 31 28 28 PRO PRO A . n A 1 32 THR 32 29 29 THR THR A . n A 1 33 LYS 33 30 30 LYS LYS A . n A 1 34 ASN 34 31 31 ASN ASN A . n A 1 35 PRO 35 32 32 PRO PRO A . n A 1 36 ASP 36 33 33 ASP ASP A . n A 1 37 GLY 37 34 34 GLY GLY A . n A 1 38 THR 38 35 35 THR THR A . n A 1 39 MET 39 36 36 MET MET A . n A 1 40 ASN 40 37 37 ASN ASN A . n A 1 41 LEU 41 38 38 LEU LEU A . n A 1 42 MET 42 39 39 MET MET A . n A 1 43 ASN 43 40 40 ASN ASN A . n A 1 44 TRP 44 41 41 TRP TRP A . n A 1 45 GLU 45 42 42 GLU GLU A . n A 1 46 CYS 46 43 43 CYS CYS A . n A 1 47 ALA 47 44 44 ALA ALA A . n A 1 48 ILE 48 45 45 ILE ILE A . n A 1 49 PRO 49 46 46 PRO PRO A . n A 1 50 GLY 50 47 47 GLY GLY A . n A 1 51 LYS 51 48 48 LYS LYS A . n A 1 52 LYS 52 49 49 LYS LYS A . n A 1 53 GLY 53 50 50 GLY GLY A . n A 1 54 THR 54 51 51 THR THR A . n A 1 55 PRO 55 52 52 PRO PRO A . n A 1 56 TRP 56 53 53 TRP TRP A . n A 1 57 GLU 57 54 54 GLU GLU A . n A 1 58 GLY 58 55 55 GLY GLY A . n A 1 59 GLY 59 56 56 GLY GLY A . n A 1 60 LEU 60 57 57 LEU LEU A . n A 1 61 PHE 61 58 58 PHE PHE A . n A 1 62 LYS 62 59 59 LYS LYS A . n A 1 63 LEU 63 60 60 LEU LEU A . n A 1 64 ARG 64 61 61 ARG ARG A . n A 1 65 MET 65 62 62 MET MET A . n A 1 66 LEU 66 63 63 LEU LEU A . n A 1 67 PHE 67 64 64 PHE PHE A . n A 1 68 LYS 68 65 65 LYS LYS A . n A 1 69 ASP 69 66 66 ASP ASP A . n A 1 70 ASP 70 67 67 ASP ASP A . n A 1 71 TYR 71 68 68 TYR TYR A . n A 1 72 PRO 72 69 69 PRO PRO A . n A 1 73 SER 73 70 70 SER SER A . n A 1 74 SER 74 71 71 SER SER A . n A 1 75 PRO 75 72 72 PRO PRO A . n A 1 76 PRO 76 73 73 PRO PRO A . n A 1 77 LYS 77 74 74 LYS LYS A . n A 1 78 CYS 78 75 75 CYS CYS A . n A 1 79 LYS 79 76 76 LYS LYS A . n A 1 80 PHE 80 77 77 PHE PHE A . n A 1 81 GLU 81 78 78 GLU GLU A . n A 1 82 PRO 82 79 79 PRO PRO A . n A 1 83 PRO 83 80 80 PRO PRO A . n A 1 84 LEU 84 81 81 LEU LEU A . n A 1 85 PHE 85 82 82 PHE PHE A . n A 1 86 HIS 86 83 83 HIS HIS A . n A 1 87 PRO 87 84 84 PRO PRO A . n A 1 88 ASN 88 85 85 ASN ASN A . n A 1 89 VAL 89 86 86 VAL VAL A . n A 1 90 TYR 90 87 87 TYR TYR A . n A 1 91 PRO 91 88 88 PRO PRO A . n A 1 92 SER 92 89 89 SER SER A . n A 1 93 GLY 93 90 90 GLY GLY A . n A 1 94 THR 94 91 91 THR THR A . n A 1 95 VAL 95 92 92 VAL VAL A . n A 1 96 CYS 96 93 93 CYS CYS A . n A 1 97 LEU 97 94 94 LEU LEU A . n A 1 98 SER 98 95 95 SER SER A . n A 1 99 ILE 99 96 96 ILE ILE A . n A 1 100 LEU 100 97 97 LEU LEU A . n A 1 101 GLU 101 98 98 GLU GLU A . n A 1 102 GLU 102 99 99 GLU GLU A . n A 1 103 ASP 103 100 100 ASP ASP A . n A 1 104 LYS 104 101 101 LYS LYS A . n A 1 105 ASP 105 102 102 ASP ASP A . n A 1 106 TRP 106 103 103 TRP TRP A . n A 1 107 ARG 107 104 104 ARG ARG A . n A 1 108 PRO 108 105 105 PRO PRO A . n A 1 109 ALA 109 106 106 ALA ALA A . n A 1 110 ILE 110 107 107 ILE ILE A . n A 1 111 THR 111 108 108 THR THR A . n A 1 112 ILE 112 109 109 ILE ILE A . n A 1 113 LDH 113 110 110 LDH LDH A . n A 1 114 GLN 114 111 111 GLN GLN A . n A 1 115 ILE 115 112 112 ILE ILE A . n A 1 116 LEU 116 113 113 LEU LEU A . n A 1 117 LEU 117 114 114 LEU LEU A . n A 1 118 GLY 118 115 115 GLY GLY A . n A 1 119 ILE 119 116 116 ILE ILE A . n A 1 120 GLN 120 117 117 GLN GLN A . n A 1 121 GLU 121 118 118 GLU GLU A . n A 1 122 LEU 122 119 119 LEU LEU A . n A 1 123 LEU 123 120 120 LEU LEU A . n A 1 124 ASN 124 121 121 ASN ASN A . n A 1 125 GLU 125 122 122 GLU GLU A . n A 1 126 PRO 126 123 123 PRO PRO A . n A 1 127 ASN 127 124 124 ASN ASN A . n A 1 128 ILE 128 125 125 ILE ILE A . n A 1 129 GLN 129 126 126 GLN GLN A . n A 1 130 ASP 130 127 127 ASP ASP A . n A 1 131 PRO 131 128 128 PRO PRO A . n A 1 132 ALA 132 129 129 ALA ALA A . n A 1 133 GLN 133 130 130 GLN GLN A . n A 1 134 ALA 134 131 131 ALA ALA A . n A 1 135 GLU 135 132 132 GLU GLU A . n A 1 136 ALA 136 133 133 ALA ALA A . n A 1 137 TYR 137 134 134 TYR TYR A . n A 1 138 THR 138 135 135 THR THR A . n A 1 139 ILE 139 136 136 ILE ILE A . n A 1 140 TYR 140 137 137 TYR TYR A . n A 1 141 CYS 141 138 138 CYS CYS A . n A 1 142 GLN 142 139 139 GLN GLN A . n A 1 143 ASN 143 140 140 ASN ASN A . n A 1 144 ARG 144 141 141 ARG ARG A . n A 1 145 VAL 145 142 142 VAL VAL A . n A 1 146 GLU 146 143 143 GLU GLU A . n A 1 147 TYR 147 144 144 TYR TYR A . n A 1 148 GLU 148 145 145 GLU GLU A . n A 1 149 LYS 149 146 146 LYS LYS A . n A 1 150 ARG 150 147 147 ARG ARG A . n A 1 151 VAL 151 148 148 VAL VAL A . n A 1 152 ARG 152 149 149 ARG ARG A . n A 1 153 ALA 153 150 150 ALA ALA A . n A 1 154 GLN 154 151 151 GLN GLN A . n A 1 155 ALA 155 152 152 ALA ALA A . n A 1 156 LYS 156 153 153 LYS LYS A . n A 1 157 LYS 157 154 154 LYS LYS A . n A 1 158 PHE 158 155 155 PHE PHE A . n A 1 159 ALA 159 156 156 ALA ALA A . n A 1 160 PRO 160 157 157 PRO PRO A . n A 1 161 SER 161 158 158 SER SER A . n B 2 1 GLY 1 443 ? ? ? B . n B 2 2 SER 2 444 ? ? ? B . n B 2 3 HIS 3 445 ? ? ? B . n B 2 4 SER 4 446 ? ? ? B . n B 2 5 LYS 5 447 447 LYS LYS B . n B 2 6 PRO 6 448 448 PRO PRO B . n B 2 7 GLU 7 449 449 GLU GLU B . n B 2 8 VAL 8 450 450 VAL VAL B . n B 2 9 THR 9 451 451 THR THR B . n B 2 10 VAL 10 452 452 VAL VAL B . n B 2 11 ARG 11 453 453 ARG ARG B . n B 2 12 LEU 12 454 454 LEU LEU B . n B 2 13 ASN 13 455 455 ASN ASN B . n B 2 14 VAL 14 456 456 VAL VAL B . n B 2 15 HIS 15 457 457 HIS HIS B . n B 2 16 LYS 16 458 458 LYS LYS B . n B 2 17 VAL 17 459 459 VAL VAL B . n B 2 18 THR 18 460 460 THR THR B . n B 2 19 VAL 19 461 461 VAL VAL B . n B 2 20 LEU 20 462 462 LEU LEU B . n B 2 21 THR 21 463 463 THR THR B . n B 2 22 LEU 22 464 464 LEU LEU B . n B 2 23 GLN 23 465 465 GLN GLN B . n B 2 24 ASP 24 466 466 ASP ASP B . n B 2 25 LYS 25 467 467 LYS LYS B . n B 2 26 ILE 26 468 468 ILE ILE B . n B 2 27 VAL 27 469 469 VAL VAL B . n B 2 28 LYS 28 470 470 LYS LYS B . n B 2 29 GLU 29 471 471 GLU GLU B . n B 2 30 LYS 30 472 472 LYS LYS B . n B 2 31 PHE 31 473 473 PHE PHE B . n B 2 32 ALA 32 474 474 ALA ALA B . n B 2 33 MET 33 475 475 MET MET B . n B 2 34 VAL 34 476 476 VAL VAL B . n B 2 35 ALA 35 477 477 ALA ALA B . n B 2 36 PRO 36 478 478 PRO PRO B . n B 2 37 ASP 37 479 479 ASP ASP B . n B 2 38 VAL 38 480 480 VAL VAL B . n B 2 39 GLN 39 481 481 GLN GLN B . n B 2 40 ILE 40 482 482 ILE ILE B . n B 2 41 GLU 41 483 483 GLU GLU B . n B 2 42 ASP 42 484 484 ASP ASP B . n B 2 43 GLY 43 485 485 GLY GLY B . n B 2 44 LYS 44 486 486 LYS LYS B . n B 2 45 GLY 45 487 487 GLY GLY B . n B 2 46 THR 46 488 488 THR THR B . n B 2 47 ILE 47 489 489 ILE ILE B . n B 2 48 LEU 48 490 490 LEU LEU B . n B 2 49 ILE 49 491 491 ILE ILE B . n B 2 50 SER 50 492 492 SER SER B . n B 2 51 SER 51 493 493 SER SER B . n B 2 52 GLU 52 494 494 GLU GLU B . n B 2 53 GLU 53 495 495 GLU GLU B . n B 2 54 GLY 54 496 496 GLY GLY B . n B 2 55 GLU 55 497 497 GLU GLU B . n B 2 56 THR 56 498 498 THR THR B . n B 2 57 GLU 57 499 499 GLU GLU B . n B 2 58 ALA 58 500 500 ALA ALA B . n B 2 59 ASN 59 501 501 ASN ASN B . n B 2 60 ASN 60 502 502 ASN ASN B . n B 2 61 HIS 61 503 503 HIS HIS B . n B 2 62 LYS 62 504 504 LYS LYS B . n B 2 63 MLZ 63 505 505 MLZ MLZ B . n B 2 64 LEU 64 506 506 LEU LEU B . n B 2 65 SER 65 507 507 SER SER B . n B 2 66 GLU 66 508 508 GLU GLU B . n B 2 67 PHE 67 509 509 PHE PHE B . n B 2 68 GLY 68 510 510 GLY GLY B . n B 2 69 ILE 69 511 511 ILE ILE B . n B 2 70 ARG 70 512 512 ARG ARG B . n B 2 71 ASN 71 513 513 ASN ASN B . n B 2 72 GLY 72 514 514 GLY GLY B . n B 2 73 SER 73 515 515 SER SER B . n B 2 74 ARG 74 516 516 ARG ARG B . n B 2 75 LEU 75 517 517 LEU LEU B . n B 2 76 GLN 76 518 518 GLN GLN B . n B 2 77 ALA 77 519 519 ALA ALA B . n B 2 78 ASP 78 520 520 ASP ASP B . n B 2 79 ASP 79 521 521 ASP ASP B . n B 2 80 PHE 80 522 522 PHE PHE B . n B 2 81 LEU 81 523 523 LEU LEU B . n B 2 82 GLN 82 524 524 GLN GLN B . n B 2 83 ASP 83 525 525 ASP ASP B . n B 2 84 TYR 84 526 526 TYR TYR B . n B 2 85 THR 85 527 527 THR THR B . n B 2 86 LEU 86 528 528 LEU LEU B . n B 2 87 LEU 87 529 529 LEU LEU B . n B 2 88 ILE 88 530 530 ILE ILE B . n B 2 89 ASN 89 531 531 ASN ASN B . n B 2 90 ILE 90 532 532 ILE ILE B . n B 2 91 LEU 91 533 533 LEU LEU B . n B 2 92 HIS 92 534 534 HIS HIS B . n B 2 93 SER 93 535 535 SER SER B . n B 2 94 GLU 94 536 536 GLU GLU B . n B 2 95 ASP 95 537 537 ASP ASP B . n B 2 96 LEU 96 538 538 LEU LEU B . n B 2 97 GLY 97 539 539 GLY GLY B . n B 2 98 LYS 98 540 540 LYS LYS B . n B 2 99 ASP 99 541 541 ASP ASP B . n B 2 100 VAL 100 542 542 VAL VAL B . n B 2 101 GLU 101 543 543 GLU GLU B . n B 2 102 PHE 102 544 544 PHE PHE B . n B 2 103 GLU 103 545 545 GLU GLU B . n B 2 104 VAL 104 546 546 VAL VAL B . n B 2 105 VAL 105 547 547 VAL VAL B . 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 HOH 1 2001 2001 HOH HOH A . C 3 HOH 2 2002 2002 HOH HOH A . C 3 HOH 3 2003 2003 HOH HOH A . C 3 HOH 4 2004 2004 HOH HOH A . C 3 HOH 5 2005 2005 HOH HOH A . C 3 HOH 6 2006 2006 HOH HOH A . C 3 HOH 7 2007 2007 HOH HOH A . C 3 HOH 8 2008 2008 HOH HOH A . C 3 HOH 9 2009 2009 HOH HOH A . C 3 HOH 10 2010 2010 HOH HOH A . C 3 HOH 11 2011 2011 HOH HOH A . C 3 HOH 12 2012 2012 HOH HOH A . C 3 HOH 13 2013 2013 HOH HOH A . C 3 HOH 14 2014 2014 HOH HOH A . C 3 HOH 15 2015 2015 HOH HOH A . C 3 HOH 16 2016 2016 HOH HOH A . C 3 HOH 17 2017 2017 HOH HOH A . C 3 HOH 18 2018 2018 HOH HOH A . C 3 HOH 19 2019 2019 HOH HOH A . C 3 HOH 20 2020 2020 HOH HOH A . C 3 HOH 21 2021 2021 HOH HOH A . C 3 HOH 22 2022 2022 HOH HOH A . D 3 HOH 1 2001 2001 HOH HOH B . D 3 HOH 2 2002 2002 HOH HOH B . D 3 HOH 3 2003 2003 HOH HOH B . D 3 HOH 4 2004 2004 HOH HOH B . D 3 HOH 5 2005 2005 HOH HOH B . D 3 HOH 6 2006 2006 HOH HOH B . D 3 HOH 7 2007 2007 HOH HOH B . D 3 HOH 8 2008 2008 HOH HOH B . D 3 HOH 9 2009 2009 HOH HOH B . D 3 HOH 10 2010 2010 HOH HOH B . D 3 HOH 11 2011 2011 HOH HOH B . D 3 HOH 12 2012 2012 HOH HOH B . D 3 HOH 13 2013 2013 HOH HOH B . D 3 HOH 14 2014 2014 HOH HOH B . D 3 HOH 15 2015 2015 HOH HOH B . D 3 HOH 16 2016 2016 HOH HOH B . # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A LDH 113 A LDH 110 ? LYS N~6~-ETHYL-L-LYSINE 2 B MLZ 63 B MLZ 505 ? LYS N-METHYL-LYSINE # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PQS _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 # 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)' 1740 ? 1 MORE -2.4 ? 1 'SSA (A^2)' 16320 ? # _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 # _pdbx_audit_revision_history.ordinal 1 _pdbx_audit_revision_history.data_content_type 'Structure model' _pdbx_audit_revision_history.major_revision 1 _pdbx_audit_revision_history.minor_revision 0 _pdbx_audit_revision_history.revision_date 2016-11-16 # _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_refine_tls.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls.id 1 _pdbx_refine_tls.details ? _pdbx_refine_tls.method refined _pdbx_refine_tls.origin_x 30.6666 _pdbx_refine_tls.origin_y 124.7904 _pdbx_refine_tls.origin_z 13.2245 _pdbx_refine_tls.T[1][1] 0.4080 _pdbx_refine_tls.T[2][2] 0.4243 _pdbx_refine_tls.T[3][3] 0.4343 _pdbx_refine_tls.T[1][2] -0.0283 _pdbx_refine_tls.T[1][3] 0.0617 _pdbx_refine_tls.T[2][3] -0.0141 _pdbx_refine_tls.L[1][1] 0.6376 _pdbx_refine_tls.L[2][2] 5.0730 _pdbx_refine_tls.L[3][3] 0.3453 _pdbx_refine_tls.L[1][2] -1.8015 _pdbx_refine_tls.L[1][3] 0.1082 _pdbx_refine_tls.L[2][3] 0.1130 _pdbx_refine_tls.S[1][1] -0.0723 _pdbx_refine_tls.S[1][2] -0.0809 _pdbx_refine_tls.S[1][3] -0.0548 _pdbx_refine_tls.S[2][1] 0.0106 _pdbx_refine_tls.S[2][2] 0.0570 _pdbx_refine_tls.S[2][3] 0.1050 _pdbx_refine_tls.S[3][1] -0.0032 _pdbx_refine_tls.S[3][2] 0.0477 _pdbx_refine_tls.S[3][3] 0.0253 # _pdbx_refine_tls_group.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls_group.id 1 _pdbx_refine_tls_group.refine_tls_id 1 _pdbx_refine_tls_group.beg_auth_asym_id ? _pdbx_refine_tls_group.beg_auth_seq_id ? _pdbx_refine_tls_group.beg_label_asym_id ? _pdbx_refine_tls_group.beg_label_seq_id ? _pdbx_refine_tls_group.end_auth_asym_id ? _pdbx_refine_tls_group.end_auth_seq_id ? _pdbx_refine_tls_group.end_label_asym_id ? _pdbx_refine_tls_group.end_label_seq_id ? _pdbx_refine_tls_group.selection ? _pdbx_refine_tls_group.selection_details ALL # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal PHENIX refinement '(PHENIX.REFINE)' ? 1 XDS 'data reduction' . ? 2 SCALA 'data scaling' . ? 3 PHASER phasing . ? 4 # _pdbx_entry_details.entry_id 5FQ2 _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ;LYSINE METHYLATION AT POSITION LYS110 LYSINE METHYLATION AT POSITION LYS505 ; # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 ND2 _pdbx_validate_close_contact.auth_asym_id_1 B _pdbx_validate_close_contact.auth_comp_id_1 ASN _pdbx_validate_close_contact.auth_seq_id_1 501 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 O _pdbx_validate_close_contact.auth_asym_id_2 A _pdbx_validate_close_contact.auth_comp_id_2 HOH _pdbx_validate_close_contact.auth_seq_id_2 2008 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 2.14 # 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 ASP A 19 ? ? -166.68 107.34 2 1 HIS A 83 ? ? -171.50 136.75 3 1 LYS A 101 ? ? -120.18 -107.57 4 1 ILE B 468 ? ? -91.70 -60.91 5 1 TYR B 526 ? ? -165.44 104.98 # 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 GLY -2 ? A GLY 1 2 1 Y 1 A SER -1 ? A SER 2 3 1 Y 1 A HIS 0 ? A HIS 3 4 1 Y 1 A MET 1 ? A MET 4 5 1 Y 1 B GLY 443 ? B GLY 1 6 1 Y 1 B SER 444 ? B SER 2 7 1 Y 1 B HIS 445 ? B HIS 3 8 1 Y 1 B SER 446 ? B SER 4 # _pdbx_entity_nonpoly.entity_id 3 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH #