data_2C7M # _entry.id 2C7M # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.308 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 2C7M PDBE EBI-26558 WWPDB D_1290026558 # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.content_type _pdbx_database_related.details PDB 1AAR unspecified DI-UBIQUITIN PDB 1E0Q unspecified 'MUTANT PEPTIDE FROM THE FIRST N-TERMINAL 17 AMINO-ACID OF UBIQUITIN' PDB 1P3Q unspecified 'MECHANISM OF UBIQUITIN RECOGNITION BY THE CUE DOMAIN OF VPS9' PDB 1UZX unspecified 'A COMPLEX OF THE VPS23 UEV WITH UBIQUITIN' PDB 1V80 unspecified 'SOLUTION STRUCTURES OF UBIQUITIN AT 30 BAR AND 3 KBAR' PDB 1V81 unspecified 'SOLUTION STRUCTURES OF UBIQUITIN AT 30 BAR AND 3 KBAR' PDB 1WR6 unspecified 'CRYSTAL STRUCTURE OF GGA3 GAT DOMAIN IN COMPLEX WITHUBIQUITIN' PDB 1WRD unspecified 'CRYSTAL STRUCTURE OF TOM1 GAT DOMAIN IN COMPLEX WITHUBIQUITIN' PDB 1YD8 unspecified 'COMPLEX OF HUMAN GGA3 GAT DOMAIN AND UBIQUITIN' PDB 2BGF unspecified 'NMR STRUCTURE OF LYS48-LINKED DI-UBIQUITIN USING CHEMICAL SHIFT PERTURBATION DATA TOGETHER WITH RDCS AND 15N-RELAXATION DATA' PDB 2C7N unspecified 'HUMAN RABEX-5 RESIDUES 1-74 IN COMPLEX WITH UBIQUITIN' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2C7M _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.SG_entry . _pdbx_database_status.recvd_initial_deposition_date 2005-11-25 _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 'Penengo, L.' 1 ? 'Mapelli, M.' 2 ? 'Murachelli, A.G.' 3 ? 'Confalioneri, S.' 4 ? 'Magri, L.' 5 ? 'Musacchio, A.' 6 ? 'Di Fiore, P.P.' 7 ? 'Polo, S.' 8 ? 'Schneider, T.R.' 9 ? # _citation.id primary _citation.title 'Crystal structure of the ubiquitin binding domains of rabex-5 reveals two modes of interaction with ubiquitin.' _citation.journal_abbrev Cell _citation.journal_volume 124 _citation.page_first 1183 _citation.page_last 1195 _citation.year 2006 _citation.journal_id_ASTM CELLB5 _citation.country US _citation.journal_id_ISSN 0092-8674 _citation.journal_id_CSD 0998 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 16499958 _citation.pdbx_database_id_DOI 10.1016/j.cell.2006.02.020 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Penengo, L.' 1 ? primary 'Mapelli, M.' 2 ? primary 'Murachelli, A.G.' 3 ? primary 'Confalonieri, S.' 4 ? primary 'Magri, L.' 5 ? primary 'Musacchio, A.' 6 ? primary 'Di Fiore, P.P.' 7 ? primary 'Polo, S.' 8 ? primary 'Schneider, T.R.' 9 ? # _cell.entry_id 2C7M _cell.length_a 81.900 _cell.length_b 81.900 _cell.length_c 55.100 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2C7M _symmetry.space_group_name_H-M 'P 61' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 # 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 'RAB GUANINE NUCLEOTIDE EXCHANGE FACTOR 1' 8784.761 1 ? ? 'TWO UBIQUTIN BINDING DOMAINS, RESIDUES 1-74' ? 2 polymer nat UBIQUITIN 8576.831 1 ? ? ? ? 3 non-polymer syn 'ZINC ION' 65.409 1 ? ? ? ? 4 water nat water 18.015 37 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'RABEX-5, GEF 1' # 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 MSLKSERRGIHVDQSDLLCKKGCGYYGNPAWQGFCSKCWREEYHKARQKQIQEDWELAERLQREEEEAFASSQS MSLKSERRGIHVDQSDLLCKKGCGYYGNPAWQGFCSKCWREEYHKARQKQIQEDWELAERLQREEEEAFASSQS A ? 2 'polypeptide(L)' no no MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG B ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 MET n 1 2 SER n 1 3 LEU n 1 4 LYS n 1 5 SER n 1 6 GLU n 1 7 ARG n 1 8 ARG n 1 9 GLY n 1 10 ILE n 1 11 HIS n 1 12 VAL n 1 13 ASP n 1 14 GLN n 1 15 SER n 1 16 ASP n 1 17 LEU n 1 18 LEU n 1 19 CYS n 1 20 LYS n 1 21 LYS n 1 22 GLY n 1 23 CYS n 1 24 GLY n 1 25 TYR n 1 26 TYR n 1 27 GLY n 1 28 ASN n 1 29 PRO n 1 30 ALA n 1 31 TRP n 1 32 GLN n 1 33 GLY n 1 34 PHE n 1 35 CYS n 1 36 SER n 1 37 LYS n 1 38 CYS n 1 39 TRP n 1 40 ARG n 1 41 GLU n 1 42 GLU n 1 43 TYR n 1 44 HIS n 1 45 LYS n 1 46 ALA n 1 47 ARG n 1 48 GLN n 1 49 LYS n 1 50 GLN n 1 51 ILE n 1 52 GLN n 1 53 GLU n 1 54 ASP n 1 55 TRP n 1 56 GLU n 1 57 LEU n 1 58 ALA n 1 59 GLU n 1 60 ARG n 1 61 LEU n 1 62 GLN n 1 63 ARG n 1 64 GLU n 1 65 GLU n 1 66 GLU n 1 67 GLU n 1 68 ALA n 1 69 PHE n 1 70 ALA n 1 71 SER n 1 72 SER n 1 73 GLN n 1 74 SER n 2 1 MET n 2 2 GLN n 2 3 ILE n 2 4 PHE n 2 5 VAL n 2 6 LYS n 2 7 THR n 2 8 LEU n 2 9 THR n 2 10 GLY n 2 11 LYS n 2 12 THR n 2 13 ILE n 2 14 THR n 2 15 LEU n 2 16 GLU n 2 17 VAL n 2 18 GLU n 2 19 PRO n 2 20 SER n 2 21 ASP n 2 22 THR n 2 23 ILE n 2 24 GLU n 2 25 ASN n 2 26 VAL n 2 27 LYS n 2 28 ALA n 2 29 LYS n 2 30 ILE n 2 31 GLN n 2 32 ASP n 2 33 LYS n 2 34 GLU n 2 35 GLY n 2 36 ILE n 2 37 PRO n 2 38 PRO n 2 39 ASP n 2 40 GLN n 2 41 GLN n 2 42 ARG n 2 43 LEU n 2 44 ILE n 2 45 PHE n 2 46 ALA n 2 47 GLY n 2 48 LYS n 2 49 GLN n 2 50 LEU n 2 51 GLU n 2 52 ASP n 2 53 GLY n 2 54 ARG n 2 55 THR n 2 56 LEU n 2 57 SER n 2 58 ASP n 2 59 TYR n 2 60 ASN n 2 61 ILE n 2 62 GLN n 2 63 LYS n 2 64 GLU n 2 65 SER n 2 66 THR n 2 67 LEU n 2 68 HIS n 2 69 LEU n 2 70 VAL n 2 71 LEU n 2 72 ARG n 2 73 LEU n 2 74 ARG n 2 75 GLY n 2 76 GLY 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 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 ? _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 ? # _entity_src_nat.entity_id 2 _entity_src_nat.pdbx_src_id 1 _entity_src_nat.pdbx_alt_source_flag sample _entity_src_nat.pdbx_beg_seq_num ? _entity_src_nat.pdbx_end_seq_num ? _entity_src_nat.common_name BOVINE _entity_src_nat.pdbx_organism_scientific 'BOS TAURUS' _entity_src_nat.pdbx_ncbi_taxonomy_id 9913 _entity_src_nat.genus ? _entity_src_nat.species ? _entity_src_nat.strain ? _entity_src_nat.tissue ? _entity_src_nat.tissue_fraction ? _entity_src_nat.pdbx_secretion ? _entity_src_nat.pdbx_fragment ? _entity_src_nat.pdbx_variant ? _entity_src_nat.pdbx_cell_line ? _entity_src_nat.pdbx_atcc ? _entity_src_nat.pdbx_cellular_location ? _entity_src_nat.pdbx_organ ? _entity_src_nat.pdbx_organelle ? _entity_src_nat.pdbx_cell ? _entity_src_nat.pdbx_plasmid_name ? _entity_src_nat.pdbx_plasmid_details ? _entity_src_nat.details 'BOSTON BIOCHEM' # 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 Q53FG0_HUMAN 1 ? ? Q53FG0 ? 2 UNP UBIQ_BOVIN 2 ? ? P62990 ? # 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 2C7M A 1 ? 74 ? Q53FG0 1 ? 74 ? 2 75 2 2 2C7M B 1 ? 76 ? P62990 1 ? 76 ? 1 76 # 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 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 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 2C7M _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 3.07 _exptl_crystal.density_percent_sol 59.97 _exptl_crystal.description ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.temp ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.50 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details 'SITTING DROP 300 NL PLUS 300 NL 20 MG/ML PROTEIN SOLUTION 0.2 M LIS2SO4, 0.1 MES PH 6.5 25% PEG3350' # _diffrn.id 1 _diffrn.ambient_temp 100.0 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC CCD' _diffrn_detector.pdbx_collection_date 2005-09-03 _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 0.9793 _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 0.9793 _diffrn_source.pdbx_wavelength_list ? # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 2C7M _reflns.observed_criterion_sigma_I -4.000 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 20.000 _reflns.d_resolution_high 2.400 _reflns.number_obs 8066 _reflns.number_all ? _reflns.percent_possible_obs 96.1 _reflns.pdbx_Rmerge_I_obs 0.04000 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 43.1100 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 18.500 _reflns.pdbx_CC_half ? _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_Rrim_I_all ? # _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_ordinal 1 _reflns_shell.d_res_high 2.40 _reflns_shell.d_res_low 2.50 _reflns_shell.percent_possible_all 76.9 _reflns_shell.Rmerge_I_obs 0.22000 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 6.000 _reflns_shell.pdbx_redundancy 6.00 _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_all ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_CC_half ? _reflns_shell.pdbx_Rpim_I_all ? _reflns_shell.pdbx_Rrim_I_all ? # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 2C7M _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 7655 _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 19.67 _refine.ls_d_res_high 2.40 _refine.ls_percent_reflns_obs 100.0 _refine.ls_R_factor_obs 0.184 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.183 _refine.ls_R_factor_R_free 0.214 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.900 _refine.ls_number_reflns_R_free 392 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.962 _refine.correlation_coeff_Fo_to_Fc_free 0.949 _refine.B_iso_mean 66.85 _refine.aniso_B[1][1] -4.64000 _refine.aniso_B[2][2] -4.64000 _refine.aniso_B[3][3] 6.95000 _refine.aniso_B[1][2] -2.32000 _refine.aniso_B[1][3] 0.00000 _refine.aniso_B[2][3] 0.00000 _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.' _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct SAD _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 0.262 _refine.pdbx_overall_ESU_R_Free 0.199 _refine.overall_SU_ML 0.168 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 14.866 _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 1070 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 1 _refine_hist.number_atoms_solvent 37 _refine_hist.number_atoms_total 1108 _refine_hist.d_res_high 2.40 _refine_hist.d_res_low 19.67 # 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 0.029 0.022 ? 1088 'X-RAY DIFFRACTION' ? r_bond_other_d ? ? ? ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 2.380 1.965 ? 1462 'X-RAY DIFFRACTION' ? r_angle_other_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 6.924 5.000 ? 129 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 35.947 25.179 ? 56 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 19.987 15.000 ? 212 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 24.842 15.000 ? 7 'X-RAY DIFFRACTION' ? r_chiral_restr 0.162 0.200 ? 155 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.009 0.020 ? 821 'X-RAY DIFFRACTION' ? r_gen_planes_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_refined 0.226 0.200 ? 398 'X-RAY DIFFRACTION' ? r_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_refined 0.312 0.200 ? 720 'X-RAY DIFFRACTION' ? r_nbtor_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.167 0.200 ? 39 '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 0.169 0.200 ? 33 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.089 0.200 ? 7 '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 1.306 1.500 ? 683 'X-RAY DIFFRACTION' ? r_mcbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_it 2.068 2.000 ? 1046 'X-RAY DIFFRACTION' ? r_mcangle_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_scbond_it 3.979 3.000 ? 483 'X-RAY DIFFRACTION' ? r_scbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_scangle_it 6.065 4.500 ? 416 '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 ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_free ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_bonded ? ? ? ? '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 2.40 _refine_ls_shell.d_res_low 2.46 _refine_ls_shell.number_reflns_R_work 417 _refine_ls_shell.R_factor_R_work 0.2380 _refine_ls_shell.percent_reflns_obs ? _refine_ls_shell.R_factor_R_free 0.3340 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 26 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_obs ? _refine_ls_shell.number_reflns_obs ? # _struct.entry_id 2C7M _struct.title 'Human Rabex-5 residues 1-74 in complex with Ubiquitin' _struct.pdbx_descriptor 'RAB GUANINE NUCLEOTIDE EXCHANGE FACTOR 1, UBIQUITIN' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2C7M _struct_keywords.pdbx_keywords 'PROTEIN BINDING' _struct_keywords.text ;PROTEIN-BINDING, UBIQUITIN COMPLEX, UBIQUITIN BINDING DOMAIN, ENDOCYTOSIS, NUCLEAR PROTEIN, POLYPROTEIN, UBL CONJUGATION, PROTEIN BINDING ; # 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 4 ? E N N 4 ? # _struct_biol.id 1 _struct_biol.details ;THE QUATERNARY STRUCTURE FOR THIS ENTRY IS NOT RELEVANTSINCE THE COMPLEX IS ONLY MADE UP OF FRAGMENTS OF RABEX-5IN COMPLEX WITH UBIQUITIN. HOWEVER, THESE REMARKSONLY INDICATE THE COMPLEX AS SEEN IN THE PDB FILE, ANDDO NOT HAVE RELEVANCE TO THE BIOLOGICAL STATE OF THEMOLECULE. ; # 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 ASN A 28 ? GLN A 32 ? ASN A 29 GLN A 33 5 ? 5 HELX_P HELX_P2 2 CYS A 35 ? SER A 74 ? CYS A 36 SER A 75 1 ? 40 HELX_P HELX_P3 3 THR B 22 ? GLY B 35 ? THR B 22 GLY B 35 1 ? 14 HELX_P HELX_P4 4 PRO B 37 ? ASP B 39 ? PRO B 37 ASP B 39 5 ? 3 HELX_P HELX_P5 5 LEU B 56 ? ASN B 60 ? LEU B 56 ASN B 60 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 metalc1 metalc ? ? C ZN . ZN ? ? ? 1_555 A CYS 19 SG ? ? A ZN 500 A CYS 20 1_555 ? ? ? ? ? ? ? 2.252 ? metalc2 metalc ? ? C ZN . ZN ? ? ? 1_555 A CYS 23 SG ? ? A ZN 500 A CYS 24 1_555 ? ? ? ? ? ? ? 2.651 ? metalc3 metalc ? ? C ZN . ZN ? ? ? 1_555 A CYS 35 SG ? ? A ZN 500 A CYS 36 1_555 ? ? ? ? ? ? ? 2.538 ? metalc4 metalc ? ? C ZN . ZN ? ? ? 1_555 A CYS 38 SG ? ? A ZN 500 A CYS 39 1_555 ? ? ? ? ? ? ? 2.294 ? # _struct_conn_type.id metalc _struct_conn_type.criteria ? _struct_conn_type.reference ? # _struct_sheet.id BA _struct_sheet.type ? _struct_sheet.number_strands 5 _struct_sheet.details ? # 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 BA 1 2 ? anti-parallel BA 2 3 ? parallel BA 3 4 ? anti-parallel BA 4 5 ? 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 BA 1 THR B 12 ? GLU B 16 ? THR B 12 GLU B 16 BA 2 GLN B 2 ? LYS B 6 ? GLN B 2 LYS B 6 BA 3 THR B 66 ? LEU B 71 ? THR B 66 LEU B 71 BA 4 GLN B 41 ? PHE B 45 ? GLN B 41 PHE B 45 BA 5 LYS B 48 ? GLN B 49 ? LYS B 48 GLN B 49 # 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 BA 1 2 N LEU B 15 ? N LEU B 15 O ILE B 3 ? O ILE B 3 BA 2 3 N LYS B 6 ? N LYS B 6 O LEU B 67 ? O LEU B 67 BA 3 4 N VAL B 70 ? N VAL B 70 O ARG B 42 ? O ARG B 42 BA 4 5 N PHE B 45 ? N PHE B 45 O LYS B 48 ? O LYS B 48 # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _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 4 _struct_site.details 'BINDING SITE FOR RESIDUE ZN A 500' # 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 19 ? CYS A 20 . ? 1_555 ? 2 AC1 4 CYS A 23 ? CYS A 24 . ? 1_555 ? 3 AC1 4 CYS A 35 ? CYS A 36 . ? 1_555 ? 4 AC1 4 CYS A 38 ? CYS A 39 . ? 1_555 ? # _database_PDB_matrix.entry_id 2C7M _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 2C7M _atom_sites.fract_transf_matrix[1][1] 0.012210 _atom_sites.fract_transf_matrix[1][2] 0.007049 _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] 0.014099 _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] 0.018149 _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 MET 1 2 ? ? ? A . n A 1 2 SER 2 3 ? ? ? A . n A 1 3 LEU 3 4 ? ? ? A . n A 1 4 LYS 4 5 ? ? ? A . n A 1 5 SER 5 6 ? ? ? A . n A 1 6 GLU 6 7 ? ? ? A . n A 1 7 ARG 7 8 ? ? ? A . n A 1 8 ARG 8 9 ? ? ? A . n A 1 9 GLY 9 10 ? ? ? A . n A 1 10 ILE 10 11 ? ? ? A . n A 1 11 HIS 11 12 ? ? ? A . n A 1 12 VAL 12 13 ? ? ? A . n A 1 13 ASP 13 14 ? ? ? A . n A 1 14 GLN 14 15 ? ? ? A . n A 1 15 SER 15 16 ? ? ? A . n A 1 16 ASP 16 17 ? ? ? A . n A 1 17 LEU 17 18 18 LEU LEU A . n A 1 18 LEU 18 19 19 LEU LEU A . n A 1 19 CYS 19 20 20 CYS CYS A . n A 1 20 LYS 20 21 21 LYS LYS A . n A 1 21 LYS 21 22 22 LYS LYS A . n A 1 22 GLY 22 23 23 GLY GLY A . n A 1 23 CYS 23 24 24 CYS CYS A . n A 1 24 GLY 24 25 25 GLY GLY A . n A 1 25 TYR 25 26 26 TYR TYR A . n A 1 26 TYR 26 27 27 TYR TYR A . n A 1 27 GLY 27 28 28 GLY GLY A . n A 1 28 ASN 28 29 29 ASN ASN A . n A 1 29 PRO 29 30 30 PRO PRO A . n A 1 30 ALA 30 31 31 ALA ALA A . n A 1 31 TRP 31 32 32 TRP TRP A . n A 1 32 GLN 32 33 33 GLN GLN A . n A 1 33 GLY 33 34 34 GLY GLY A . n A 1 34 PHE 34 35 35 PHE PHE A . n A 1 35 CYS 35 36 36 CYS CYS A . n A 1 36 SER 36 37 37 SER SER A . n A 1 37 LYS 37 38 38 LYS LYS A . n A 1 38 CYS 38 39 39 CYS CYS A . n A 1 39 TRP 39 40 40 TRP TRP A . n A 1 40 ARG 40 41 41 ARG ARG A . n A 1 41 GLU 41 42 42 GLU GLU A . n A 1 42 GLU 42 43 43 GLU GLU A . n A 1 43 TYR 43 44 44 TYR TYR A . n A 1 44 HIS 44 45 45 HIS HIS A . n A 1 45 LYS 45 46 46 LYS LYS A . n A 1 46 ALA 46 47 47 ALA ALA A . n A 1 47 ARG 47 48 48 ARG ARG A . n A 1 48 GLN 48 49 49 GLN GLN A . n A 1 49 LYS 49 50 50 LYS LYS A . n A 1 50 GLN 50 51 51 GLN GLN A . n A 1 51 ILE 51 52 52 ILE ILE A . n A 1 52 GLN 52 53 53 GLN GLN A . n A 1 53 GLU 53 54 54 GLU GLU A . n A 1 54 ASP 54 55 55 ASP ASP A . n A 1 55 TRP 55 56 56 TRP TRP A . n A 1 56 GLU 56 57 57 GLU GLU A . n A 1 57 LEU 57 58 58 LEU LEU A . n A 1 58 ALA 58 59 59 ALA ALA A . n A 1 59 GLU 59 60 60 GLU GLU A . n A 1 60 ARG 60 61 61 ARG ARG A . n A 1 61 LEU 61 62 62 LEU LEU A . n A 1 62 GLN 62 63 63 GLN GLN A . n A 1 63 ARG 63 64 64 ARG ARG A . n A 1 64 GLU 64 65 65 GLU GLU A . n A 1 65 GLU 65 66 66 GLU GLU A . n A 1 66 GLU 66 67 67 GLU GLU A . n A 1 67 GLU 67 68 68 GLU GLU A . n A 1 68 ALA 68 69 69 ALA ALA A . n A 1 69 PHE 69 70 70 PHE PHE A . n A 1 70 ALA 70 71 71 ALA ALA A . n A 1 71 SER 71 72 72 SER SER A . n A 1 72 SER 72 73 73 SER SER A . n A 1 73 GLN 73 74 74 GLN GLN A . n A 1 74 SER 74 75 75 SER SER A . n B 2 1 MET 1 1 1 MET MET B . n B 2 2 GLN 2 2 2 GLN GLN B . n B 2 3 ILE 3 3 3 ILE ILE B . n B 2 4 PHE 4 4 4 PHE PHE B . n B 2 5 VAL 5 5 5 VAL VAL B . n B 2 6 LYS 6 6 6 LYS LYS B . n B 2 7 THR 7 7 7 THR THR B . n B 2 8 LEU 8 8 8 LEU LEU B . n B 2 9 THR 9 9 9 THR THR B . n B 2 10 GLY 10 10 10 GLY GLY B . n B 2 11 LYS 11 11 11 LYS LYS B . n B 2 12 THR 12 12 12 THR THR B . n B 2 13 ILE 13 13 13 ILE ILE B . n B 2 14 THR 14 14 14 THR THR B . n B 2 15 LEU 15 15 15 LEU LEU B . n B 2 16 GLU 16 16 16 GLU GLU B . n B 2 17 VAL 17 17 17 VAL VAL B . n B 2 18 GLU 18 18 18 GLU GLU B . n B 2 19 PRO 19 19 19 PRO PRO B . n B 2 20 SER 20 20 20 SER SER B . n B 2 21 ASP 21 21 21 ASP ASP B . n B 2 22 THR 22 22 22 THR THR B . n B 2 23 ILE 23 23 23 ILE ILE B . n B 2 24 GLU 24 24 24 GLU GLU B . n B 2 25 ASN 25 25 25 ASN ASN B . n B 2 26 VAL 26 26 26 VAL VAL B . n B 2 27 LYS 27 27 27 LYS LYS B . n B 2 28 ALA 28 28 28 ALA ALA B . n B 2 29 LYS 29 29 29 LYS LYS B . n B 2 30 ILE 30 30 30 ILE ILE B . n B 2 31 GLN 31 31 31 GLN GLN B . n B 2 32 ASP 32 32 32 ASP ASP B . n B 2 33 LYS 33 33 33 LYS LYS B . n B 2 34 GLU 34 34 34 GLU GLU B . n B 2 35 GLY 35 35 35 GLY GLY B . n B 2 36 ILE 36 36 36 ILE ILE B . n B 2 37 PRO 37 37 37 PRO PRO B . n B 2 38 PRO 38 38 38 PRO PRO B . n B 2 39 ASP 39 39 39 ASP ASP B . n B 2 40 GLN 40 40 40 GLN GLN B . n B 2 41 GLN 41 41 41 GLN GLN B . n B 2 42 ARG 42 42 42 ARG ARG B . n B 2 43 LEU 43 43 43 LEU LEU B . n B 2 44 ILE 44 44 44 ILE ILE B . n B 2 45 PHE 45 45 45 PHE PHE B . n B 2 46 ALA 46 46 46 ALA ALA B . n B 2 47 GLY 47 47 47 GLY GLY B . n B 2 48 LYS 48 48 48 LYS LYS B . n B 2 49 GLN 49 49 49 GLN GLN B . n B 2 50 LEU 50 50 50 LEU LEU B . n B 2 51 GLU 51 51 51 GLU GLU B . n B 2 52 ASP 52 52 52 ASP ASP B . n B 2 53 GLY 53 53 53 GLY GLY B . n B 2 54 ARG 54 54 54 ARG ARG B . n B 2 55 THR 55 55 55 THR THR B . n B 2 56 LEU 56 56 56 LEU LEU B . n B 2 57 SER 57 57 57 SER SER B . n B 2 58 ASP 58 58 58 ASP ASP B . n B 2 59 TYR 59 59 59 TYR TYR B . n B 2 60 ASN 60 60 60 ASN ASN B . n B 2 61 ILE 61 61 61 ILE ILE B . n B 2 62 GLN 62 62 62 GLN GLN B . n B 2 63 LYS 63 63 63 LYS LYS B . n B 2 64 GLU 64 64 64 GLU GLU B . n B 2 65 SER 65 65 65 SER SER B . n B 2 66 THR 66 66 66 THR THR B . n B 2 67 LEU 67 67 67 LEU LEU B . n B 2 68 HIS 68 68 68 HIS HIS B . n B 2 69 LEU 69 69 69 LEU LEU B . n B 2 70 VAL 70 70 70 VAL VAL B . n B 2 71 LEU 71 71 71 LEU LEU B . n B 2 72 ARG 72 72 72 ARG ARG B . n B 2 73 LEU 73 73 73 LEU LEU B . n B 2 74 ARG 74 74 74 ARG ARG B . n B 2 75 GLY 75 75 ? ? ? B . n B 2 76 GLY 76 76 ? ? ? 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 ZN 1 500 500 ZN ZN A . D 4 HOH 1 2001 2001 HOH HOH A . D 4 HOH 2 2002 2002 HOH HOH A . D 4 HOH 3 2003 2003 HOH HOH A . D 4 HOH 4 2004 2004 HOH HOH A . D 4 HOH 5 2005 2005 HOH HOH A . D 4 HOH 6 2006 2006 HOH HOH A . D 4 HOH 7 2007 2007 HOH HOH A . D 4 HOH 8 2008 2008 HOH HOH A . D 4 HOH 9 2009 2009 HOH HOH A . D 4 HOH 10 2010 2010 HOH HOH A . D 4 HOH 11 2011 2011 HOH HOH A . D 4 HOH 12 2012 2012 HOH HOH A . D 4 HOH 13 2013 2013 HOH HOH A . E 4 HOH 1 2001 2001 HOH HOH B . E 4 HOH 2 2002 2002 HOH HOH B . E 4 HOH 3 2003 2003 HOH HOH B . E 4 HOH 4 2004 2004 HOH HOH B . E 4 HOH 5 2005 2005 HOH HOH B . E 4 HOH 6 2006 2006 HOH HOH B . E 4 HOH 7 2007 2007 HOH HOH B . E 4 HOH 8 2008 2008 HOH HOH B . E 4 HOH 9 2009 2009 HOH HOH B . E 4 HOH 10 2010 2010 HOH HOH B . E 4 HOH 11 2011 2011 HOH HOH B . E 4 HOH 12 2012 2012 HOH HOH B . E 4 HOH 13 2013 2013 HOH HOH B . E 4 HOH 14 2014 2014 HOH HOH B . E 4 HOH 15 2015 2015 HOH HOH B . E 4 HOH 16 2016 2016 HOH HOH B . E 4 HOH 17 2017 2017 HOH HOH B . E 4 HOH 18 2018 2018 HOH HOH B . E 4 HOH 19 2019 2019 HOH HOH B . E 4 HOH 20 2020 2020 HOH HOH B . E 4 HOH 21 2021 2021 HOH HOH B . E 4 HOH 22 2022 2022 HOH HOH B . E 4 HOH 23 2023 2023 HOH HOH B . E 4 HOH 24 2024 2024 HOH HOH B . # _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,E # _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 19 ? A CYS 20 ? 1_555 ZN ? C ZN . ? A ZN 500 ? 1_555 SG ? A CYS 23 ? A CYS 24 ? 1_555 129.6 ? 2 SG ? A CYS 19 ? A CYS 20 ? 1_555 ZN ? C ZN . ? A ZN 500 ? 1_555 SG ? A CYS 35 ? A CYS 36 ? 1_555 112.2 ? 3 SG ? A CYS 23 ? A CYS 24 ? 1_555 ZN ? C ZN . ? A ZN 500 ? 1_555 SG ? A CYS 35 ? A CYS 36 ? 1_555 93.1 ? 4 SG ? A CYS 19 ? A CYS 20 ? 1_555 ZN ? C ZN . ? A ZN 500 ? 1_555 SG ? A CYS 38 ? A CYS 39 ? 1_555 114.6 ? 5 SG ? A CYS 23 ? A CYS 24 ? 1_555 ZN ? C ZN . ? A ZN 500 ? 1_555 SG ? A CYS 38 ? A CYS 39 ? 1_555 100.0 ? 6 SG ? A CYS 35 ? A CYS 36 ? 1_555 ZN ? C ZN . ? A ZN 500 ? 1_555 SG ? A CYS 38 ? A CYS 39 ? 1_555 102.8 ? # 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 2006-02-15 2 'Structure model' 1 1 2011-05-08 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2018-06-13 5 'Structure model' 1 4 2019-05-08 # _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 ? # 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' 'Version format compliance' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Refinement description' 6 4 'Structure model' 'Structure summary' 7 5 'Structure model' 'Data collection' 8 5 'Structure model' 'Experimental preparation' # 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 4 'Structure model' citation 2 4 'Structure model' diffrn_radiation 3 4 'Structure model' software 4 4 'Structure model' struct 5 5 'Structure model' exptl_crystal_grow # 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 4 'Structure model' '_citation.journal_abbrev' 2 4 'Structure model' '_citation.page_last' 3 4 'Structure model' '_citation.pdbx_database_id_DOI' 4 4 'Structure model' '_citation.title' 5 4 'Structure model' '_diffrn_radiation.pdbx_diffrn_protocol' 6 4 'Structure model' '_software.name' 7 4 'Structure model' '_struct.title' 8 5 'Structure model' '_exptl_crystal_grow.method' # loop_ _pdbx_refine_tls.pdbx_refine_id _pdbx_refine_tls.id _pdbx_refine_tls.details _pdbx_refine_tls.method _pdbx_refine_tls.origin_x _pdbx_refine_tls.origin_y _pdbx_refine_tls.origin_z _pdbx_refine_tls.T[1][1] _pdbx_refine_tls.T[2][2] _pdbx_refine_tls.T[3][3] _pdbx_refine_tls.T[1][2] _pdbx_refine_tls.T[1][3] _pdbx_refine_tls.T[2][3] _pdbx_refine_tls.L[1][1] _pdbx_refine_tls.L[2][2] _pdbx_refine_tls.L[3][3] _pdbx_refine_tls.L[1][2] _pdbx_refine_tls.L[1][3] _pdbx_refine_tls.L[2][3] _pdbx_refine_tls.S[1][1] _pdbx_refine_tls.S[1][2] _pdbx_refine_tls.S[1][3] _pdbx_refine_tls.S[2][1] _pdbx_refine_tls.S[2][2] _pdbx_refine_tls.S[2][3] _pdbx_refine_tls.S[3][1] _pdbx_refine_tls.S[3][2] _pdbx_refine_tls.S[3][3] 'X-RAY DIFFRACTION' 1 ? refined 22.0590 14.3470 18.0530 -0.2579 -0.1325 -0.1985 0.0039 -0.0941 -0.0645 11.5810 5.5790 6.0194 0.3270 -1.8505 2.3088 -0.1043 -0.8194 0.6825 0.5793 0.0637 -0.3693 0.0125 0.4354 0.0407 'X-RAY DIFFRACTION' 2 ? refined 40.0410 11.3680 10.0760 -0.2148 0.2136 0.2582 -0.0317 -0.0873 -0.1450 21.5103 3.3604 9.2796 -0.4141 6.0266 -1.6423 -0.2477 1.0629 0.6526 -0.4938 0.1376 -0.7555 0.0292 1.0855 0.1101 'X-RAY DIFFRACTION' 3 ? refined 66.3220 6.1470 26.9930 -0.1399 -0.2962 -0.2530 -0.0287 0.0653 -0.0138 52.4317 2.1364 18.3496 -3.6484 25.4856 -1.7316 0.7266 -0.0299 -1.0441 -0.0002 -0.2880 0.1608 0.3688 0.2154 -0.4386 # loop_ _pdbx_refine_tls_group.pdbx_refine_id _pdbx_refine_tls_group.id _pdbx_refine_tls_group.refine_tls_id _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 'X-RAY DIFFRACTION' 1 1 B 1 ? ? B 73 ? ? ? ? 'X-RAY DIFFRACTION' 2 2 A 18 ? ? A 39 ? ? ? ? 'X-RAY DIFFRACTION' 3 3 A 40 ? ? A 75 ? ? ? ? # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal _software.date _software.type _software.location _software.language REFMAC refinement 5.2.0005 ? 1 ? ? ? ? DENZO 'data reduction' . ? 2 ? ? ? ? SCALEPACK 'data scaling' . ? 3 ? ? ? ? HKL2Map phasing . ? 4 ? ? ? ? # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 O _pdbx_validate_close_contact.auth_asym_id_1 B _pdbx_validate_close_contact.auth_comp_id_1 HOH _pdbx_validate_close_contact.auth_seq_id_1 2016 _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 B _pdbx_validate_close_contact.auth_comp_id_2 HOH _pdbx_validate_close_contact.auth_seq_id_2 2017 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 2.12 # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 CG A GLU 65 ? ? CD A GLU 65 ? ? 1.607 1.515 0.092 0.015 N 2 1 CD B GLU 16 ? ? OE1 B GLU 16 ? ? 1.328 1.252 0.076 0.011 N 3 1 CD B GLU 16 ? ? OE2 B GLU 16 ? ? 1.322 1.252 0.070 0.011 N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 CA A LEU 18 ? ? CB A LEU 18 ? ? CG A LEU 18 ? ? 133.03 115.30 17.73 2.30 N 2 1 CB A ARG 48 ? ? CA A ARG 48 ? ? C A ARG 48 ? ? 123.54 110.40 13.14 2.00 N 3 1 CB A LEU 62 ? ? CG A LEU 62 ? ? CD2 A LEU 62 ? ? 96.67 111.00 -14.33 1.70 N # 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 CYS A 20 ? ? -39.84 131.20 2 1 PRO B 38 ? ? -39.08 -35.34 # 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 B ARG 74 ? CA ? B ARG 74 CA 2 1 Y 1 B ARG 74 ? C ? B ARG 74 C 3 1 Y 1 B ARG 74 ? O ? B ARG 74 O 4 1 Y 1 B ARG 74 ? CB ? B ARG 74 CB 5 1 Y 1 B ARG 74 ? CG ? B ARG 74 CG 6 1 Y 1 B ARG 74 ? CD ? B ARG 74 CD 7 1 Y 1 B ARG 74 ? NE ? B ARG 74 NE 8 1 Y 1 B ARG 74 ? CZ ? B ARG 74 CZ 9 1 Y 1 B ARG 74 ? NH1 ? B ARG 74 NH1 10 1 Y 1 B ARG 74 ? NH2 ? B ARG 74 NH2 # 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 MET 2 ? A MET 1 2 1 Y 1 A SER 3 ? A SER 2 3 1 Y 1 A LEU 4 ? A LEU 3 4 1 Y 1 A LYS 5 ? A LYS 4 5 1 Y 1 A SER 6 ? A SER 5 6 1 Y 1 A GLU 7 ? A GLU 6 7 1 Y 1 A ARG 8 ? A ARG 7 8 1 Y 1 A ARG 9 ? A ARG 8 9 1 Y 1 A GLY 10 ? A GLY 9 10 1 Y 1 A ILE 11 ? A ILE 10 11 1 Y 1 A HIS 12 ? A HIS 11 12 1 Y 1 A VAL 13 ? A VAL 12 13 1 Y 1 A ASP 14 ? A ASP 13 14 1 Y 1 A GLN 15 ? A GLN 14 15 1 Y 1 A SER 16 ? A SER 15 16 1 Y 1 A ASP 17 ? A ASP 16 17 1 Y 1 B GLY 75 ? B GLY 75 18 1 Y 1 B GLY 76 ? B GLY 76 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 3 'ZINC ION' ZN 4 water HOH #