data_6RAD # _model_server_result.job_id D1vNXwRM0mTP00ILSNPHeA _model_server_result.datetime_utc '2025-03-06 09:24:18' _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 6rad # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 6RAD # _exptl.entry_id 6RAD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _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 6RAD _cell.length_a 107.449 _cell.length_b 107.449 _cell.length_c 73.511 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6RAD _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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,F,G,H,I,J,K,L _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 B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id ADP _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-5'-DIPHOSPHATE" _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 PB O1B ADP doub 1 n n PB O2B ADP sing 2 n n PB O3B ADP sing 3 n n PB O3A ADP sing 4 n n O2B HOB2 ADP sing 5 n n O3B HOB3 ADP sing 6 n n PA O1A ADP doub 7 n n PA O2A ADP sing 8 n n PA O3A ADP sing 9 n n PA O5' ADP sing 10 n n O2A HOA2 ADP sing 11 n n O5' C5' ADP sing 12 n n C5' C4' ADP sing 13 n n C5' "H5'1" ADP sing 14 n n C5' "H5'2" ADP sing 15 n n C4' O4' ADP sing 16 n n C4' C3' ADP sing 17 n n C4' H4' ADP sing 18 n n O4' C1' ADP sing 19 n n C3' O3' ADP sing 20 n n C3' C2' ADP sing 21 n n C3' H3' ADP sing 22 n n O3' HO3' ADP sing 23 n n C2' O2' ADP sing 24 n n C2' C1' ADP sing 25 n n C2' H2' ADP sing 26 n n O2' HO2' ADP sing 27 n n C1' N9 ADP sing 28 n n C1' H1' ADP sing 29 n n N9 C8 ADP sing 30 n y N9 C4 ADP sing 31 n y C8 N7 ADP doub 32 n y C8 H8 ADP sing 33 n n N7 C5 ADP sing 34 n y C5 C6 ADP sing 35 n y C5 C4 ADP doub 36 n y C6 N6 ADP sing 37 n n C6 N1 ADP doub 38 n y N6 HN61 ADP sing 39 n n N6 HN62 ADP sing 40 n n N1 C2 ADP sing 41 n y C2 N3 ADP doub 42 n y C2 H2 ADP sing 43 n n N3 C4 ADP sing 44 n y # _atom_sites.entry_id 6RAD _atom_sites.fract_transf_matrix[1][1] 0.009307 _atom_sites.fract_transf_matrix[1][2] 0.005373 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010746 _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] 0.013603 _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 ADP A 1 501 1 ADP ADP . C 3 MES A 1 502 2 MES MES . D 4 GOL A 1 503 3 GOL GOL . E 4 GOL A 1 504 4 GOL GOL . F 4 GOL A 1 505 5 GOL GOL . G 4 GOL A 1 506 6 GOL GOL . H 4 GOL A 1 507 7 GOL GOL . I 4 GOL A 1 508 8 GOL GOL . J 4 GOL A 1 509 9 GOL GOL . K 5 SO4 A 1 510 10 SO4 SO4 . L 6 HOH A 1 601 2 HOH HOH . L 6 HOH A 2 602 12 HOH HOH . L 6 HOH A 3 603 1 HOH HOH . L 6 HOH A 4 604 10 HOH HOH . L 6 HOH A 5 605 6 HOH HOH . L 6 HOH A 6 606 11 HOH HOH . L 6 HOH A 7 607 9 HOH HOH . L 6 HOH A 8 608 8 HOH HOH . L 6 HOH A 9 609 7 HOH HOH . L 6 HOH A 10 610 5 HOH HOH . L 6 HOH A 11 611 4 HOH HOH . L 6 HOH A 12 612 13 HOH HOH . L 6 HOH A 13 613 3 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 P PB ADP . . . B 2 33.605 -7.042 14.226 1 166.78 ? PB ADP 501 A 1 HETATM 2 O O1B ADP . . . B 2 33.193 -6.176 13.06 1 166.13 ? O1B ADP 501 A 1 HETATM 3 O O2B ADP . . . B 2 33.151 -6.54 15.576 1 165.22 ? O2B ADP 501 A 1 HETATM 4 O O3B ADP . . . B 2 35.049 -7.483 14.197 1 160.23 ? O3B ADP 501 A 1 HETATM 5 P PA ADP . . . B 2 33.087 -9.685 14.952 1 197.15 ? PA ADP 501 A 1 HETATM 6 O O1A ADP . . . B 2 34.323 -10.366 14.415 1 193.85 ? O1A ADP 501 A 1 HETATM 7 O O2A ADP . . . B 2 33.038 -9.24 16.394 1 211.11 ? O2A ADP 501 A 1 HETATM 8 O O3A ADP . . . B 2 32.785 -8.412 14.014 1 180.85 ? O3A ADP 501 A 1 HETATM 9 O O5' ADP . . . B 2 31.831 -10.66 14.691 1 204.9 ? O5' ADP 501 A 1 HETATM 10 C C5' ADP . . . B 2 31.628 -11.787 15.542 1 207.03 ? C5' ADP 501 A 1 HETATM 11 C C4' ADP . . . B 2 30.497 -12.661 15.012 1 204.22 ? C4' ADP 501 A 1 HETATM 12 O O4' ADP . . . B 2 31.001 -13.688 14.151 1 199.61 ? O4' ADP 501 A 1 HETATM 13 C C3' ADP . . . B 2 29.763 -13.365 16.142 1 204.03 ? C3' ADP 501 A 1 HETATM 14 O O3' ADP . . . B 2 28.469 -12.786 16.325 1 208.28 ? O3' ADP 501 A 1 HETATM 15 C C2' ADP . . . B 2 29.623 -14.81 15.708 1 199.44 ? C2' ADP 501 A 1 HETATM 16 O O2' ADP . . . B 2 28.241 -15.175 15.667 1 202.91 ? O2' ADP 501 A 1 HETATM 17 C C1' ADP . . . B 2 30.222 -14.878 14.312 1 191.43 ? C1' ADP 501 A 1 HETATM 18 N N9 ADP . . . B 2 31.053 -16.102 14.16 1 175.12 ? N9 ADP 501 A 1 HETATM 19 C C8 ADP . . . B 2 32.372 -16.139 13.89 1 167.49 ? C8 ADP 501 A 1 HETATM 20 N N7 ADP . . . B 2 32.82 -17.419 13.807 1 165.55 ? N7 ADP 501 A 1 HETATM 21 C C5 ADP . . . B 2 31.767 -18.231 14.023 1 164.76 ? C5 ADP 501 A 1 HETATM 22 C C6 ADP . . . B 2 31.536 -19.694 14.077 1 159.04 ? C6 ADP 501 A 1 HETATM 23 N N6 ADP . . . B 2 32.548 -20.574 13.879 1 155.9 ? N6 ADP 501 A 1 HETATM 24 N N1 ADP . . . B 2 30.28 -20.124 14.331 1 159.14 ? N1 ADP 501 A 1 HETATM 25 C C2 ADP . . . B 2 29.261 -19.266 14.53 1 161.99 ? C2 ADP 501 A 1 HETATM 26 N N3 ADP . . . B 2 29.4 -17.929 14.495 1 165.23 ? N3 ADP 501 A 1 HETATM 27 C C4 ADP . . . B 2 30.604 -17.358 14.249 1 168.34 ? C4 ADP 501 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 251 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 27 #