data_5XJA # _model_server_result.job_id CpJ95l317Ce0cWNuDoi_9Q _model_server_result.datetime_utc '2024-10-18 15:29:19' _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 5xja # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":602}' # _entry.id 5XJA # _exptl.entry_id 5XJA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 2 _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 90 _cell.entry_id 5XJA _cell.length_a 91.098 _cell.length_b 166.989 _cell.length_c 74.991 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5XJA _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,I 1 1 B,F,G,H,J 2 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 G N 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 OG1 THR 185 A THR 351 1_555 C MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.567 ? metalc ? metalc2 C MG MG . A MG 601 1_555 D O1B ADP . A ADP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.86 ? metalc ? metalc3 C MG MG . A MG 601 1_555 D O1A ADP . A ADP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.701 ? metalc ? metalc4 C MG MG . A MG 601 1_555 D O2A ADP . A ADP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.9 ? metalc ? metalc5 C MG MG . A MG 601 1_555 D O3A ADP . A ADP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.754 ? metalc ? metalc6 B OG1 THR 185 B THR 351 1_555 F MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.259 ? metalc ? metalc7 F MG MG . B MG 601 1_555 G O3B ADP . B ADP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? metalc ? metalc8 F MG MG . B MG 601 1_555 G O2A ADP . B ADP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.697 ? # _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 5XJA _atom_sites.fract_transf_matrix[1][1] 0.010977 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.005988 _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] 0.013335 _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 MG A 1 601 601 MG MG . D 3 ADP A 1 602 1 ADP ADP . E 4 AF3 A 1 603 1 AF3 AF3 . F 2 MG B 1 601 601 MG MG . G 3 ADP B 1 602 2 ADP ADP . H 4 AF3 B 1 603 2 AF3 AF3 . I 5 HOH A 1 701 8 HOH HOH . I 5 HOH A 2 702 3 HOH HOH . I 5 HOH A 3 703 6 HOH HOH . I 5 HOH A 4 704 9 HOH HOH . J 5 HOH B 1 701 5 HOH HOH . J 5 HOH B 2 702 7 HOH HOH . J 5 HOH B 3 703 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 P PB ADP . . . D 3 21.477 -10.531 -24.686 1 46.99 ? PB ADP 602 A 1 HETATM 2 O O1B ADP . . . D 3 20.316 -11.432 -24.644 1 54.2 ? O1B ADP 602 A 1 HETATM 3 O O2B ADP . . . D 3 22.556 -10.95 -25.615 1 46.45 ? O2B ADP 602 A 1 HETATM 4 O O3B ADP . . . D 3 22.006 -10.151 -23.338 1 49.81 ? O3B ADP 602 A 1 HETATM 5 P PA ADP . . . D 3 19.998 -9.158 -26.757 1 50.68 ? PA ADP 602 A 1 HETATM 6 O O1A ADP . . . D 3 20.764 -9.875 -27.838 1 49.5 ? O1A ADP 602 A 1 HETATM 7 O O2A ADP . . . D 3 18.574 -9.529 -26.43 1 51.38 ? O2A ADP 602 A 1 HETATM 8 O O3A ADP . . . D 3 20.853 -9.214 -25.374 1 50.59 ? O3A ADP 602 A 1 HETATM 9 O O5' ADP . . . D 3 20.016 -7.637 -27.242 1 46.82 ? O5' ADP 602 A 1 HETATM 10 C C5' ADP . . . D 3 19.475 -6.626 -26.429 1 50.39 ? C5' ADP 602 A 1 HETATM 11 C C4' ADP . . . D 3 18.815 -5.64 -27.358 1 53.04 ? C4' ADP 602 A 1 HETATM 12 O O4' ADP . . . D 3 19.857 -4.979 -28.046 1 54.83 ? O4' ADP 602 A 1 HETATM 13 C C3' ADP . . . D 3 17.933 -6.272 -28.419 1 56.61 ? C3' ADP 602 A 1 HETATM 14 O O3' ADP . . . D 3 16.757 -5.495 -28.686 1 57.92 ? O3' ADP 602 A 1 HETATM 15 C C2' ADP . . . D 3 18.75 -6.231 -29.668 1 57.34 ? C2' ADP 602 A 1 HETATM 16 O O2' ADP . . . D 3 17.868 -6.124 -30.787 1 66.01 ? O2' ADP 602 A 1 HETATM 17 C C1' ADP . . . D 3 19.651 -5.021 -29.446 1 55.29 ? C1' ADP 602 A 1 HETATM 18 N N9 ADP . . . D 3 20.95 -5.189 -30.138 1 53.69 ? N9 ADP 602 A 1 HETATM 19 C C8 ADP . . . D 3 21.948 -6.016 -29.764 1 55.64 ? C8 ADP 602 A 1 HETATM 20 N N7 ADP . . . D 3 23.013 -5.982 -30.616 1 55.9 ? N7 ADP 602 A 1 HETATM 21 C C5 ADP . . . D 3 22.667 -5.091 -31.548 1 56.09 ? C5 ADP 602 A 1 HETATM 22 C C6 ADP . . . D 3 23.325 -4.575 -32.744 1 58.29 ? C6 ADP 602 A 1 HETATM 23 N N6 ADP . . . D 3 24.558 -5.043 -33.044 1 61.94 ? N6 ADP 602 A 1 HETATM 24 N N1 ADP . . . D 3 22.662 -3.653 -33.474 1 54.72 ? N1 ADP 602 A 1 HETATM 25 C C2 ADP . . . D 3 21.434 -3.23 -33.116 1 52.2 ? C2 ADP 602 A 1 HETATM 26 N N3 ADP . . . D 3 20.775 -3.661 -32.03 1 48.27 ? N3 ADP 602 A 1 HETATM 27 C C4 ADP . . . D 3 21.33 -4.572 -31.234 1 51.56 ? C4 ADP 602 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 311 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #