data_4YDF # _model_server_result.job_id wONdy5yn2lQmCnIGjLueBw _model_server_result.datetime_utc '2024-11-17 07:26:32' _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 4ydf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":201}' # _entry.id 4YDF # _exptl.entry_id 4YDF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 651.71 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N-benzyl-N-[(3S,4S)-4-{benzyl[(4-nitrophenyl)sulfonyl]amino}pyrrolidin-3-yl]-3-nitrobenzenesulfonamide _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 4YDF _cell.length_a 77.35 _cell.length_b 77.35 _cell.length_c 160.05 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YDF _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,F _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 2 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C30 H29 N5 O8 S2' _chem_comp.formula_weight 651.71 _chem_comp.id 4B1 _chem_comp.mon_nstd_flag . _chem_comp.name N-benzyl-N-[(3S,4S)-4-{benzyl[(4-nitrophenyl)sulfonyl]amino}pyrrolidin-3-yl]-3-nitrobenzenesulfonamide _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 C1 C3 4B1 sing 1 n n C1 N3 4B1 sing 2 n n C2 C4 4B1 sing 3 n n C2 C5 4B1 sing 4 n n C2 N2 4B1 sing 5 n n C3 C7 4B1 doub 6 n y C3 C8 4B1 sing 7 n y C4 C6 4B1 sing 8 n n C4 N3 4B1 sing 9 n n N1 C5 4B1 sing 10 n n N1 C6 4B1 sing 11 n n N2 C18 4B1 sing 12 n n N2 S2 4B1 sing 13 n n N3 S1 4B1 sing 14 n n S1 C13 4B1 sing 15 n n S1 O5 4B1 doub 16 n n S1 O6 4B1 doub 17 n n C7 C9 4B1 sing 18 n y C8 C10 4B1 doub 19 n y C9 C11 4B1 doub 20 n y C10 C11 4B1 sing 21 n y C12 C13 4B1 doub 22 n y C12 C14 4B1 sing 23 n y C13 C15 4B1 sing 24 n y C14 C16 4B1 doub 25 n y C15 C17 4B1 doub 26 n y C16 C17 4B1 sing 27 n y C17 N4 4B1 sing 28 n n N4 O1 4B1 doub 29 n n N4 O2 4B1 sing 30 n n C18 C19 4B1 sing 31 n n S2 C25 4B1 sing 32 n n S2 O3 4B1 doub 33 n n S2 O4 4B1 doub 34 n n C19 C20 4B1 doub 35 n y C19 C21 4B1 sing 36 n y C20 C22 4B1 sing 37 n y C21 C23 4B1 doub 38 n y C22 C24 4B1 doub 39 n y C23 C24 4B1 sing 40 n y C25 C26 4B1 doub 41 n y C25 C27 4B1 sing 42 n y C26 C28 4B1 sing 43 n y C27 C29 4B1 doub 44 n y C28 C30 4B1 doub 45 n y C29 C30 4B1 sing 46 n y C30 N5 4B1 sing 47 n n N5 O7 4B1 sing 48 n n N5 O8 4B1 doub 49 n n C1 H1 4B1 sing 50 n n C1 H2 4B1 sing 51 n n C4 H3 4B1 sing 52 n n N1 H4 4B1 sing 53 n n C5 H6 4B1 sing 54 n n C5 H7 4B1 sing 55 n n C6 H8 4B1 sing 56 n n C6 H9 4B1 sing 57 n n C7 H10 4B1 sing 58 n n C8 H11 4B1 sing 59 n n C9 H12 4B1 sing 60 n n C10 H13 4B1 sing 61 n n C11 H14 4B1 sing 62 n n C14 H15 4B1 sing 63 n n C15 H16 4B1 sing 64 n n C16 H17 4B1 sing 65 n n C18 H18 4B1 sing 66 n n C18 H19 4B1 sing 67 n n C20 H20 4B1 sing 68 n n C21 H21 4B1 sing 69 n n C22 H22 4B1 sing 70 n n C23 H23 4B1 sing 71 n n C24 H24 4B1 sing 72 n n C26 H25 4B1 sing 73 n n C27 H26 4B1 sing 74 n n C28 H27 4B1 sing 75 n n C29 H28 4B1 sing 76 n n C2 H5 4B1 sing 77 n n C12 H33 4B1 sing 78 n n # _atom_sites.entry_id 4YDF _atom_sites.fract_transf_matrix[1][1] 0.012928 _atom_sites.fract_transf_matrix[1][2] 0.007464 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014928 _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] 0.006248 _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 4B1 A 1 201 1 4B1 ZZZ . D 3 SO4 A 1 202 1 SO4 SO4 . E 4 HOH A 1 301 1 HOH HOH . F 4 HOH B 1 201 2 HOH HOH . F 4 HOH B 2 202 3 HOH HOH . F 4 HOH B 3 203 4 HOH HOH . # 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 C1 4B1 . . . C 2 59.359 31.339 25.226 1 39.83 ? C1 4B1 201 A 1 HETATM 2 C C2 4B1 . . . C 2 57.802 34.183 25.18 1 49.11 ? C2 4B1 201 A 1 HETATM 3 C C3 4B1 . . . C 2 58.053 31.017 25.476 1 29.06 ? C3 4B1 201 A 1 HETATM 4 C C4 4B1 . . . C 2 59.254 33.892 24.996 1 42.42 ? C4 4B1 201 A 1 HETATM 5 N N1 4B1 . . . C 2 58.173 33.428 23.013 1 20.75 ? N1 4B1 201 A 1 HETATM 6 C C5 4B1 . . . C 2 57.13 33.686 23.937 1 26.07 ? C5 4B1 201 A 1 HETATM 7 C C6 4B1 . . . C 2 59.373 34.019 23.532 1 23.48 ? C6 4B1 201 A 1 HETATM 8 N N2 4B1 . . . C 2 57.486 35.563 25.626 1 43.49 ? N2 4B1 201 A 1 HETATM 9 N N3 4B1 . . . C 2 59.773 32.664 25.66 1 42.05 ? N3 4B1 201 A 1 HETATM 10 S S1 4B1 . . . C 2 60.773 32.707 26.607 1 49.5 ? S1 4B1 201 A 1 HETATM 11 C C7 4B1 . . . C 2 57.533 31.054 26.721 1 40.63 ? C7 4B1 201 A 1 HETATM 12 C C8 4B1 . . . C 2 57.275 30.625 24.451 1 26.88 ? C8 4B1 201 A 1 HETATM 13 C C9 4B1 . . . C 2 56.238 30.705 26.936 1 34.43 ? C9 4B1 201 A 1 HETATM 14 C C10 4B1 . . . C 2 55.975 30.305 24.696 1 33.34 ? C10 4B1 201 A 1 HETATM 15 C C11 4B1 . . . C 2 55.427 30.332 25.931 1 25.48 ? C11 4B1 201 A 1 HETATM 16 C C12 4B1 . . . C 2 62.037 32.952 25.937 1 45.39 ? C12 4B1 201 A 1 HETATM 17 C C13 4B1 . . . C 2 62.596 31.884 25.304 1 33.45 ? C13 4B1 201 A 1 HETATM 18 C C14 4B1 . . . C 2 62.651 34.174 25.922 1 38.57 ? C14 4B1 201 A 1 HETATM 19 C C15 4B1 . . . C 2 63.784 32.075 24.679 1 23.03 ? C15 4B1 201 A 1 HETATM 20 C C16 4B1 . . . C 2 63.844 34.327 25.284 1 23.41 ? C16 4B1 201 A 1 HETATM 21 C C17 4B1 . . . C 2 64.427 33.276 24.665 1 20.18 ? C17 4B1 201 A 1 HETATM 22 N N4 4B1 . . . C 2 65.551 33.404 24.021 1 24.65 ? N4 4B1 201 A 1 HETATM 23 O O1 4B1 . . . C 2 66.063 32.331 23.272 1 22.76 ? O1 4B1 201 A 1 HETATM 24 O O2 4B1 . . . C 2 66.208 34.622 24.023 1 28.18 ? O2 4B1 201 A 1 HETATM 25 C C18 4B1 . . . C 2 57.918 36.684 24.832 1 34.87 ? C18 4B1 201 A 1 HETATM 26 S S2 4B1 . . . C 2 56.71 35.709 26.668 1 53.39 ? S2 4B1 201 A 1 HETATM 27 C C19 4B1 . . . C 2 59.208 37.047 24.954 1 27.07 ? C19 4B1 201 A 1 HETATM 28 C C20 4B1 . . . C 2 59.83 37.023 26.154 1 34.66 ? C20 4B1 201 A 1 HETATM 29 C C21 4B1 . . . C 2 59.871 37.495 23.857 1 25.62 ? C21 4B1 201 A 1 HETATM 30 C C22 4B1 . . . C 2 61.12 37.434 26.301 1 28.38 ? C22 4B1 201 A 1 HETATM 31 C C23 4B1 . . . C 2 61.163 37.907 23.984 1 36.43 ? C23 4B1 201 A 1 HETATM 32 C C24 4B1 . . . C 2 61.794 37.877 25.207 1 24.71 ? C24 4B1 201 A 1 HETATM 33 C C25 4B1 . . . C 2 55.258 35.229 26.388 1 42.42 ? C25 4B1 201 A 1 HETATM 34 C C26 4B1 . . . C 2 54.892 34 26.839 1 42.97 ? C26 4B1 201 A 1 HETATM 35 C C27 4B1 . . . C 2 54.321 35.988 25.717 1 36 ? C27 4B1 201 A 1 HETATM 36 C C28 4B1 . . . C 2 53.629 33.544 26.635 1 31.35 ? C28 4B1 201 A 1 HETATM 37 C C29 4B1 . . . C 2 53.057 35.513 25.482 1 22.28 ? C29 4B1 201 A 1 HETATM 38 C C30 4B1 . . . C 2 52.712 34.274 25.93 1 30.89 ? C30 4B1 201 A 1 HETATM 39 O O3 4B1 . . . C 2 57.277 34.902 27.731 1 54.67 ? O3 4B1 201 A 1 HETATM 40 O O4 4B1 . . . C 2 56.615 37.09 27.192 1 54.05 ? O4 4B1 201 A 1 HETATM 41 O O5 4B1 . . . C 2 60.566 33.755 27.592 1 67.65 ? O5 4B1 201 A 1 HETATM 42 O O6 4B1 . . . C 2 60.951 31.472 27.408 1 55.37 ? O6 4B1 201 A 1 HETATM 43 N N5 4B1 . . . C 2 51.521 33.772 25.726 1 44.51 ? N5 4B1 201 A 1 HETATM 44 O O7 4B1 . . . C 2 50.627 34.458 24.958 1 25.89 ? O7 4B1 201 A 1 HETATM 45 O O8 4B1 . . . C 2 51.113 32.597 26.384 1 35.07 ? O8 4B1 201 A 1 # _model_server_stats.io_time_ms 30 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 831 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 45 #