data_3S9A # _entry.id 3S9A # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.329 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 3S9A RCSB RCSB065922 WWPDB D_1000065922 # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 3S9B . unspecified PDB 3S9C . unspecified PDB 3SBK . unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3S9A _pdbx_database_status.recvd_initial_deposition_date 2011-06-01 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Nakayama, D.' 1 'Ben Ammar, Y.' 2 'Takeda, S.' 3 # loop_ _citation.id _citation.title _citation.journal_abbrev _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 _citation.book_publisher _citation.pdbx_database_id_PubMed _citation.pdbx_database_id_DOI primary 'Structural basis of coagulation factor V recognition for cleavage by RVV-V' 'Febs Lett.' 585 3020 3025 2011 FEBLAL NE 0014-5793 0165 ? 21871889 10.1016/j.febslet.2011.08.022 1 ;Crystallization and preliminary X-ray crystallographic analysis of blood coagulation factor V-activating proteinase (RVV-V) from Russell's viper venom ; 'Acta Crystallogr.,Sect.F' 65 1306 1308 2009 ? DK 1744-3091 ? ? 20054136 10.1107/S1744309109046697 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Nakayama, D.' 1 ? primary 'Ben Ammar, Y.' 2 ? primary 'Miyata, T.' 3 ? primary 'Takeda, S.' 4 ? 1 'Nakayama, D.' 5 ? 1 'Ben Ammar, Y.' 6 ? 1 'Takeda, S.' 7 ? # _cell.entry_id 3S9A _cell.length_a 78.928 _cell.length_b 78.928 _cell.length_c 157.370 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 12 _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 3S9A _symmetry.space_group_name_H-M 'P 65 2 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _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 nat 'Vipera russelli proteinase RVV-V gamma' 25960.971 1 3.4.21.95 ? ? ? 2 non-polymer man 2-acetamido-2-deoxy-beta-D-glucopyranose 221.208 1 ? ? ? ? 3 water nat water 18.015 170 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'Factor V-activating proteinase gamma, Snake venom factor V activator gamma' # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code ;VVGGDECNINEHPFLVALYTSASSTIHCAGALINREWVLTAAHCDRRNIRIKLGMHSKNIRNEDEQIRVPRGKYFCLNTK FPNGLDKDIMLIRLRRPVTYSTHIAPVSLPSRSRGVGSRCRIMGWGKISTTTYPDVPHCTNIFIVKHKWCEPLYPWVPAD SRTLCAGILKGGRDTCHGDSGGPLICNGEMHGIVAGGSEPCGQHLKPAVYTKVFDYNNWIQSIIAGNRTVTCPP ; _entity_poly.pdbx_seq_one_letter_code_can ;VVGGDECNINEHPFLVALYTSASSTIHCAGALINREWVLTAAHCDRRNIRIKLGMHSKNIRNEDEQIRVPRGKYFCLNTK FPNGLDKDIMLIRLRRPVTYSTHIAPVSLPSRSRGVGSRCRIMGWGKISTTTYPDVPHCTNIFIVKHKWCEPLYPWVPAD SRTLCAGILKGGRDTCHGDSGGPLICNGEMHGIVAGGSEPCGQHLKPAVYTKVFDYNNWIQSIIAGNRTVTCPP ; _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 VAL n 1 2 VAL n 1 3 GLY n 1 4 GLY n 1 5 ASP n 1 6 GLU n 1 7 CYS n 1 8 ASN n 1 9 ILE n 1 10 ASN n 1 11 GLU n 1 12 HIS n 1 13 PRO n 1 14 PHE n 1 15 LEU n 1 16 VAL n 1 17 ALA n 1 18 LEU n 1 19 TYR n 1 20 THR n 1 21 SER n 1 22 ALA n 1 23 SER n 1 24 SER n 1 25 THR n 1 26 ILE n 1 27 HIS n 1 28 CYS n 1 29 ALA n 1 30 GLY n 1 31 ALA n 1 32 LEU n 1 33 ILE n 1 34 ASN n 1 35 ARG n 1 36 GLU n 1 37 TRP n 1 38 VAL n 1 39 LEU n 1 40 THR n 1 41 ALA n 1 42 ALA n 1 43 HIS n 1 44 CYS n 1 45 ASP n 1 46 ARG n 1 47 ARG n 1 48 ASN n 1 49 ILE n 1 50 ARG n 1 51 ILE n 1 52 LYS n 1 53 LEU n 1 54 GLY n 1 55 MET n 1 56 HIS n 1 57 SER n 1 58 LYS n 1 59 ASN n 1 60 ILE n 1 61 ARG n 1 62 ASN n 1 63 GLU n 1 64 ASP n 1 65 GLU n 1 66 GLN n 1 67 ILE n 1 68 ARG n 1 69 VAL n 1 70 PRO n 1 71 ARG n 1 72 GLY n 1 73 LYS n 1 74 TYR n 1 75 PHE n 1 76 CYS n 1 77 LEU n 1 78 ASN n 1 79 THR n 1 80 LYS n 1 81 PHE n 1 82 PRO n 1 83 ASN n 1 84 GLY n 1 85 LEU n 1 86 ASP n 1 87 LYS n 1 88 ASP n 1 89 ILE n 1 90 MET n 1 91 LEU n 1 92 ILE n 1 93 ARG n 1 94 LEU n 1 95 ARG n 1 96 ARG n 1 97 PRO n 1 98 VAL n 1 99 THR n 1 100 TYR n 1 101 SER n 1 102 THR n 1 103 HIS n 1 104 ILE n 1 105 ALA n 1 106 PRO n 1 107 VAL n 1 108 SER n 1 109 LEU n 1 110 PRO n 1 111 SER n 1 112 ARG n 1 113 SER n 1 114 ARG n 1 115 GLY n 1 116 VAL n 1 117 GLY n 1 118 SER n 1 119 ARG n 1 120 CYS n 1 121 ARG n 1 122 ILE n 1 123 MET n 1 124 GLY n 1 125 TRP n 1 126 GLY n 1 127 LYS n 1 128 ILE n 1 129 SER n 1 130 THR n 1 131 THR n 1 132 THR n 1 133 TYR n 1 134 PRO n 1 135 ASP n 1 136 VAL n 1 137 PRO n 1 138 HIS n 1 139 CYS n 1 140 THR n 1 141 ASN n 1 142 ILE n 1 143 PHE n 1 144 ILE n 1 145 VAL n 1 146 LYS n 1 147 HIS n 1 148 LYS n 1 149 TRP n 1 150 CYS n 1 151 GLU n 1 152 PRO n 1 153 LEU n 1 154 TYR n 1 155 PRO n 1 156 TRP n 1 157 VAL n 1 158 PRO n 1 159 ALA n 1 160 ASP n 1 161 SER n 1 162 ARG n 1 163 THR n 1 164 LEU n 1 165 CYS n 1 166 ALA n 1 167 GLY n 1 168 ILE n 1 169 LEU n 1 170 LYS n 1 171 GLY n 1 172 GLY n 1 173 ARG n 1 174 ASP n 1 175 THR n 1 176 CYS n 1 177 HIS n 1 178 GLY n 1 179 ASP n 1 180 SER n 1 181 GLY n 1 182 GLY n 1 183 PRO n 1 184 LEU n 1 185 ILE n 1 186 CYS n 1 187 ASN n 1 188 GLY n 1 189 GLU n 1 190 MET n 1 191 HIS n 1 192 GLY n 1 193 ILE n 1 194 VAL n 1 195 ALA n 1 196 GLY n 1 197 GLY n 1 198 SER n 1 199 GLU n 1 200 PRO n 1 201 CYS n 1 202 GLY n 1 203 GLN n 1 204 HIS n 1 205 LEU n 1 206 LYS n 1 207 PRO n 1 208 ALA n 1 209 VAL n 1 210 TYR n 1 211 THR n 1 212 LYS n 1 213 VAL n 1 214 PHE n 1 215 ASP n 1 216 TYR n 1 217 ASN n 1 218 ASN n 1 219 TRP n 1 220 ILE n 1 221 GLN n 1 222 SER n 1 223 ILE n 1 224 ILE n 1 225 ALA n 1 226 GLY n 1 227 ASN n 1 228 ARG n 1 229 THR n 1 230 VAL n 1 231 THR n 1 232 CYS n 1 233 PRO n 1 234 PRO n # _entity_src_nat.entity_id 1 _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 ;Siamese Russell's viper ; _entity_src_nat.pdbx_organism_scientific 'Daboia russellii siamensis' _entity_src_nat.pdbx_ncbi_taxonomy_id 343250 _entity_src_nat.genus ? _entity_src_nat.species ? _entity_src_nat.strain ? _entity_src_nat.tissue venom _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 ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code VSPG_DABRU _struct_ref.pdbx_db_accession P18965 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;VVGGDECNINEHPFLVALYTSASSTIHCAGALINREWVLTAAHCDRRNIRIKLGMHSKNIRNEDEQIRVPRGKYFCLNTK FPNGLDKDIMLIRLRRPVTYSTHIAPVSLPSRSRGVGSRCRIMGWGKISTTEDTYPDVPHCTNIFIVKHKWCEPLYPWVP ADSRTLCAGILKGGRDTCHGDSGGPLICNGEMHGIVAGGSEPCGQHLKPAVYTKVFDYNNWIQSIIAGNRTVTCPP ; _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3S9A _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 234 _struct_ref_seq.pdbx_seq_align_end_ins_code G _struct_ref_seq.pdbx_db_accession P18965 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 236 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 16 _struct_ref_seq.pdbx_auth_seq_align_end 245 # 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 3S9A ? A ? ? UNP P18965 GLU 132 deletion ? 1 1 3S9A ? A ? ? UNP P18965 ASP 133 deletion ? 2 # 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 NAG 'D-saccharide, beta linking' . 2-acetamido-2-deoxy-beta-D-glucopyranose ? 'C8 H15 N O6' 221.208 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 3S9A _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.73 _exptl_crystal.density_percent_sol 54.87 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 5.0 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details '16% PEG 3350, 50mM sodium citrate, 50mM bis-tris propane , pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K' # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'RAYONIX MX225HE' _diffrn_detector.pdbx_collection_date 2009-04-21 _diffrn_detector.details mirrors # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'Rotated-inclined double-crystal' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.0 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'SPRING-8 BEAMLINE BL41XU' _diffrn_source.pdbx_synchrotron_site SPring-8 _diffrn_source.pdbx_synchrotron_beamline BL41XU _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.0 # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 3S9A _reflns.observed_criterion_sigma_I 0 _reflns.observed_criterion_sigma_F 0 _reflns.d_resolution_low 50 _reflns.d_resolution_high 1.9 _reflns.number_obs 23547 _reflns.number_all 23594 _reflns.percent_possible_obs 99.8 _reflns.pdbx_Rmerge_I_obs 0.063 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 22.8 _reflns.B_iso_Wilson_estimate 18.3 _reflns.pdbx_redundancy 7.0 _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_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_ordinal 1 _reflns_shell.d_res_high 1.90 _reflns_shell.d_res_low 1.97 _reflns_shell.percent_possible_all 100 _reflns_shell.Rmerge_I_obs 0.255 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 8.6 _reflns_shell.pdbx_redundancy ? _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 ? # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 3S9A _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 23544 _refine.ls_number_reflns_all 23594 _refine.pdbx_ls_sigma_I 0 _refine.pdbx_ls_sigma_F 0.0 _refine.pdbx_data_cutoff_high_absF 2221293.05 _refine.pdbx_data_cutoff_low_absF 0.000000 _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 35.28 _refine.ls_d_res_high 1.90 _refine.ls_percent_reflns_obs 99.6 _refine.ls_R_factor_obs 0.220 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.2190 _refine.ls_R_factor_R_free 0.2555 _refine.ls_R_factor_R_free_error 0.008 _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.9 _refine.ls_number_reflns_R_free 1149 _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 29.6516 _refine.aniso_B[1][1] -1.2530 _refine.aniso_B[2][2] -1.2530 _refine.aniso_B[3][3] 2.5060 _refine.aniso_B[1][2] 0.0000 _refine.aniso_B[1][3] 0.0000 _refine.aniso_B[2][3] 0.0000 _refine.solvent_model_details 'FLAT MODEL' _refine.solvent_model_param_ksol 0.4 _refine.solvent_model_param_bsol 54.4674 _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'BULK SOLVENT MODEL USED' _refine.pdbx_starting_model 'PDB ENTRY 2AIQ' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model RESTRAINED _refine.pdbx_stereochemistry_target_values 'Engh & Huber' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.pdbx_overall_phase_error ? _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.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _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_overall_ESU_R ? # _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_analyze.entry_id 3S9A _refine_analyze.Luzzati_coordinate_error_obs 0.23 _refine_analyze.Luzzati_sigma_a_obs 0.14 _refine_analyze.Luzzati_d_res_low_obs 5.00 _refine_analyze.Luzzati_coordinate_error_free 0.28 _refine_analyze.Luzzati_sigma_a_free 0.17 _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.pdbx_Luzzati_d_res_high_obs ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 1817 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 14 _refine_hist.number_atoms_solvent 170 _refine_hist.number_atoms_total 2001 _refine_hist.d_res_high 1.90 _refine_hist.d_res_low 35.28 # 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 c_bond_d 0.005 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg 1.3 ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d 24.7 ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 2.61 ? ? ? 'X-RAY DIFFRACTION' ? c_mcbond_it 1.276 1.500 ? ? 'X-RAY DIFFRACTION' ? c_scbond_it 1.893 2.000 ? ? 'X-RAY DIFFRACTION' ? c_mcangle_it 1.928 2.000 ? ? 'X-RAY DIFFRACTION' ? c_scangle_it 2.843 2.500 ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.pdbx_total_number_of_bins_used 6 _refine_ls_shell.d_res_high 1.90 _refine_ls_shell.d_res_low 2.02 _refine_ls_shell.number_reflns_R_work 3618 _refine_ls_shell.R_factor_R_work 0.242 _refine_ls_shell.percent_reflns_obs 99.2 _refine_ls_shell.R_factor_R_free 0.269 _refine_ls_shell.R_factor_R_free_error 0.019 _refine_ls_shell.percent_reflns_R_free 5.1 _refine_ls_shell.number_reflns_R_free 196 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.number_reflns_obs ? # loop_ _pdbx_xplor_file.pdbx_refine_id _pdbx_xplor_file.serial_no _pdbx_xplor_file.param_file _pdbx_xplor_file.topol_file 'X-RAY DIFFRACTION' 1 protein_rep.param protein.top 'X-RAY DIFFRACTION' 2 water_rep.param water.top 'X-RAY DIFFRACTION' 3 ion.param ion.top 'X-RAY DIFFRACTION' 4 carbohydrate.param carbohydrate.top # _struct_ncs_dom.id 1 _struct_ncs_dom.details ? _struct_ncs_dom.pdbx_ens_id 1 # _struct_ncs_ens.id 1 _struct_ncs_ens.details ? # _struct.entry_id 3S9A _struct.title ;Russell's viper venom serine proteinase, RVV-V (closed-form) ; _struct.pdbx_descriptor 'Vipera russelli proteinase RVV-V gamma (E.C.3.4.21.95)' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3S9A _struct_keywords.pdbx_keywords HYDROLASE _struct_keywords.text 'serine proteinase, double six-stranded beta-barrels, Hydrolase, glycosylation' # 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 ALA A 41 ? ASP A 45 ? ALA A 55 ASP A 59 5 ? 5 HELX_P HELX_P2 2 GLY A 84 ? ASP A 88 ? GLY A 98 ASP A 102 5 ? 5 HELX_P HELX_P3 3 LYS A 146 ? CYS A 150 ? LYS A 164 CYS A 168 5 ? 5 HELX_P HELX_P4 4 TYR A 216 ? ALA A 225 ? TYR A 234 ALA A 243 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 _struct_conn.pdbx_role disulf1 disulf ? ? A CYS 7 SG ? ? ? 1_555 A CYS 139 SG ? ? A CYS 22 A CYS 157 1_555 ? ? ? ? ? ? ? 2.023 ? ? disulf2 disulf ? ? A CYS 28 SG ? ? ? 1_555 A CYS 44 SG ? ? A CYS 42 A CYS 58 1_555 ? ? ? ? ? ? ? 2.032 ? ? disulf3 disulf ? ? A CYS 76 SG ? ? ? 1_555 A CYS 232 SG ? E A CYS 91 A CYS 245 1_555 ? ? ? ? ? ? ? 2.026 ? ? disulf4 disulf ? ? A CYS 120 SG ? ? ? 1_555 A CYS 186 SG ? ? A CYS 136 A CYS 201 1_555 ? ? ? ? ? ? ? 2.034 ? ? disulf5 disulf ? ? A CYS 150 SG ? ? ? 1_555 A CYS 165 SG ? ? A CYS 168 A CYS 182 1_555 ? ? ? ? ? ? ? 2.035 ? ? disulf6 disulf ? ? A CYS 176 SG ? ? ? 1_555 A CYS 201 SG ? ? A CYS 191 A CYS 220 1_555 ? ? ? ? ? ? ? 2.036 ? ? covale1 covale one ? A ASN 227 ND2 ? ? ? 1_555 B NAG . C1 ? ? A ASN 245 A NAG 301 1_555 ? ? ? ? ? ? ? 1.155 ? N-Glycosylation # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference disulf ? ? covale ? ? # _struct_mon_prot_cis.pdbx_id 1 _struct_mon_prot_cis.label_comp_id GLU _struct_mon_prot_cis.label_seq_id 199 _struct_mon_prot_cis.label_asym_id A _struct_mon_prot_cis.label_alt_id . _struct_mon_prot_cis.pdbx_PDB_ins_code ? _struct_mon_prot_cis.auth_comp_id GLU _struct_mon_prot_cis.auth_seq_id 218 _struct_mon_prot_cis.auth_asym_id A _struct_mon_prot_cis.pdbx_label_comp_id_2 PRO _struct_mon_prot_cis.pdbx_label_seq_id_2 200 _struct_mon_prot_cis.pdbx_label_asym_id_2 A _struct_mon_prot_cis.pdbx_PDB_ins_code_2 ? _struct_mon_prot_cis.pdbx_auth_comp_id_2 PRO _struct_mon_prot_cis.pdbx_auth_seq_id_2 219 _struct_mon_prot_cis.pdbx_auth_asym_id_2 A _struct_mon_prot_cis.pdbx_PDB_model_num 1 _struct_mon_prot_cis.pdbx_omega_angle -0.16 # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details A ? 8 ? B ? 7 ? # 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 A 3 4 ? anti-parallel A 4 5 ? anti-parallel A 5 6 ? anti-parallel A 6 7 ? anti-parallel A 7 8 ? anti-parallel B 1 2 ? anti-parallel B 2 3 ? anti-parallel B 3 4 ? anti-parallel B 4 5 ? anti-parallel B 5 6 ? anti-parallel B 6 7 ? 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 ASP A 5 ? GLU A 6 ? ASP A 20 GLU A 21 A 2 HIS A 138 ? VAL A 145 ? HIS A 156 VAL A 163 A 3 THR A 163 ? GLY A 167 ? THR A 180 GLY A 184 A 4 ALA A 208 ? LYS A 212 ? ALA A 226 LYS A 230 A 5 GLU A 189 ? GLY A 196 ? GLU A 208 GLY A 215 A 6 PRO A 183 ? CYS A 186 ? PRO A 198 CYS A 201 A 7 ARG A 119 ? GLY A 124 ? ARG A 135 GLY A 140 A 8 HIS A 138 ? VAL A 145 ? HIS A 156 VAL A 163 B 1 GLN A 66 ? ARG A 68 ? GLN A 81 ARG A 83 B 2 ILE A 49 ? LEU A 53 ? ILE A 64 LEU A 68 B 3 LEU A 15 ? THR A 20 ? LEU A 30 THR A 35 B 4 CYS A 28 ? ASN A 34 ? CYS A 42 ASN A 48 B 5 TRP A 37 ? THR A 40 ? TRP A 51 THR A 54 B 6 MET A 90 ? LEU A 94 ? MET A 104 LEU A 108 B 7 PRO A 70 ? PHE A 75 ? PRO A 85 PHE A 90 # 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 ASP A 5 ? N ASP A 20 O CYS A 139 ? O CYS A 157 A 2 3 N VAL A 145 ? N VAL A 163 O CYS A 165 ? O CYS A 182 A 3 4 N LEU A 164 ? N LEU A 181 O TYR A 210 ? O TYR A 228 A 4 5 O VAL A 209 ? O VAL A 227 N GLY A 196 ? N GLY A 215 A 5 6 O GLU A 189 ? O GLU A 208 N CYS A 186 ? N CYS A 201 A 6 7 O ILE A 185 ? O ILE A 200 N ARG A 121 ? N ARG A 137 A 7 8 N CYS A 120 ? N CYS A 136 O ILE A 142 ? O ILE A 160 B 1 2 O GLN A 66 ? O GLN A 81 N LEU A 53 ? N LEU A 68 B 2 3 O ARG A 50 ? O ARG A 65 N TYR A 19 ? N TYR A 34 B 3 4 N LEU A 18 ? N LEU A 33 O CYS A 28 ? O CYS A 42 B 4 5 N ALA A 31 ? N ALA A 45 O LEU A 39 ? O LEU A 53 B 5 6 N VAL A 38 ? N VAL A 52 O ILE A 92 ? O ILE A 106 B 6 7 O ARG A 93 ? O ARG A 107 N GLY A 72 ? N GLY A 87 # _database_PDB_matrix.entry_id 3S9A _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 3S9A _atom_sites.fract_transf_matrix[1][1] 0.012670 _atom_sites.fract_transf_matrix[1][2] 0.007315 _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] 0.014630 _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] 0.006354 _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 VAL 1 16 16 VAL VAL A . n A 1 2 VAL 2 17 17 VAL VAL A . n A 1 3 GLY 3 18 18 GLY GLY A . n A 1 4 GLY 4 19 19 GLY GLY A . n A 1 5 ASP 5 20 20 ASP ASP A . n A 1 6 GLU 6 21 21 GLU GLU A . n A 1 7 CYS 7 22 22 CYS CYS A . n A 1 8 ASN 8 23 23 ASN ASN A . n A 1 9 ILE 9 24 24 ILE ILE A . n A 1 10 ASN 10 25 25 ASN ASN A . n A 1 11 GLU 11 26 26 GLU GLU A . n A 1 12 HIS 12 27 27 HIS HIS A . n A 1 13 PRO 13 28 28 PRO PRO A . n A 1 14 PHE 14 29 29 PHE PHE A . n A 1 15 LEU 15 30 30 LEU LEU A . n A 1 16 VAL 16 31 31 VAL VAL A . n A 1 17 ALA 17 32 32 ALA ALA A . n A 1 18 LEU 18 33 33 LEU LEU A . n A 1 19 TYR 19 34 34 TYR TYR A . n A 1 20 THR 20 35 35 THR THR A . n A 1 21 SER 21 36 36 SER SER A . n A 1 22 ALA 22 36 36 ALA ALA A A n A 1 23 SER 23 37 37 SER SER A . n A 1 24 SER 24 38 38 SER SER A . n A 1 25 THR 25 39 39 THR THR A . n A 1 26 ILE 26 40 40 ILE ILE A . n A 1 27 HIS 27 41 41 HIS HIS A . n A 1 28 CYS 28 42 42 CYS CYS A . n A 1 29 ALA 29 43 43 ALA ALA A . n A 1 30 GLY 30 44 44 GLY GLY A . n A 1 31 ALA 31 45 45 ALA ALA A . n A 1 32 LEU 32 46 46 LEU LEU A . n A 1 33 ILE 33 47 47 ILE ILE A . n A 1 34 ASN 34 48 48 ASN ASN A . n A 1 35 ARG 35 49 49 ARG ARG A . n A 1 36 GLU 36 50 50 GLU GLU A . n A 1 37 TRP 37 51 51 TRP TRP A . n A 1 38 VAL 38 52 52 VAL VAL A . n A 1 39 LEU 39 53 53 LEU LEU A . n A 1 40 THR 40 54 54 THR THR A . n A 1 41 ALA 41 55 55 ALA ALA A . n A 1 42 ALA 42 56 56 ALA ALA A . n A 1 43 HIS 43 57 57 HIS HIS A . n A 1 44 CYS 44 58 58 CYS CYS A . n A 1 45 ASP 45 59 59 ASP ASP A . n A 1 46 ARG 46 60 60 ARG ARG A . n A 1 47 ARG 47 62 62 ARG ARG A . n A 1 48 ASN 48 63 63 ASN ASN A . n A 1 49 ILE 49 64 64 ILE ILE A . n A 1 50 ARG 50 65 65 ARG ARG A . n A 1 51 ILE 51 66 66 ILE ILE A . n A 1 52 LYS 52 67 67 LYS LYS A . n A 1 53 LEU 53 68 68 LEU LEU A . n A 1 54 GLY 54 69 69 GLY GLY A . n A 1 55 MET 55 70 70 MET MET A . n A 1 56 HIS 56 71 71 HIS HIS A . n A 1 57 SER 57 72 72 SER SER A . n A 1 58 LYS 58 73 73 LYS LYS A . n A 1 59 ASN 59 74 74 ASN ASN A . n A 1 60 ILE 60 75 75 ILE ILE A . n A 1 61 ARG 61 76 76 ARG ARG A . n A 1 62 ASN 62 77 77 ASN ASN A . n A 1 63 GLU 63 78 78 GLU GLU A . n A 1 64 ASP 64 79 79 ASP ASP A . n A 1 65 GLU 65 80 80 GLU GLU A . n A 1 66 GLN 66 81 81 GLN GLN A . n A 1 67 ILE 67 82 82 ILE ILE A . n A 1 68 ARG 68 83 83 ARG ARG A . n A 1 69 VAL 69 84 84 VAL VAL A . n A 1 70 PRO 70 85 85 PRO PRO A . n A 1 71 ARG 71 86 86 ARG ARG A . n A 1 72 GLY 72 87 87 GLY GLY A . n A 1 73 LYS 73 88 88 LYS LYS A . n A 1 74 TYR 74 89 89 TYR TYR A . n A 1 75 PHE 75 90 90 PHE PHE A . n A 1 76 CYS 76 91 91 CYS CYS A . n A 1 77 LEU 77 92 92 LEU LEU A . n A 1 78 ASN 78 93 93 ASN ASN A . n A 1 79 THR 79 94 94 THR THR A . n A 1 80 LYS 80 95 95 LYS LYS A . n A 1 81 PHE 81 95 95 PHE PHE A A n A 1 82 PRO 82 96 96 PRO PRO A . n A 1 83 ASN 83 97 97 ASN ASN A . n A 1 84 GLY 84 98 98 GLY GLY A . n A 1 85 LEU 85 99 99 LEU LEU A . n A 1 86 ASP 86 100 100 ASP ASP A . n A 1 87 LYS 87 101 101 LYS LYS A . n A 1 88 ASP 88 102 102 ASP ASP A . n A 1 89 ILE 89 103 103 ILE ILE A . n A 1 90 MET 90 104 104 MET MET A . n A 1 91 LEU 91 105 105 LEU LEU A . n A 1 92 ILE 92 106 106 ILE ILE A . n A 1 93 ARG 93 107 107 ARG ARG A . n A 1 94 LEU 94 108 108 LEU LEU A . n A 1 95 ARG 95 109 109 ARG ARG A . n A 1 96 ARG 96 110 110 ARG ARG A . n A 1 97 PRO 97 111 111 PRO PRO A . n A 1 98 VAL 98 112 112 VAL VAL A . n A 1 99 THR 99 113 113 THR THR A . n A 1 100 TYR 100 114 114 TYR TYR A . n A 1 101 SER 101 115 115 SER SER A . n A 1 102 THR 102 116 116 THR THR A . n A 1 103 HIS 103 117 117 HIS HIS A . n A 1 104 ILE 104 118 118 ILE ILE A . n A 1 105 ALA 105 119 119 ALA ALA A . n A 1 106 PRO 106 120 120 PRO PRO A . n A 1 107 VAL 107 121 121 VAL VAL A . n A 1 108 SER 108 122 122 SER SER A . n A 1 109 LEU 109 123 123 LEU LEU A . n A 1 110 PRO 110 124 124 PRO PRO A . n A 1 111 SER 111 125 125 SER SER A . n A 1 112 ARG 112 127 127 ARG ARG A . n A 1 113 SER 113 128 128 SER SER A . n A 1 114 ARG 114 129 129 ARG ARG A . n A 1 115 GLY 115 131 131 GLY GLY A . n A 1 116 VAL 116 132 132 VAL VAL A . n A 1 117 GLY 117 133 133 GLY GLY A . n A 1 118 SER 118 134 134 SER SER A . n A 1 119 ARG 119 135 135 ARG ARG A . n A 1 120 CYS 120 136 136 CYS CYS A . n A 1 121 ARG 121 137 137 ARG ARG A . n A 1 122 ILE 122 138 138 ILE ILE A . n A 1 123 MET 123 139 139 MET MET A . n A 1 124 GLY 124 140 140 GLY GLY A . n A 1 125 TRP 125 141 141 TRP TRP A . n A 1 126 GLY 126 142 142 GLY GLY A . n A 1 127 LYS 127 143 143 LYS LYS A . n A 1 128 ILE 128 144 144 ILE ILE A . n A 1 129 SER 129 145 145 SER SER A . n A 1 130 THR 130 146 146 THR THR A . n A 1 131 THR 131 147 147 THR THR A . n A 1 132 THR 132 148 148 THR THR A . n A 1 133 TYR 133 149 149 TYR TYR A . n A 1 134 PRO 134 152 152 PRO PRO A . n A 1 135 ASP 135 153 153 ASP ASP A . n A 1 136 VAL 136 154 154 VAL VAL A . n A 1 137 PRO 137 155 155 PRO PRO A . n A 1 138 HIS 138 156 156 HIS HIS A . n A 1 139 CYS 139 157 157 CYS CYS A . n A 1 140 THR 140 158 158 THR THR A . n A 1 141 ASN 141 159 159 ASN ASN A . n A 1 142 ILE 142 160 160 ILE ILE A . n A 1 143 PHE 143 161 161 PHE PHE A . n A 1 144 ILE 144 162 162 ILE ILE A . n A 1 145 VAL 145 163 163 VAL VAL A . n A 1 146 LYS 146 164 164 LYS LYS A . n A 1 147 HIS 147 165 165 HIS HIS A . n A 1 148 LYS 148 166 166 LYS LYS A . n A 1 149 TRP 149 167 167 TRP TRP A . n A 1 150 CYS 150 168 168 CYS CYS A . n A 1 151 GLU 151 169 169 GLU GLU A . n A 1 152 PRO 152 170 170 PRO PRO A . n A 1 153 LEU 153 171 171 LEU LEU A . n A 1 154 TYR 154 172 172 TYR TYR A . n A 1 155 PRO 155 172 172 PRO PRO A A n A 1 156 TRP 156 173 173 TRP TRP A . n A 1 157 VAL 157 174 174 VAL VAL A . n A 1 158 PRO 158 175 175 PRO PRO A . n A 1 159 ALA 159 176 176 ALA ALA A . n A 1 160 ASP 160 177 177 ASP ASP A . n A 1 161 SER 161 178 178 SER SER A . n A 1 162 ARG 162 179 179 ARG ARG A . n A 1 163 THR 163 180 180 THR THR A . n A 1 164 LEU 164 181 181 LEU LEU A . n A 1 165 CYS 165 182 182 CYS CYS A . n A 1 166 ALA 166 183 183 ALA ALA A . n A 1 167 GLY 167 184 184 GLY GLY A . n A 1 168 ILE 168 185 185 ILE ILE A . n A 1 169 LEU 169 186 186 LEU LEU A . n A 1 170 LYS 170 186 186 LYS LYS A A n A 1 171 GLY 171 186 186 GLY GLY A B n A 1 172 GLY 172 187 187 GLY GLY A . n A 1 173 ARG 173 188 188 ARG ARG A . n A 1 174 ASP 174 189 189 ASP ASP A . n A 1 175 THR 175 190 190 THR THR A . n A 1 176 CYS 176 191 191 CYS CYS A . n A 1 177 HIS 177 192 192 HIS HIS A . n A 1 178 GLY 178 193 193 GLY GLY A . n A 1 179 ASP 179 194 194 ASP ASP A . n A 1 180 SER 180 195 195 SER SER A . n A 1 181 GLY 181 196 196 GLY GLY A . n A 1 182 GLY 182 197 197 GLY GLY A . n A 1 183 PRO 183 198 198 PRO PRO A . n A 1 184 LEU 184 199 199 LEU LEU A . n A 1 185 ILE 185 200 200 ILE ILE A . n A 1 186 CYS 186 201 201 CYS CYS A . n A 1 187 ASN 187 202 202 ASN ASN A . n A 1 188 GLY 188 207 207 GLY GLY A . n A 1 189 GLU 189 208 208 GLU GLU A . n A 1 190 MET 190 209 209 MET MET A . n A 1 191 HIS 191 210 210 HIS HIS A . n A 1 192 GLY 192 211 211 GLY GLY A . n A 1 193 ILE 193 212 212 ILE ILE A . n A 1 194 VAL 194 213 213 VAL VAL A . n A 1 195 ALA 195 214 214 ALA ALA A . n A 1 196 GLY 196 215 215 GLY GLY A . n A 1 197 GLY 197 216 216 GLY GLY A . n A 1 198 SER 198 217 217 SER SER A . n A 1 199 GLU 199 218 218 GLU GLU A . n A 1 200 PRO 200 219 219 PRO PRO A . n A 1 201 CYS 201 220 220 CYS CYS A . n A 1 202 GLY 202 221 221 GLY GLY A . n A 1 203 GLN 203 221 221 GLN GLN A A n A 1 204 HIS 204 222 222 HIS HIS A . n A 1 205 LEU 205 223 223 LEU LEU A . n A 1 206 LYS 206 224 224 LYS LYS A . n A 1 207 PRO 207 225 225 PRO PRO A . n A 1 208 ALA 208 226 226 ALA ALA A . n A 1 209 VAL 209 227 227 VAL VAL A . n A 1 210 TYR 210 228 228 TYR TYR A . n A 1 211 THR 211 229 229 THR THR A . n A 1 212 LYS 212 230 230 LYS LYS A . n A 1 213 VAL 213 231 231 VAL VAL A . n A 1 214 PHE 214 232 232 PHE PHE A . n A 1 215 ASP 215 233 233 ASP ASP A . n A 1 216 TYR 216 234 234 TYR TYR A . n A 1 217 ASN 217 235 235 ASN ASN A . n A 1 218 ASN 218 236 236 ASN ASN A . n A 1 219 TRP 219 237 237 TRP TRP A . n A 1 220 ILE 220 238 238 ILE ILE A . n A 1 221 GLN 221 239 239 GLN GLN A . n A 1 222 SER 222 240 240 SER SER A . n A 1 223 ILE 223 241 241 ILE ILE A . n A 1 224 ILE 224 242 242 ILE ILE A . n A 1 225 ALA 225 243 243 ALA ALA A . n A 1 226 GLY 226 244 244 GLY GLY A . n A 1 227 ASN 227 245 245 ASN ASN A . n A 1 228 ARG 228 245 245 ARG ARG A A n A 1 229 THR 229 245 245 THR THR A B n A 1 230 VAL 230 245 245 VAL VAL A C n A 1 231 THR 231 245 245 THR THR A D n A 1 232 CYS 232 245 245 CYS CYS A E n A 1 233 PRO 233 245 245 PRO PRO A F n A 1 234 PRO 234 245 245 PRO PRO A G 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 NAG 1 301 301 NAG NAG A . C 3 HOH 1 1 1 HOH TIP A . C 3 HOH 2 2 2 HOH TIP A . C 3 HOH 3 3 3 HOH TIP A . C 3 HOH 4 4 4 HOH TIP A . C 3 HOH 5 5 5 HOH TIP A . C 3 HOH 6 6 6 HOH TIP A . C 3 HOH 7 7 7 HOH TIP A . C 3 HOH 8 8 8 HOH TIP A . C 3 HOH 9 9 9 HOH TIP A . C 3 HOH 10 10 10 HOH TIP A . C 3 HOH 11 11 11 HOH TIP A . C 3 HOH 12 12 12 HOH TIP A . C 3 HOH 13 13 13 HOH TIP A . C 3 HOH 14 14 14 HOH TIP A . C 3 HOH 15 15 15 HOH TIP A . C 3 HOH 16 61 61 HOH TIP A . C 3 HOH 17 126 126 HOH TIP A . C 3 HOH 18 130 130 HOH TIP A . C 3 HOH 19 150 150 HOH TIP A . C 3 HOH 20 151 151 HOH TIP A . C 3 HOH 21 246 16 HOH TIP A . C 3 HOH 22 247 17 HOH TIP A . C 3 HOH 23 248 18 HOH TIP A . C 3 HOH 24 249 19 HOH TIP A . C 3 HOH 25 250 20 HOH TIP A . C 3 HOH 26 251 21 HOH TIP A . C 3 HOH 27 252 22 HOH TIP A . C 3 HOH 28 253 23 HOH TIP A . C 3 HOH 29 254 24 HOH TIP A . C 3 HOH 30 255 25 HOH TIP A . C 3 HOH 31 256 26 HOH TIP A . C 3 HOH 32 257 27 HOH TIP A . C 3 HOH 33 258 28 HOH TIP A . C 3 HOH 34 259 29 HOH TIP A . C 3 HOH 35 260 30 HOH TIP A . C 3 HOH 36 261 31 HOH TIP A . C 3 HOH 37 262 32 HOH TIP A . C 3 HOH 38 263 33 HOH TIP A . C 3 HOH 39 264 34 HOH TIP A . C 3 HOH 40 265 35 HOH TIP A . C 3 HOH 41 266 36 HOH TIP A . C 3 HOH 42 267 37 HOH TIP A . C 3 HOH 43 268 38 HOH TIP A . C 3 HOH 44 269 39 HOH TIP A . C 3 HOH 45 270 40 HOH TIP A . C 3 HOH 46 271 41 HOH TIP A . C 3 HOH 47 272 42 HOH TIP A . C 3 HOH 48 273 43 HOH TIP A . C 3 HOH 49 274 44 HOH TIP A . C 3 HOH 50 275 45 HOH TIP A . C 3 HOH 51 276 46 HOH TIP A . C 3 HOH 52 277 47 HOH TIP A . C 3 HOH 53 278 48 HOH TIP A . C 3 HOH 54 279 49 HOH TIP A . C 3 HOH 55 280 50 HOH TIP A . C 3 HOH 56 281 51 HOH TIP A . C 3 HOH 57 282 52 HOH TIP A . C 3 HOH 58 283 53 HOH TIP A . C 3 HOH 59 284 54 HOH TIP A . C 3 HOH 60 285 55 HOH TIP A . C 3 HOH 61 286 56 HOH TIP A . C 3 HOH 62 287 57 HOH TIP A . C 3 HOH 63 288 58 HOH TIP A . C 3 HOH 64 289 59 HOH TIP A . C 3 HOH 65 290 60 HOH TIP A . C 3 HOH 66 291 62 HOH TIP A . C 3 HOH 67 292 63 HOH TIP A . C 3 HOH 68 293 64 HOH TIP A . C 3 HOH 69 294 65 HOH TIP A . C 3 HOH 70 295 66 HOH TIP A . C 3 HOH 71 296 67 HOH TIP A . C 3 HOH 72 297 68 HOH TIP A . C 3 HOH 73 298 69 HOH TIP A . C 3 HOH 74 299 70 HOH TIP A . C 3 HOH 75 300 71 HOH TIP A . C 3 HOH 76 302 72 HOH TIP A . C 3 HOH 77 303 73 HOH TIP A . C 3 HOH 78 304 74 HOH TIP A . C 3 HOH 79 305 75 HOH TIP A . C 3 HOH 80 306 76 HOH TIP A . C 3 HOH 81 307 77 HOH TIP A . C 3 HOH 82 308 78 HOH TIP A . C 3 HOH 83 309 79 HOH TIP A . C 3 HOH 84 310 80 HOH TIP A . C 3 HOH 85 311 81 HOH TIP A . C 3 HOH 86 312 82 HOH TIP A . C 3 HOH 87 313 83 HOH TIP A . C 3 HOH 88 314 84 HOH TIP A . C 3 HOH 89 315 85 HOH TIP A . C 3 HOH 90 316 86 HOH TIP A . C 3 HOH 91 317 87 HOH TIP A . C 3 HOH 92 318 88 HOH TIP A . C 3 HOH 93 319 89 HOH TIP A . C 3 HOH 94 320 90 HOH TIP A . C 3 HOH 95 321 91 HOH TIP A . C 3 HOH 96 322 92 HOH TIP A . C 3 HOH 97 323 93 HOH TIP A . C 3 HOH 98 324 94 HOH TIP A . C 3 HOH 99 325 95 HOH TIP A . C 3 HOH 100 326 96 HOH TIP A . C 3 HOH 101 327 97 HOH TIP A . C 3 HOH 102 328 98 HOH TIP A . C 3 HOH 103 329 99 HOH TIP A . C 3 HOH 104 330 100 HOH TIP A . C 3 HOH 105 331 101 HOH TIP A . C 3 HOH 106 332 102 HOH TIP A . C 3 HOH 107 333 103 HOH TIP A . C 3 HOH 108 334 104 HOH TIP A . C 3 HOH 109 335 105 HOH TIP A . C 3 HOH 110 336 106 HOH TIP A . C 3 HOH 111 337 107 HOH TIP A . C 3 HOH 112 338 108 HOH TIP A . C 3 HOH 113 339 109 HOH TIP A . C 3 HOH 114 340 110 HOH TIP A . C 3 HOH 115 341 111 HOH TIP A . C 3 HOH 116 342 112 HOH TIP A . C 3 HOH 117 343 113 HOH TIP A . C 3 HOH 118 344 114 HOH TIP A . C 3 HOH 119 345 115 HOH TIP A . C 3 HOH 120 346 116 HOH TIP A . C 3 HOH 121 347 117 HOH TIP A . C 3 HOH 122 348 118 HOH TIP A . C 3 HOH 123 349 119 HOH TIP A . C 3 HOH 124 350 120 HOH TIP A . C 3 HOH 125 351 121 HOH TIP A . C 3 HOH 126 352 122 HOH TIP A . C 3 HOH 127 353 123 HOH TIP A . C 3 HOH 128 354 124 HOH TIP A . C 3 HOH 129 355 125 HOH TIP A . C 3 HOH 130 356 127 HOH TIP A . C 3 HOH 131 357 128 HOH TIP A . C 3 HOH 132 358 129 HOH TIP A . C 3 HOH 133 359 131 HOH TIP A . C 3 HOH 134 360 132 HOH TIP A . C 3 HOH 135 361 133 HOH TIP A . C 3 HOH 136 362 134 HOH TIP A . C 3 HOH 137 363 135 HOH TIP A . C 3 HOH 138 364 136 HOH TIP A . C 3 HOH 139 365 137 HOH TIP A . C 3 HOH 140 366 138 HOH TIP A . C 3 HOH 141 367 139 HOH TIP A . C 3 HOH 142 368 140 HOH TIP A . C 3 HOH 143 369 141 HOH TIP A . C 3 HOH 144 370 142 HOH TIP A . C 3 HOH 145 371 143 HOH TIP A . C 3 HOH 146 372 144 HOH TIP A . C 3 HOH 147 373 145 HOH TIP A . C 3 HOH 148 374 146 HOH TIP A . C 3 HOH 149 375 147 HOH TIP A . C 3 HOH 150 376 148 HOH TIP A . C 3 HOH 151 377 149 HOH TIP A . C 3 HOH 152 378 152 HOH TIP A . C 3 HOH 153 379 153 HOH TIP A . C 3 HOH 154 380 154 HOH TIP A . C 3 HOH 155 381 155 HOH TIP A . C 3 HOH 156 382 156 HOH TIP A . C 3 HOH 157 383 157 HOH TIP A . C 3 HOH 158 384 158 HOH TIP A . C 3 HOH 159 385 159 HOH TIP A . C 3 HOH 160 386 160 HOH TIP A . C 3 HOH 161 387 161 HOH TIP A . C 3 HOH 162 388 162 HOH TIP A . C 3 HOH 163 389 163 HOH TIP A . C 3 HOH 164 390 164 HOH TIP A . C 3 HOH 165 391 165 HOH TIP A . C 3 HOH 166 392 166 HOH TIP A . C 3 HOH 167 393 167 HOH TIP A . C 3 HOH 168 394 168 HOH TIP A . C 3 HOH 169 395 169 HOH TIP A . C 3 HOH 170 396 170 HOH TIP A . # _pdbx_struct_mod_residue.id 1 _pdbx_struct_mod_residue.label_asym_id A _pdbx_struct_mod_residue.label_comp_id ASN _pdbx_struct_mod_residue.label_seq_id 227 _pdbx_struct_mod_residue.auth_asym_id A _pdbx_struct_mod_residue.auth_comp_id ASN _pdbx_struct_mod_residue.auth_seq_id 245 _pdbx_struct_mod_residue.PDB_ins_code ? _pdbx_struct_mod_residue.parent_comp_id ASN _pdbx_struct_mod_residue.details 'GLYCOSYLATION SITE' # _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 2011-09-07 2 'Structure model' 1 1 2013-07-03 3 'Structure model' 1 2 2020-07-29 # loop_ _pdbx_audit_revision_details.ordinal _pdbx_audit_revision_details.revision_ordinal _pdbx_audit_revision_details.data_content_type _pdbx_audit_revision_details.provider _pdbx_audit_revision_details.type _pdbx_audit_revision_details.description _pdbx_audit_revision_details.details 1 1 'Structure model' repository 'Initial release' ? ? 2 3 'Structure model' repository Remediation 'Carbohydrate remediation' ? # 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' 'Database references' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' 5 3 'Structure model' 'Structure summary' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' chem_comp 2 3 'Structure model' entity 3 3 'Structure model' pdbx_chem_comp_identifier 4 3 'Structure model' pdbx_entity_nonpoly 5 3 'Structure model' struct_conn 6 3 'Structure model' struct_ref_seq_dif 7 3 'Structure model' struct_site 8 3 'Structure model' struct_site_gen # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_chem_comp.name' 2 3 'Structure model' '_chem_comp.type' 3 3 'Structure model' '_entity.pdbx_description' 4 3 'Structure model' '_pdbx_entity_nonpoly.name' 5 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 6 3 'Structure model' '_struct_conn.pdbx_role' 7 3 'Structure model' '_struct_ref_seq_dif.details' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal CNS refinement 1.3 ? 1 HKL-2000 'data collection' . ? 2 HKL-2000 'data reduction' . ? 3 HKL-2000 'data scaling' . ? 4 MOLREP phasing . ? 5 # _pdbx_entry_details.entry_id 3S9A _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details 'THE RESIDUE NUMBERING IS NOT SEQUENTIAL. THE RESIDUE NUMBERING IS BASED ON THE TOPOLOGICAL EQUIVALENCE TO CHYMOTRYPSINOGEN.' _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.has_ligand_of_interest ? # _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 A _pdbx_validate_close_contact.auth_comp_id_1 ASN _pdbx_validate_close_contact.auth_seq_id_1 245 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 C2 _pdbx_validate_close_contact.auth_asym_id_2 A _pdbx_validate_close_contact.auth_comp_id_2 NAG _pdbx_validate_close_contact.auth_seq_id_2 301 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 2.09 # 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 HIS A 71 ? ? -127.80 -82.04 2 1 ASN A 93 ? ? -103.48 76.81 # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier NAG 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1.0 DGlcpNAcb NAG 'COMMON NAME' GMML 1.0 N-acetyl-b-D-glucopyranosamine NAG 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1.0 b-D-GlcpNAc NAG 'SNFG CARBOHYDRATE SYMBOL' GMML 1.0 GlcNAc # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 2-acetamido-2-deoxy-beta-D-glucopyranose NAG 3 water HOH #