data_4YDG # _model_server_result.job_id KeTaTmPaQ4W3UeCb2TqrZQ _model_server_result.datetime_utc '2025-06-29 02:38:43' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 4ydg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":201}' # _entry.id 4YDG # _exptl.entry_id 4YDG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 591.744 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "N,N'-(3S,4S)-PYRROLIDINE-3,4-DIYLBIS(4-AMINO-N-BENZYLBENZENESULFONAMIDE)" _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 120 _cell.entry_id 4YDG _cell.length_a 77.61 _cell.length_b 77.61 _cell.length_c 160.23 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YDG _symmetry.cell_setting ? _symmetry.Int_Tables_number 182 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _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 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C30 H33 N5 O4 S2' _chem_comp.formula_weight 591.744 _chem_comp.id G3G _chem_comp.mon_nstd_flag . _chem_comp.name "N,N'-(3S,4S)-PYRROLIDINE-3,4-DIYLBIS(4-AMINO-N-BENZYLBENZENESULFONAMIDE)" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag C2 C6 G3G doub 83 n y C2 C18 G3G sing 84 n y C2 H2 G3G sing 85 n n C6 C5 G3G sing 86 n y C6 N43 G3G sing 87 n n C5 C20 G3G doub 88 n y C5 H5 G3G sing 89 n n C20 C27 G3G sing 90 n y C20 H20 G3G sing 91 n n C27 S9 G3G sing 92 n n C27 C18 G3G doub 93 n y C18 H18 G3G sing 94 n n S9 O11 G3G doub 95 n n S9 N32 G3G sing 96 n n S9 O40 G3G doub 97 n n N32 C24 G3G sing 98 n n N32 C33 G3G sing 99 n n C33 C34 G3G sing 100 n n C33 H331 G3G sing 101 n n C33 H332 G3G sing 102 n n C34 C35 G3G sing 103 n y C34 C38 G3G doub 104 n y C38 C39 G3G sing 105 n y C38 H38 G3G sing 106 n n C39 C37 G3G doub 107 n y C39 H39 G3G sing 108 n n C37 C36 G3G sing 109 n y C37 H37 G3G sing 110 n n C36 C35 G3G doub 111 n y C36 H36 G3G sing 112 n n C35 H35 G3G sing 113 n n C24 C23 G3G sing 114 n n C24 C25 G3G sing 115 n n C24 H24 G3G sing 116 n n C25 N22 G3G sing 117 n n C25 H251 G3G sing 118 n n C25 H252 G3G sing 119 n n N22 C21 G3G sing 120 n n N22 HN22 G3G sing 121 n n C21 C23 G3G sing 122 n n C21 H211 G3G sing 123 n n C21 H212 G3G sing 124 n n C23 N28 G3G sing 125 n n C23 H23 G3G sing 126 n n N28 S8 G3G sing 127 n n N28 C7 G3G sing 128 n n C7 C12 G3G sing 129 n n C7 H71 G3G sing 130 n n C7 H72 G3G sing 131 n n C12 C13 G3G sing 132 n y C12 C14 G3G doub 133 n y C14 C30 G3G sing 134 n y C14 H14 G3G sing 135 n n C30 C31 G3G doub 136 n y C30 H30 G3G sing 137 n n C31 C29 G3G sing 138 n y C31 H31 G3G sing 139 n n C29 C13 G3G doub 140 n y C29 H29 G3G sing 141 n n C13 H13 G3G sing 142 n n S8 O41 G3G doub 143 n n S8 C26 G3G sing 144 n n S8 O10 G3G doub 145 n n C26 C17 G3G sing 146 n y C26 C19 G3G doub 147 n y C17 C1 G3G doub 148 n y C17 H17 G3G sing 149 n n C1 C4 G3G sing 150 n y C1 H1 G3G sing 151 n n C4 N42 G3G sing 152 n n C4 C3 G3G doub 153 n y C3 C19 G3G sing 154 n y C3 H3 G3G sing 155 n n C19 H19 G3G sing 156 n n N42 H421 G3G sing 157 n n N42 H422 G3G sing 158 n n N43 H431 G3G sing 159 n n N43 H432 G3G sing 160 n n # _atom_sites.entry_id 4YDG _atom_sites.fract_transf_matrix[1][1] 0.012885 _atom_sites.fract_transf_matrix[1][2] 0.007439 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014878 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.006241 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_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_ins_code C 2 SO4 A 1 201 1 SO4 SO4 . D 2 SO4 A 1 202 2 SO4 SO4 . E 3 G3G B 1 201 1 G3G G3G . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 C C2 G3G . . . E 3 2.779 71.585 186.476 1 45.86 ? C2 G3G 201 B 1 HETATM 2 C C6 G3G . . . E 3 3.923 71.774 185.708 1 46.01 ? C6 G3G 201 B 1 HETATM 3 C C5 G3G . . . E 3 4.608 70.675 185.204 1 46.1 ? C5 G3G 201 B 1 HETATM 4 C C20 G3G . . . E 3 4.149 69.388 185.465 1 46.29 ? C20 G3G 201 B 1 HETATM 5 C C27 G3G . . . E 3 3 69.198 186.227 1 46.16 ? C27 G3G 201 B 1 HETATM 6 C C18 G3G . . . E 3 2.322 70.298 186.739 1 45.77 ? C18 G3G 201 B 1 HETATM 7 S S9 G3G . . . E 3 2.476 67.721 186.539 1 43.7 ? S9 G3G 201 B 1 HETATM 8 O O40 G3G . . . E 3 3.588 66.96 187.029 1 43.1 ? O40 G3G 201 B 1 HETATM 9 O O11 G3G . . . E 3 1.456 67.781 187.547 1 43.94 ? O11 G3G 201 B 1 HETATM 10 N N32 G3G . . . E 3 1.91 67.064 185.281 1 42.97 ? N32 G3G 201 B 1 HETATM 11 C C33 G3G . . . E 3 2.675 66.083 184.509 1 42.95 ? C33 G3G 201 B 1 HETATM 12 C C34 G3G . . . E 3 2.45 64.644 184.939 1 42.71 ? C34 G3G 201 B 1 HETATM 13 C C38 G3G . . . E 3 2.606 64.264 186.267 1 42.62 ? C38 G3G 201 B 1 HETATM 14 C C39 G3G . . . E 3 2.393 62.946 186.651 1 42.92 ? C39 G3G 201 B 1 HETATM 15 C C37 G3G . . . E 3 2.015 62.001 185.706 1 43.11 ? C37 G3G 201 B 1 HETATM 16 C C36 G3G . . . E 3 1.853 62.376 184.377 1 42.93 ? C36 G3G 201 B 1 HETATM 17 C C35 G3G . . . E 3 2.067 63.696 183.996 1 42.75 ? C35 G3G 201 B 1 HETATM 18 C C24 G3G . . . E 3 0.581 67.428 184.776 1 41.71 ? C24 G3G 201 B 1 HETATM 19 C C25 G3G . . . E 3 0.765 67.873 183.328 1 41.2 ? C25 G3G 201 B 1 HETATM 20 N N22 G3G . . . E 3 0.092 66.86 182.539 1 40.94 ? N22 G3G 201 B 1 HETATM 21 C C21 G3G . . . E 3 -0.763 65.977 183.307 1 40.95 ? C21 G3G 201 B 1 HETATM 22 C C23 G3G . . . E 3 -0.34 66.203 184.755 1 41.18 ? C23 G3G 201 B 1 HETATM 23 N N28 G3G . . . E 3 -1.57 66.452 185.513 1 41.18 ? N28 G3G 201 B 1 HETATM 24 C C7 G3G . . . E 3 -2.413 67.568 185.077 1 40.99 ? C7 G3G 201 B 1 HETATM 25 C C12 G3G . . . E 3 -2.135 68.883 185.784 1 40.2 ? C12 G3G 201 B 1 HETATM 26 C C14 G3G . . . E 3 -1.747 69.995 185.043 1 39.98 ? C14 G3G 201 B 1 HETATM 27 C C30 G3G . . . E 3 -1.49 71.206 185.676 1 39.89 ? C30 G3G 201 B 1 HETATM 28 C C31 G3G . . . E 3 -1.628 71.312 187.055 1 39.92 ? C31 G3G 201 B 1 HETATM 29 C C29 G3G . . . E 3 -2.021 70.205 187.798 1 39.83 ? C29 G3G 201 B 1 HETATM 30 C C13 G3G . . . E 3 -2.277 68.997 187.162 1 39.82 ? C13 G3G 201 B 1 HETATM 31 S S8 G3G . . . E 3 -1.961 65.532 186.667 1 40.81 ? S8 G3G 201 B 1 HETATM 32 C C26 G3G . . . E 3 -2.509 64.139 186.111 1 41.76 ? C26 G3G 201 B 1 HETATM 33 C C17 G3G . . . E 3 -3.865 63.985 185.846 1 41.69 ? C17 G3G 201 B 1 HETATM 34 C C1 G3G . . . E 3 -4.351 62.773 185.367 1 41.5 ? C1 G3G 201 B 1 HETATM 35 C C4 G3G . . . E 3 -3.48 61.711 185.157 1 41.31 ? C4 G3G 201 B 1 HETATM 36 C C3 G3G . . . E 3 -2.125 61.861 185.425 1 41.64 ? C3 G3G 201 B 1 HETATM 37 C C19 G3G . . . E 3 -1.639 63.073 185.905 1 41.76 ? C19 G3G 201 B 1 HETATM 38 O O41 G3G . . . E 3 -0.81 65.284 187.489 1 40.64 ? O41 G3G 201 B 1 HETATM 39 O O10 G3G . . . E 3 -2.995 66.125 187.466 1 40.67 ? O10 G3G 201 B 1 HETATM 40 N N42 G3G . . . E 3 -3.953 60.53 184.69 1 40.98 ? N42 G3G 201 B 1 HETATM 41 N N43 G3G . . . E 3 4.369 73.029 185.453 1 46.06 ? N43 G3G 201 B 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 260 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 41 #