data_4PD5 # _model_server_result.job_id 1FxLRJEjen3bmWbMQfAx1w _model_server_result.datetime_utc '2024-11-01 19:44:05' _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 4pd5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 4PD5 # _exptl.entry_id 4PD5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 263.198 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GEMCITABINE _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 4PD5 _cell.length_a 119.046 _cell.length_b 119.046 _cell.length_c 82.285 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4PD5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 63' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_and_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 1,2,3 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_665 -y+1,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 59.523 103.09686 0 3 'crystal symmetry operation' 3_565 -x+y,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -59.523 103.09686 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_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_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 A O ASN 155 A ASN 149 1_555 C NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.462 ? metalc ? metalc2 A OD1 ASN 155 A ASN 149 1_555 C NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.458 ? metalc ? metalc3 A O VAL 158 A VAL 152 1_555 C NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.448 ? metalc ? metalc4 A OG SER 189 A SER 183 1_555 C NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.407 ? metalc ? metalc5 A O ILE 190 A ILE 184 1_555 C NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.485 ? metalc ? metalc6 C NA NA . A NA 502 1_555 E O HOH . A HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.367 ? # _chem_comp.formula 'C9 H11 F2 N3 O4' _chem_comp.formula_weight 263.198 _chem_comp.id GEO _chem_comp.mon_nstd_flag . _chem_comp.name GEMCITABINE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "2',2'-DIFLUORODEOXYCYTIDINE" # 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 O5' C5' GEO sing 159 n n O5' H5' GEO sing 160 n n C5' C4' GEO sing 161 n n C5' "H5'1" GEO sing 162 n n C5' "H5'2" GEO sing 163 n n C4' O4' GEO sing 164 n n C4' C3' GEO sing 165 n n C4' H4' GEO sing 166 n n O4' C1' GEO sing 167 n n C1' N1 GEO sing 168 n n C1' C2' GEO sing 169 n n C1' H1' GEO sing 170 n n N1 C6 GEO sing 171 n y N1 C2 GEO sing 172 n y C6 C5 GEO doub 173 n y C6 H6 GEO sing 174 n n C5 C4 GEO sing 175 n y C5 H5 GEO sing 176 n n C4 N3 GEO doub 177 n y C4 N4 GEO sing 178 n n N3 C2 GEO sing 179 n y C2 O2 GEO doub 180 n n N4 HN41 GEO sing 181 n n N4 HN42 GEO sing 182 n n C2' F1 GEO sing 183 n n C2' F2 GEO sing 184 n n C2' C3' GEO sing 185 n n C3' O3' GEO sing 186 n n C3' H3' GEO sing 187 n n O3' H1 GEO sing 188 n n # _atom_sites.entry_id 4PD5 _atom_sites.fract_transf_matrix[1][1] 0.0084 _atom_sites.fract_transf_matrix[1][2] 0.00485 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.0097 _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] 0.012153 _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 B 2 GEO A 1 501 2 GEO GCE . C 3 NA A 1 502 1 NA NA . D 4 DMU A 1 503 503 DMU DMU . E 5 HOH A 1 601 5 HOH HOH . E 5 HOH A 2 602 3 HOH HOH . E 5 HOH A 3 603 1 HOH HOH . E 5 HOH A 4 604 2 HOH HOH . E 5 HOH A 5 605 4 HOH HOH . E 5 HOH A 6 606 6 HOH HOH . E 5 HOH A 7 607 7 HOH HOH . E 5 HOH A 8 608 8 HOH HOH . E 5 HOH A 9 609 9 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 O O5' GEO . . . B 2 -9.145 53.942 0.291 1 59.57 ? O5' GEO 501 A 1 HETATM 2 C C5' GEO . . . B 2 -10.3 54.789 0.121 1 59.57 ? C5' GEO 501 A 1 HETATM 3 C C4' GEO . . . B 2 -10.597 54.901 -1.368 1 59.57 ? C4' GEO 501 A 1 HETATM 4 O O4' GEO . . . B 2 -9.456 55.478 -2.07 1 59.57 ? O4' GEO 501 A 1 HETATM 5 C C1' GEO . . . B 2 -9.324 54.849 -3.338 1 59.57 ? C1' GEO 501 A 1 HETATM 6 N N1 GEO . . . B 2 -7.996 54.22 -3.449 1 59.57 ? N1 GEO 501 A 1 HETATM 7 C C6 GEO . . . B 2 -7.251 54.003 -2.322 1 59.57 ? C6 GEO 501 A 1 HETATM 8 C C5 GEO . . . B 2 -6.042 53.436 -2.418 1 59.57 ? C5 GEO 501 A 1 HETATM 9 C C4 GEO . . . B 2 -5.533 53.065 -3.696 1 59.57 ? C4 GEO 501 A 1 HETATM 10 N N3 GEO . . . B 2 -6.263 53.282 -4.794 1 59.57 ? N3 GEO 501 A 1 HETATM 11 C C2 GEO . . . B 2 -7.485 53.857 -4.699 1 59.57 ? C2 GEO 501 A 1 HETATM 12 O O2 GEO . . . B 2 -8.154 54.051 -5.725 1 59.57 ? O2 GEO 501 A 1 HETATM 13 N N4 GEO . . . B 2 -4.328 52.5 -3.796 1 59.57 ? N4 GEO 501 A 1 HETATM 14 C C2' GEO . . . B 2 -10.452 53.815 -3.433 1 59.57 ? C2' GEO 501 A 1 HETATM 15 F F1 GEO . . . B 2 -10.048 52.694 -4.046 1 59.57 ? F1 GEO 501 A 1 HETATM 16 F F2 GEO . . . B 2 -11.509 54.347 -4.073 1 59.57 ? F2 GEO 501 A 1 HETATM 17 C C3' GEO . . . B 2 -10.801 53.541 -1.981 1 59.57 ? C3' GEO 501 A 1 HETATM 18 O O3' GEO . . . B 2 -12.154 53.13 -1.86 1 59.57 ? O3' GEO 501 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 298 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 18 #