data_3HPB # _entry.id 3HPB # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.287 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 3HPB RCSB RCSB053415 WWPDB D_1000053415 # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 3HPC _pdbx_database_related.details 'Crystal structure of SNX5-PX domain in P21 space group' _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3HPB _pdbx_database_status.recvd_initial_deposition_date 2009-06-03 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Koharudin, L.M.I.' 1 'Furey, W.' 2 'Gronenborn, A.M.' 3 # _citation.id primary _citation.title 'The Phox domain of sorting nexin 5 lacks ptdins(3)p specificity and preferentially binds to ptdins(4,5)P2' _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 'Koharudin, L.M.I.' 1 primary 'Furey, W.' 2 primary 'Liu, H.' 3 primary 'Liu, Y.-J.' 4 primary 'Gronenborn, A.M.' 5 # _cell.entry_id 3HPB _cell.length_a 42.957 _cell.length_b 75.874 _cell.length_c 77.512 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 3HPB _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? # 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 'Snx5 protein' 18649.512 1 ? ? 'Residues 20-180' ? 2 non-polymer syn 'CHLORIDE ION' 35.453 1 ? ? ? ? 3 water nat water 18.015 135 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code ;SVSVDLNVDPSLQIDIPDALSERDKVKFTVHTKTTLPTFQSPEFSVTRQHEDFVWLHDTLTETTDYAGLIIPPAPTKPDF DGPREK(MSE)QKLGEGEGS(MSE)TKEEFAK(MSE)KQELEAEYLAVFKKTVSSHEVFLQRLSSHPVLSKDRNFHVFLE YDQDLSVRRKNTK ; _entity_poly.pdbx_seq_one_letter_code_can ;SVSVDLNVDPSLQIDIPDALSERDKVKFTVHTKTTLPTFQSPEFSVTRQHEDFVWLHDTLTETTDYAGLIIPPAPTKPDF DGPREKMQKLGEGEGSMTKEEFAKMKQELEAEYLAVFKKTVSSHEVFLQRLSSHPVLSKDRNFHVFLEYDQDLSVRRKNT K ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 SER n 1 2 VAL n 1 3 SER n 1 4 VAL n 1 5 ASP n 1 6 LEU n 1 7 ASN n 1 8 VAL n 1 9 ASP n 1 10 PRO n 1 11 SER n 1 12 LEU n 1 13 GLN n 1 14 ILE n 1 15 ASP n 1 16 ILE n 1 17 PRO n 1 18 ASP n 1 19 ALA n 1 20 LEU n 1 21 SER n 1 22 GLU n 1 23 ARG n 1 24 ASP n 1 25 LYS n 1 26 VAL n 1 27 LYS n 1 28 PHE n 1 29 THR n 1 30 VAL n 1 31 HIS n 1 32 THR n 1 33 LYS n 1 34 THR n 1 35 THR n 1 36 LEU n 1 37 PRO n 1 38 THR n 1 39 PHE n 1 40 GLN n 1 41 SER n 1 42 PRO n 1 43 GLU n 1 44 PHE n 1 45 SER n 1 46 VAL n 1 47 THR n 1 48 ARG n 1 49 GLN n 1 50 HIS n 1 51 GLU n 1 52 ASP n 1 53 PHE n 1 54 VAL n 1 55 TRP n 1 56 LEU n 1 57 HIS n 1 58 ASP n 1 59 THR n 1 60 LEU n 1 61 THR n 1 62 GLU n 1 63 THR n 1 64 THR n 1 65 ASP n 1 66 TYR n 1 67 ALA n 1 68 GLY n 1 69 LEU n 1 70 ILE n 1 71 ILE n 1 72 PRO n 1 73 PRO n 1 74 ALA n 1 75 PRO n 1 76 THR n 1 77 LYS n 1 78 PRO n 1 79 ASP n 1 80 PHE n 1 81 ASP n 1 82 GLY n 1 83 PRO n 1 84 ARG n 1 85 GLU n 1 86 LYS n 1 87 MSE n 1 88 GLN n 1 89 LYS n 1 90 LEU n 1 91 GLY n 1 92 GLU n 1 93 GLY n 1 94 GLU n 1 95 GLY n 1 96 SER n 1 97 MSE n 1 98 THR n 1 99 LYS n 1 100 GLU n 1 101 GLU n 1 102 PHE n 1 103 ALA n 1 104 LYS n 1 105 MSE n 1 106 LYS n 1 107 GLN n 1 108 GLU n 1 109 LEU n 1 110 GLU n 1 111 ALA n 1 112 GLU n 1 113 TYR n 1 114 LEU n 1 115 ALA n 1 116 VAL n 1 117 PHE n 1 118 LYS n 1 119 LYS n 1 120 THR n 1 121 VAL n 1 122 SER n 1 123 SER n 1 124 HIS n 1 125 GLU n 1 126 VAL n 1 127 PHE n 1 128 LEU n 1 129 GLN n 1 130 ARG n 1 131 LEU n 1 132 SER n 1 133 SER n 1 134 HIS n 1 135 PRO n 1 136 VAL n 1 137 LEU n 1 138 SER n 1 139 LYS n 1 140 ASP n 1 141 ARG n 1 142 ASN n 1 143 PHE n 1 144 HIS n 1 145 VAL n 1 146 PHE n 1 147 LEU n 1 148 GLU n 1 149 TYR n 1 150 ASP n 1 151 GLN n 1 152 ASP n 1 153 LEU n 1 154 SER n 1 155 VAL n 1 156 ARG n 1 157 ARG n 1 158 LYS n 1 159 ASN n 1 160 THR n 1 161 LYS 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 rat _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene Snx5 _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 'Rattus norvegicus' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 10116 _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 'BL21(DE3)' _entity_src_gen.pdbx_host_org_variant ? _entity_src_gen.pdbx_host_org_cell_line ? _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type plasmid _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name pET15b _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code B1H267_RAT _struct_ref.pdbx_db_accession B1H267 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;SVSVDLNVDPSLQIDIPDALSERDKVKFTVHTKTTLPTFQSPEFSVTRQHEDFVWLHDTLTETTDYAGLIIPPAPTKPDF DGPREKMQKLGEGEGSMTKEEFAKMKQELEAEYLAVFKKTVSSHEVFLQRLSSHPVLSKDRNFHVFLEYDQDLSVRRKNT K ; _struct_ref.pdbx_align_begin 20 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3HPB _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 161 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession B1H267 _struct_ref_seq.db_align_beg 20 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 180 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 20 _struct_ref_seq.pdbx_auth_seq_align_end 180 # 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 CL non-polymer . 'CHLORIDE ION' ? 'Cl -1' 35.453 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 MSE 'L-peptide linking' n SELENOMETHIONINE ? 'C5 H11 N O2 Se' 196.106 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 3HPB _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 2 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 3.39 _exptl_crystal.density_percent_sol 59.25 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method ? _exptl_crystal_grow.temp 277 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 8.0 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details ;the protein solution in the final superdex-75 buffer (20 mM Tris.HCl, 100 mM NaCl, 0.02% NaN3, pH 8.0) was concentrated to 8 mg/ml. The Se-Met derivative and the 2.19 A crystals were obtained using an optimized initial crystallization condition of 8 ul of protein vs 1 ul of reservoir solution (0.2M (NH4)2SO4, 0.1M Sodium cacodylate tryhydrate pH 6.5, 30% PEG 8000) at 4C by sitting drop vapor diffusion, VAPOR DIFFUSION, SITTING DROP, temperature 277K ; # loop_ _diffrn.id _diffrn.ambient_temp _diffrn.ambient_temp_details _diffrn.crystal_id 1 100 ? 1 2 100 ? 1 # loop_ _diffrn_detector.diffrn_id _diffrn_detector.detector _diffrn_detector.type _diffrn_detector.pdbx_collection_date _diffrn_detector.details 1 CCD 'RIGAKU SATURN 944' 2006-10-17 MIRRORS 2 CCD 'MARMOSAIC 300 mm CCD' 2008-11-18 ;ROSENBAUM-ROCK MONOCHROMATOR HIGH-RESOLUTION DOUBLE-CRYSTAL SI(220) SAGITTAL FO CUSING, ROSENBAUM- ROCK VERTICAL FOCUSING MIRROR ; # loop_ _diffrn_radiation.diffrn_id _diffrn_radiation.wavelength_id _diffrn_radiation.pdbx_monochromatic_or_laue_m_l _diffrn_radiation.monochromator _diffrn_radiation.pdbx_diffrn_protocol _diffrn_radiation.pdbx_scattering_type 1 1 M 'OSMIC MIRRORS' 'SINGLE WAVELENGTH' x-ray 2 1 M 'SI 220. ROSENBAUM-ROCK DOUBLE-CRYSTAL MONOCHROMATOR' MAD x-ray # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 1.5418 1.0 2 0.9793 1.0 3 0.9795 1.0 4 0.9718 1.0 # loop_ _diffrn_source.diffrn_id _diffrn_source.source _diffrn_source.type _diffrn_source.pdbx_synchrotron_site _diffrn_source.pdbx_synchrotron_beamline _diffrn_source.pdbx_wavelength _diffrn_source.pdbx_wavelength_list 1 'ROTATING ANODE' 'RIGAKU FR-E SUPERBRIGHT' ? ? 1.5418 ? 2 SYNCHROTRON 'APS BEAMLINE 22-ID' APS 22-ID ? 0.9793,0.9795,0.9718 # _reflns.entry_id 3HPB _reflns.observed_criterion_sigma_I 3.000 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 28.780 _reflns.d_resolution_high 2.190 _reflns.number_obs 12680 _reflns.number_all ? _reflns.percent_possible_obs 93.4 _reflns.pdbx_Rmerge_I_obs 0.03300 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 28.1000 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 4.180 _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1,2 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 2.19 _reflns_shell.d_res_low 2.27 _reflns_shell.percent_possible_all 62.3 _reflns_shell.Rmerge_I_obs 0.25600 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 3.500 _reflns_shell.pdbx_redundancy 2.05 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 3HPB _refine.ls_number_reflns_obs 11436 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 28.78 _refine.ls_d_res_high 2.19 _refine.ls_percent_reflns_obs 93.3 _refine.ls_R_factor_obs 0.240 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.236 _refine.ls_R_factor_R_free 0.284 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 9.800 _refine.ls_number_reflns_R_free 1244 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.945 _refine.correlation_coeff_Fo_to_Fc_free 0.917 _refine.B_iso_mean 48.12 _refine.aniso_B[1][1] -1.19000 _refine.aniso_B[2][2] 0.15000 _refine.aniso_B[3][3] 1.04000 _refine.aniso_B[1][2] 0.00000 _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 1.40 _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 MAD _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 0.271 _refine.pdbx_overall_ESU_R_Free 0.232 _refine.overall_SU_ML 0.157 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 6.449 _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _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 1274 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 1 _refine_hist.number_atoms_solvent 135 _refine_hist.number_atoms_total 1410 _refine_hist.d_res_high 2.19 _refine_hist.d_res_low 28.78 # 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 0.012 0.022 ? 1309 'X-RAY DIFFRACTION' ? r_bond_other_d ? ? ? ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.284 1.966 ? 1783 'X-RAY DIFFRACTION' ? r_angle_other_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 5.259 5.000 ? 161 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 43.298 25.313 ? 64 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 16.213 15.000 ? 229 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 23.943 15.000 ? 5 'X-RAY DIFFRACTION' ? r_chiral_restr 0.101 0.200 ? 198 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.008 0.021 ? 1009 '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 0.682 1.500 ? 799 'X-RAY DIFFRACTION' ? r_mcbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_it 1.324 2.000 ? 1315 'X-RAY DIFFRACTION' ? r_scbond_it 2.156 3.000 ? 510 'X-RAY DIFFRACTION' ? r_scangle_it 3.663 4.500 ? 468 '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 2.19 _refine_ls_shell.d_res_low 2.25 _refine_ls_shell.number_reflns_R_work 497 _refine_ls_shell.R_factor_R_work 0.3220 _refine_ls_shell.percent_reflns_obs 57.01 _refine_ls_shell.R_factor_R_free 0.4700 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 68 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.number_reflns_obs ? # _struct.entry_id 3HPB _struct.title 'Crystal structure of SNX5-PX domain in P212121 space group' _struct.pdbx_descriptor 'Snx5 protein' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3HPB _struct_keywords.pdbx_keywords 'PROTEIN TRANSPORT' _struct_keywords.text 'Sorting nexin, SNX5, Phox, PhosphatidylInositol, PI(4, 5)P2, PROTEIN TRANSPORT' # 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 ? # _struct_biol.id 1 _struct_biol.details ? # 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 GLN A 49 ? GLU A 62 ? GLN A 68 GLU A 81 1 ? 14 HELX_P HELX_P2 2 THR A 63 ? ALA A 67 ? THR A 82 ALA A 86 5 ? 5 HELX_P HELX_P3 3 PHE A 80 ? GLY A 93 ? PHE A 99 GLY A 112 1 ? 14 HELX_P HELX_P4 4 GLU A 94 ? MSE A 97 ? GLU A 113 MSE A 116 5 ? 4 HELX_P HELX_P5 5 THR A 98 ? HIS A 134 ? THR A 117 HIS A 153 1 ? 37 HELX_P HELX_P6 6 VAL A 136 ? LYS A 139 ? VAL A 155 LYS A 158 5 ? 4 HELX_P HELX_P7 7 ASP A 140 ? TYR A 149 ? ASP A 159 TYR A 168 1 ? 10 # _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 LYS 86 C ? ? ? 1_555 A MSE 87 N ? ? A LYS 105 A MSE 106 1_555 ? ? ? ? ? ? ? 1.331 ? covale2 covale ? ? A MSE 87 C ? ? ? 1_555 A GLN 88 N ? ? A MSE 106 A GLN 107 1_555 ? ? ? ? ? ? ? 1.329 ? covale3 covale ? ? A SER 96 C ? ? ? 1_555 A MSE 97 N ? ? A SER 115 A MSE 116 1_555 ? ? ? ? ? ? ? 1.322 ? covale4 covale ? ? A MSE 97 C ? ? ? 1_555 A THR 98 N ? ? A MSE 116 A THR 117 1_555 ? ? ? ? ? ? ? 1.331 ? covale5 covale ? ? A LYS 104 C ? ? ? 1_555 A MSE 105 N ? ? A LYS 123 A MSE 124 1_555 ? ? ? ? ? ? ? 1.326 ? covale6 covale ? ? A MSE 105 C ? ? ? 1_555 A LYS 106 N ? ? A MSE 124 A LYS 125 1_555 ? ? ? ? ? ? ? 1.326 ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details A ? 3 ? B ? 3 ? # 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 A 1 2 ? anti-parallel A 2 3 ? anti-parallel B 1 2 ? anti-parallel B 2 3 ? anti-parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id A 1 LEU A 12 ? ASP A 15 ? LEU A 31 ASP A 34 A 2 LYS A 25 ? THR A 34 ? LYS A 44 THR A 53 A 3 ALA A 19 ? GLU A 22 ? ALA A 38 GLU A 41 B 1 LEU A 12 ? ASP A 15 ? LEU A 31 ASP A 34 B 2 LYS A 25 ? THR A 34 ? LYS A 44 THR A 53 B 3 GLU A 43 ? ARG A 48 ? GLU A 62 ARG A 67 # 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 A 1 2 N GLN A 13 ? N GLN A 32 O LYS A 33 ? O LYS A 52 A 2 3 O LYS A 27 ? O LYS A 46 N LEU A 20 ? N LEU A 39 B 1 2 N GLN A 13 ? N GLN A 32 O LYS A 33 ? O LYS A 52 B 2 3 N THR A 32 ? N THR A 51 O PHE A 44 ? O PHE A 63 # _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 2 _struct_site.details 'BINDING SITE FOR RESIDUE CL A 181' # 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 2 VAL A 26 ? VAL A 45 . ? 1_555 ? 2 AC1 2 HOH C . ? HOH A 193 . ? 1_555 ? # _database_PDB_matrix.entry_id 3HPB _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 3HPB _atom_sites.fract_transf_matrix[1][1] 0.023279 _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] 0.013180 _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] 0.012901 _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 CL N O SE # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 SER 1 20 ? ? ? A . n A 1 2 VAL 2 21 21 VAL VAL A . n A 1 3 SER 3 22 22 SER SER A . n A 1 4 VAL 4 23 23 VAL VAL A . n A 1 5 ASP 5 24 24 ASP ASP A . n A 1 6 LEU 6 25 25 LEU LEU A . n A 1 7 ASN 7 26 26 ASN ASN A . n A 1 8 VAL 8 27 27 VAL VAL A . n A 1 9 ASP 9 28 28 ASP ASP A . n A 1 10 PRO 10 29 29 PRO PRO A . n A 1 11 SER 11 30 30 SER SER A . n A 1 12 LEU 12 31 31 LEU LEU A . n A 1 13 GLN 13 32 32 GLN GLN A . n A 1 14 ILE 14 33 33 ILE ILE A . n A 1 15 ASP 15 34 34 ASP ASP A . n A 1 16 ILE 16 35 35 ILE ILE A . n A 1 17 PRO 17 36 36 PRO PRO A . n A 1 18 ASP 18 37 37 ASP ASP A . n A 1 19 ALA 19 38 38 ALA ALA A . n A 1 20 LEU 20 39 39 LEU LEU A . n A 1 21 SER 21 40 40 SER SER A . n A 1 22 GLU 22 41 41 GLU GLU A . n A 1 23 ARG 23 42 42 ARG ARG A . n A 1 24 ASP 24 43 43 ASP ASP A . n A 1 25 LYS 25 44 44 LYS LYS A . n A 1 26 VAL 26 45 45 VAL VAL A . n A 1 27 LYS 27 46 46 LYS LYS A . n A 1 28 PHE 28 47 47 PHE PHE A . n A 1 29 THR 29 48 48 THR THR A . n A 1 30 VAL 30 49 49 VAL VAL A . n A 1 31 HIS 31 50 50 HIS HIS A . n A 1 32 THR 32 51 51 THR THR A . n A 1 33 LYS 33 52 52 LYS LYS A . n A 1 34 THR 34 53 53 THR THR A . n A 1 35 THR 35 54 54 THR THR A . n A 1 36 LEU 36 55 55 LEU LEU A . n A 1 37 PRO 37 56 56 PRO PRO A . n A 1 38 THR 38 57 57 THR THR A . n A 1 39 PHE 39 58 58 PHE PHE A . n A 1 40 GLN 40 59 59 GLN GLN A . n A 1 41 SER 41 60 60 SER SER A . n A 1 42 PRO 42 61 61 PRO PRO A . n A 1 43 GLU 43 62 62 GLU GLU A . n A 1 44 PHE 44 63 63 PHE PHE A . n A 1 45 SER 45 64 64 SER SER A . n A 1 46 VAL 46 65 65 VAL VAL A . n A 1 47 THR 47 66 66 THR THR A . n A 1 48 ARG 48 67 67 ARG ARG A . n A 1 49 GLN 49 68 68 GLN GLN A . n A 1 50 HIS 50 69 69 HIS HIS A . n A 1 51 GLU 51 70 70 GLU GLU A . n A 1 52 ASP 52 71 71 ASP ASP A . n A 1 53 PHE 53 72 72 PHE PHE A . n A 1 54 VAL 54 73 73 VAL VAL A . n A 1 55 TRP 55 74 74 TRP TRP A . n A 1 56 LEU 56 75 75 LEU LEU A . n A 1 57 HIS 57 76 76 HIS HIS A . n A 1 58 ASP 58 77 77 ASP ASP A . n A 1 59 THR 59 78 78 THR THR A . n A 1 60 LEU 60 79 79 LEU LEU A . n A 1 61 THR 61 80 80 THR THR A . n A 1 62 GLU 62 81 81 GLU GLU A . n A 1 63 THR 63 82 82 THR THR A . n A 1 64 THR 64 83 83 THR THR A . n A 1 65 ASP 65 84 84 ASP ASP A . n A 1 66 TYR 66 85 85 TYR TYR A . n A 1 67 ALA 67 86 86 ALA ALA A . n A 1 68 GLY 68 87 87 GLY GLY A . n A 1 69 LEU 69 88 88 LEU LEU A . n A 1 70 ILE 70 89 89 ILE ILE A . n A 1 71 ILE 71 90 90 ILE ILE A . n A 1 72 PRO 72 91 91 PRO PRO A . n A 1 73 PRO 73 92 92 PRO PRO A . n A 1 74 ALA 74 93 93 ALA ALA A . n A 1 75 PRO 75 94 94 PRO PRO A . n A 1 76 THR 76 95 95 THR THR A . n A 1 77 LYS 77 96 96 LYS LYS A . n A 1 78 PRO 78 97 97 PRO PRO A . n A 1 79 ASP 79 98 98 ASP ASP A . n A 1 80 PHE 80 99 99 PHE PHE A . n A 1 81 ASP 81 100 100 ASP ASP A . n A 1 82 GLY 82 101 101 GLY GLY A . n A 1 83 PRO 83 102 102 PRO PRO A . n A 1 84 ARG 84 103 103 ARG ARG A . n A 1 85 GLU 85 104 104 GLU GLU A . n A 1 86 LYS 86 105 105 LYS LYS A . n A 1 87 MSE 87 106 106 MSE MSE A . n A 1 88 GLN 88 107 107 GLN GLN A . n A 1 89 LYS 89 108 108 LYS LYS A . n A 1 90 LEU 90 109 109 LEU LEU A . n A 1 91 GLY 91 110 110 GLY GLY A . n A 1 92 GLU 92 111 111 GLU GLU A . n A 1 93 GLY 93 112 112 GLY GLY A . n A 1 94 GLU 94 113 113 GLU GLU A . n A 1 95 GLY 95 114 114 GLY GLY A . n A 1 96 SER 96 115 115 SER SER A . n A 1 97 MSE 97 116 116 MSE MSE A . n A 1 98 THR 98 117 117 THR THR A . n A 1 99 LYS 99 118 118 LYS LYS A . n A 1 100 GLU 100 119 119 GLU GLU A . n A 1 101 GLU 101 120 120 GLU GLU A . n A 1 102 PHE 102 121 121 PHE PHE A . n A 1 103 ALA 103 122 122 ALA ALA A . n A 1 104 LYS 104 123 123 LYS LYS A . n A 1 105 MSE 105 124 124 MSE MSE A . n A 1 106 LYS 106 125 125 LYS LYS A . n A 1 107 GLN 107 126 126 GLN GLN A . n A 1 108 GLU 108 127 127 GLU GLU A . n A 1 109 LEU 109 128 128 LEU LEU A . n A 1 110 GLU 110 129 129 GLU GLU A . n A 1 111 ALA 111 130 130 ALA ALA A . n A 1 112 GLU 112 131 131 GLU GLU A . n A 1 113 TYR 113 132 132 TYR TYR A . n A 1 114 LEU 114 133 133 LEU LEU A . n A 1 115 ALA 115 134 134 ALA ALA A . n A 1 116 VAL 116 135 135 VAL VAL A . n A 1 117 PHE 117 136 136 PHE PHE A . n A 1 118 LYS 118 137 137 LYS LYS A . n A 1 119 LYS 119 138 138 LYS LYS A . n A 1 120 THR 120 139 139 THR THR A . n A 1 121 VAL 121 140 140 VAL VAL A . n A 1 122 SER 122 141 141 SER SER A . n A 1 123 SER 123 142 142 SER SER A . n A 1 124 HIS 124 143 143 HIS HIS A . n A 1 125 GLU 125 144 144 GLU GLU A . n A 1 126 VAL 126 145 145 VAL VAL A . n A 1 127 PHE 127 146 146 PHE PHE A . n A 1 128 LEU 128 147 147 LEU LEU A . n A 1 129 GLN 129 148 148 GLN GLN A . n A 1 130 ARG 130 149 149 ARG ARG A . n A 1 131 LEU 131 150 150 LEU LEU A . n A 1 132 SER 132 151 151 SER SER A . n A 1 133 SER 133 152 152 SER SER A . n A 1 134 HIS 134 153 153 HIS HIS A . n A 1 135 PRO 135 154 154 PRO PRO A . n A 1 136 VAL 136 155 155 VAL VAL A . n A 1 137 LEU 137 156 156 LEU LEU A . n A 1 138 SER 138 157 157 SER SER A . n A 1 139 LYS 139 158 158 LYS LYS A . n A 1 140 ASP 140 159 159 ASP ASP A . n A 1 141 ARG 141 160 160 ARG ARG A . n A 1 142 ASN 142 161 161 ASN ASN A . n A 1 143 PHE 143 162 162 PHE PHE A . n A 1 144 HIS 144 163 163 HIS HIS A . n A 1 145 VAL 145 164 164 VAL VAL A . n A 1 146 PHE 146 165 165 PHE PHE A . n A 1 147 LEU 147 166 166 LEU LEU A . n A 1 148 GLU 148 167 167 GLU GLU A . n A 1 149 TYR 149 168 168 TYR TYR A . n A 1 150 ASP 150 169 169 ASP ASP A . n A 1 151 GLN 151 170 170 GLN GLN A . n A 1 152 ASP 152 171 171 ASP ASP A . n A 1 153 LEU 153 172 172 LEU LEU A . n A 1 154 SER 154 173 173 SER SER A . n A 1 155 VAL 155 174 174 VAL VAL A . n A 1 156 ARG 156 175 ? ? ? A . n A 1 157 ARG 157 176 ? ? ? A . n A 1 158 LYS 158 177 ? ? ? A . n A 1 159 ASN 159 178 ? ? ? A . n A 1 160 THR 160 179 ? ? ? A . n A 1 161 LYS 161 180 ? ? ? A . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 CL 1 181 181 CL CL A . C 3 HOH 1 182 182 HOH HOH A . C 3 HOH 2 183 183 HOH HOH A . C 3 HOH 3 184 184 HOH HOH A . C 3 HOH 4 185 185 HOH HOH A . C 3 HOH 5 186 186 HOH HOH A . C 3 HOH 6 187 187 HOH HOH A . C 3 HOH 7 188 188 HOH HOH A . C 3 HOH 8 189 189 HOH HOH A . C 3 HOH 9 191 191 HOH HOH A . C 3 HOH 10 192 192 HOH HOH A . C 3 HOH 11 193 193 HOH HOH A . C 3 HOH 12 194 194 HOH HOH A . C 3 HOH 13 196 196 HOH HOH A . C 3 HOH 14 197 197 HOH HOH A . C 3 HOH 15 198 198 HOH HOH A . C 3 HOH 16 199 199 HOH HOH A . C 3 HOH 17 200 200 HOH HOH A . C 3 HOH 18 201 201 HOH HOH A . C 3 HOH 19 202 202 HOH HOH A . C 3 HOH 20 203 203 HOH HOH A . C 3 HOH 21 204 204 HOH HOH A . C 3 HOH 22 205 205 HOH HOH A . C 3 HOH 23 206 206 HOH HOH A . C 3 HOH 24 207 207 HOH HOH A . C 3 HOH 25 208 208 HOH HOH A . C 3 HOH 26 209 209 HOH HOH A . C 3 HOH 27 210 210 HOH HOH A . C 3 HOH 28 211 211 HOH HOH A . C 3 HOH 29 212 212 HOH HOH A . C 3 HOH 30 213 213 HOH HOH A . C 3 HOH 31 214 214 HOH HOH A . C 3 HOH 32 215 215 HOH HOH A . C 3 HOH 33 216 216 HOH HOH A . C 3 HOH 34 217 217 HOH HOH A . C 3 HOH 35 218 218 HOH HOH A . C 3 HOH 36 219 219 HOH HOH A . C 3 HOH 37 220 220 HOH HOH A . C 3 HOH 38 221 221 HOH HOH A . C 3 HOH 39 222 222 HOH HOH A . C 3 HOH 40 223 223 HOH HOH A . C 3 HOH 41 224 224 HOH HOH A . C 3 HOH 42 225 225 HOH HOH A . C 3 HOH 43 226 226 HOH HOH A . C 3 HOH 44 227 227 HOH HOH A . C 3 HOH 45 228 228 HOH HOH A . C 3 HOH 46 229 229 HOH HOH A . C 3 HOH 47 230 230 HOH HOH A . C 3 HOH 48 231 231 HOH HOH A . C 3 HOH 49 232 232 HOH HOH A . C 3 HOH 50 233 233 HOH HOH A . C 3 HOH 51 234 234 HOH HOH A . C 3 HOH 52 235 235 HOH HOH A . C 3 HOH 53 236 236 HOH HOH A . C 3 HOH 54 237 237 HOH HOH A . C 3 HOH 55 238 238 HOH HOH A . C 3 HOH 56 239 239 HOH HOH A . C 3 HOH 57 240 240 HOH HOH A . C 3 HOH 58 241 241 HOH HOH A . C 3 HOH 59 242 242 HOH HOH A . C 3 HOH 60 243 243 HOH HOH A . C 3 HOH 61 244 244 HOH HOH A . C 3 HOH 62 245 245 HOH HOH A . C 3 HOH 63 246 246 HOH HOH A . C 3 HOH 64 247 247 HOH HOH A . C 3 HOH 65 248 248 HOH HOH A . C 3 HOH 66 249 249 HOH HOH A . C 3 HOH 67 250 250 HOH HOH A . C 3 HOH 68 251 251 HOH HOH A . C 3 HOH 69 253 253 HOH HOH A . C 3 HOH 70 254 254 HOH HOH A . C 3 HOH 71 255 255 HOH HOH A . C 3 HOH 72 256 256 HOH HOH A . C 3 HOH 73 257 257 HOH HOH A . C 3 HOH 74 258 258 HOH HOH A . C 3 HOH 75 259 259 HOH HOH A . C 3 HOH 76 260 260 HOH HOH A . C 3 HOH 77 261 261 HOH HOH A . C 3 HOH 78 262 262 HOH HOH A . C 3 HOH 79 263 263 HOH HOH A . C 3 HOH 80 264 264 HOH HOH A . C 3 HOH 81 265 265 HOH HOH A . C 3 HOH 82 266 266 HOH HOH A . C 3 HOH 83 267 267 HOH HOH A . C 3 HOH 84 268 268 HOH HOH A . C 3 HOH 85 269 269 HOH HOH A . C 3 HOH 86 270 270 HOH HOH A . C 3 HOH 87 271 271 HOH HOH A . C 3 HOH 88 272 272 HOH HOH A . C 3 HOH 89 273 273 HOH HOH A . C 3 HOH 90 274 274 HOH HOH A . C 3 HOH 91 275 275 HOH HOH A . C 3 HOH 92 276 276 HOH HOH A . C 3 HOH 93 277 277 HOH HOH A . C 3 HOH 94 278 278 HOH HOH A . C 3 HOH 95 279 279 HOH HOH A . C 3 HOH 96 280 280 HOH HOH A . C 3 HOH 97 281 281 HOH HOH A . C 3 HOH 98 282 282 HOH HOH A . C 3 HOH 99 283 283 HOH HOH A . C 3 HOH 100 284 284 HOH HOH A . C 3 HOH 101 285 285 HOH HOH A . C 3 HOH 102 286 286 HOH HOH A . C 3 HOH 103 287 287 HOH HOH A . C 3 HOH 104 289 289 HOH HOH A . C 3 HOH 105 290 290 HOH HOH A . C 3 HOH 106 291 291 HOH HOH A . C 3 HOH 107 292 292 HOH HOH A . C 3 HOH 108 293 293 HOH HOH A . C 3 HOH 109 294 294 HOH HOH A . C 3 HOH 110 295 295 HOH HOH A . C 3 HOH 111 297 297 HOH HOH A . C 3 HOH 112 298 298 HOH HOH A . C 3 HOH 113 300 300 HOH HOH A . C 3 HOH 114 301 301 HOH HOH A . C 3 HOH 115 302 302 HOH HOH A . C 3 HOH 116 303 303 HOH HOH A . C 3 HOH 117 304 304 HOH HOH A . C 3 HOH 118 305 305 HOH HOH A . C 3 HOH 119 306 306 HOH HOH A . C 3 HOH 120 307 307 HOH HOH A . C 3 HOH 121 308 308 HOH HOH A . C 3 HOH 122 309 309 HOH HOH A . C 3 HOH 123 310 310 HOH HOH A . C 3 HOH 124 311 311 HOH HOH A . C 3 HOH 125 312 312 HOH HOH A . C 3 HOH 126 313 313 HOH HOH A . C 3 HOH 127 314 314 HOH HOH A . C 3 HOH 128 315 315 HOH HOH A . C 3 HOH 129 316 316 HOH HOH A . C 3 HOH 130 317 317 HOH HOH A . C 3 HOH 131 318 318 HOH HOH A . C 3 HOH 132 319 319 HOH HOH A . C 3 HOH 133 320 320 HOH HOH A . C 3 HOH 134 321 321 HOH HOH A . C 3 HOH 135 322 322 HOH HOH A . # 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 MSE 87 A MSE 106 ? MET SELENOMETHIONINE 2 A MSE 97 A MSE 116 ? MET SELENOMETHIONINE 3 A MSE 105 A MSE 124 ? MET SELENOMETHIONINE # _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 monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation 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_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2009-06-23 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2017-11-01 # _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' 'Refinement description' # _pdbx_audit_revision_category.ordinal 1 _pdbx_audit_revision_category.revision_ordinal 3 _pdbx_audit_revision_category.data_content_type 'Structure model' _pdbx_audit_revision_category.category software # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal StructureStudio 'data collection' . ? 1 SnB phasing . ? 2 PHASER phasing . ? 3 REFMAC refinement 5.5.0044 ? 4 d*TREK 'data reduction' . ? 5 d*TREK 'data scaling' . ? 6 # _pdbx_entry_details.entry_id 3HPB _pdbx_entry_details.sequence_details ;THE ORIGINAL CONSTRUCT CONTAINED RESIDUES 1-180. THE FINAL CRYSTALLIZED PROTEIN CONSTRUCT SPANS FROM RESIDUES 20 TO 180 DUE TO NON-SPECIFIC CLEAVAGE BY THROMBIN PROTEASE ; _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? # 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 28 ? ? 34.84 57.16 2 1 TYR A 168 ? ? -49.03 108.33 3 1 ASP A 169 ? A -93.23 37.35 4 1 ASP A 169 ? B -96.30 39.96 # 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 SER 20 ? A SER 1 2 1 Y 1 A ARG 175 ? A ARG 156 3 1 Y 1 A ARG 176 ? A ARG 157 4 1 Y 1 A LYS 177 ? A LYS 158 5 1 Y 1 A ASN 178 ? A ASN 159 6 1 Y 1 A THR 179 ? A THR 160 7 1 Y 1 A LYS 180 ? A LYS 161 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'CHLORIDE ION' CL 3 water HOH #