data_2RIO # _model_server_result.job_id NwMM9aMUAF1T5zik63x7KQ _model_server_result.datetime_utc '2024-10-13 14:27:26' _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 2rio # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1101}' # _entry.id 2RIO # _exptl.entry_id 2RIO _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 4 _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 120 _cell.entry_id 2RIO _cell.length_a 130.307 _cell.length_b 130.307 _cell.length_c 175.011 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2RIO _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 E N N ? 4 H 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 OD1 ASN 145 A ASN 145 1_555 C MG MG . A MG 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.192 ? metalc ? metalc2 A OD2 ASP 171 A ASP 171 1_555 C MG MG . A MG 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? metalc ? metalc3 A OD1 ASP 171 A ASP 171 1_555 D SR SR . A SR 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.652 ? metalc ? metalc4 E O1A ADP . A ADP 1101 1_555 C MG MG . A MG 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.995 ? metalc ? metalc5 E O3B ADP . A ADP 1101 1_555 C MG MG . A MG 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? metalc ? metalc6 E O2B ADP . A ADP 1101 1_555 D SR SR . A SR 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.614 ? metalc ? metalc7 B OD1 ASN 145 B ASN 145 1_555 F MG MG . B MG 2102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.228 ? metalc ? metalc8 B OD2 ASP 171 B ASP 171 1_555 F MG MG . B MG 2102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.227 ? metalc ? metalc9 B OD1 ASP 171 B ASP 171 1_555 G SR SR . B SR 2103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.634 ? metalc ? metalc10 H O3B ADP . B ADP 2101 1_555 F MG MG . B MG 2102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? metalc ? metalc11 H O1A ADP . B ADP 2101 1_555 F MG MG . B MG 2102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? metalc ? metalc12 H O2B ADP . B ADP 2101 1_555 G SR SR . B SR 2103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.683 ? # _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 2RIO _atom_sites.fract_transf_matrix[1][1] 0.007674 _atom_sites.fract_transf_matrix[1][2] 0.004431 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008861 _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] 0.005714 _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 1102 1102 MG MG . D 3 SR A 1 1103 1103 SR SR . E 4 ADP A 1 1101 1101 ADP ADP . F 2 MG B 1 2102 2102 MG MG . G 3 SR B 1 2103 2103 SR SR . H 4 ADP B 1 2101 2101 ADP ADP . # 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 . . . E 4 78.416 69.981 90.283 1 25.04 ? PB ADP 1101 A 1 HETATM 2 O O1B ADP . . . E 4 79.075 71.288 89.91 1 27.35 ? O1B ADP 1101 A 1 HETATM 3 O O2B ADP . . . E 4 76.958 69.887 89.902 1 24.55 ? O2B ADP 1101 A 1 HETATM 4 O O3B ADP . . . E 4 79.229 68.754 89.945 1 25.67 ? O3B ADP 1101 A 1 HETATM 5 P PA ADP . . . E 4 77.951 68.695 92.721 1 19.89 ? PA ADP 1101 A 1 HETATM 6 O O1A ADP . . . E 4 78.165 67.484 91.844 1 18.45 ? O1A ADP 1101 A 1 HETATM 7 O O2A ADP . . . E 4 76.592 68.958 93.325 1 20.88 ? O2A ADP 1101 A 1 HETATM 8 O O3A ADP . . . E 4 78.396 70.002 91.893 1 20.54 ? O3A ADP 1101 A 1 HETATM 9 O O5' ADP . . . E 4 79.032 68.65 93.914 1 23.63 ? O5' ADP 1101 A 1 HETATM 10 C C5' ADP . . . E 4 80.197 69.471 93.867 1 22.09 ? C5' ADP 1101 A 1 HETATM 11 C C4' ADP . . . E 4 81.23 68.945 94.856 1 22.95 ? C4' ADP 1101 A 1 HETATM 12 O O4' ADP . . . E 4 80.874 69.354 96.18 1 26.01 ? O4' ADP 1101 A 1 HETATM 13 C C3' ADP . . . E 4 81.278 67.423 94.836 1 23.72 ? C3' ADP 1101 A 1 HETATM 14 O O3' ADP . . . E 4 82.605 66.992 94.513 1 26.46 ? O3' ADP 1101 A 1 HETATM 15 C C2' ADP . . . E 4 80.927 66.969 96.242 1 21.54 ? C2' ADP 1101 A 1 HETATM 16 O O2' ADP . . . E 4 82.031 66.25 96.801 1 26.92 ? O2' ADP 1101 A 1 HETATM 17 C C1' ADP . . . E 4 80.683 68.235 97.05 1 25.1 ? C1' ADP 1101 A 1 HETATM 18 N N9 ADP . . . E 4 79.289 68.237 97.56 1 27.39 ? N9 ADP 1101 A 1 HETATM 19 C C8 ADP . . . E 4 78.182 68.456 96.825 1 20.95 ? C8 ADP 1101 A 1 HETATM 20 N N7 ADP . . . E 4 77.064 68.389 97.591 1 19.7 ? N7 ADP 1101 A 1 HETATM 21 C C5 ADP . . . E 4 77.453 68.121 98.851 1 23.42 ? C5 ADP 1101 A 1 HETATM 22 C C6 ADP . . . E 4 76.78 67.919 100.157 1 22.45 ? C6 ADP 1101 A 1 HETATM 23 N N6 ADP . . . E 4 75.432 67.993 100.27 1 23.01 ? N6 ADP 1101 A 1 HETATM 24 N N1 ADP . . . E 4 77.558 67.659 101.231 1 22.52 ? N1 ADP 1101 A 1 HETATM 25 C C2 ADP . . . E 4 78.898 67.582 101.132 1 22.12 ? C2 ADP 1101 A 1 HETATM 26 N N3 ADP . . . E 4 79.574 67.754 99.982 1 29.03 ? N3 ADP 1101 A 1 HETATM 27 C C4 ADP . . . E 4 78.92 68.022 98.826 1 25.5 ? C4 ADP 1101 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 278 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 27 #