data_2RIO # _model_server_result.job_id mUrgwAeGnXiPYj_8WvAB4Q _model_server_result.datetime_utc '2024-10-13 14:20:36' _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":"H","auth_seq_id":2101}' # _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 . . . H 4 47.579 67.587 117.331 1 20.67 ? PB ADP 2101 B 1 HETATM 2 O O1B ADP . . . H 4 46.691 68.763 117.658 1 25.69 ? O1B ADP 2101 B 1 HETATM 3 O O2B ADP . . . H 4 49.006 67.732 117.802 1 22.37 ? O2B ADP 2101 B 1 HETATM 4 O O3B ADP . . . H 4 46.961 66.24 117.62 1 21.69 ? O3B ADP 2101 B 1 HETATM 5 P PA ADP . . . H 4 48.278 66.358 114.919 1 18.62 ? PA ADP 2101 B 1 HETATM 6 O O1A ADP . . . H 4 48.185 65.144 115.813 1 18.57 ? O1A ADP 2101 B 1 HETATM 7 O O2A ADP . . . H 4 49.606 66.751 114.319 1 18.44 ? O2A ADP 2101 B 1 HETATM 8 O O3A ADP . . . H 4 47.695 67.623 115.725 1 19.34 ? O3A ADP 2101 B 1 HETATM 9 O O5' ADP . . . H 4 47.216 66.184 113.721 1 18.66 ? O5' ADP 2101 B 1 HETATM 10 C C5' ADP . . . H 4 45.952 66.842 113.774 1 19.55 ? C5' ADP 2101 B 1 HETATM 11 C C4' ADP . . . H 4 44.992 66.176 112.795 1 22.7 ? C4' ADP 2101 B 1 HETATM 12 O O4' ADP . . . H 4 45.291 66.61 111.465 1 26.55 ? O4' ADP 2101 B 1 HETATM 13 C C3' ADP . . . H 4 45.137 64.661 112.834 1 21.31 ? C3' ADP 2101 B 1 HETATM 14 O O3' ADP . . . H 4 43.876 64.069 113.167 1 23.72 ? O3' ADP 2101 B 1 HETATM 15 C C2' ADP . . . H 4 45.54 64.236 111.433 1 24.05 ? C2' ADP 2101 B 1 HETATM 16 O O2' ADP . . . H 4 44.535 63.376 110.886 1 24.45 ? O2' ADP 2101 B 1 HETATM 17 C C1' ADP . . . H 4 45.619 65.513 110.607 1 23.91 ? C1' ADP 2101 B 1 HETATM 18 N N9 ADP . . . H 4 47.001 65.685 110.091 1 25.11 ? N9 ADP 2101 B 1 HETATM 19 C C8 ADP . . . H 4 48.082 66.006 110.827 1 20.56 ? C8 ADP 2101 B 1 HETATM 20 N N7 ADP . . . H 4 49.195 66.085 110.054 1 19.58 ? N7 ADP 2101 B 1 HETATM 21 C C5 ADP . . . H 4 48.829 65.809 108.789 1 20.97 ? C5 ADP 2101 B 1 HETATM 22 C C6 ADP . . . H 4 49.51 65.72 107.476 1 21.5 ? C6 ADP 2101 B 1 HETATM 23 N N6 ADP . . . H 4 50.84 65.947 107.359 1 20.12 ? N6 ADP 2101 B 1 HETATM 24 N N1 ADP . . . H 4 48.758 65.403 106.398 1 18.97 ? N1 ADP 2101 B 1 HETATM 25 C C2 ADP . . . H 4 47.435 65.175 106.501 1 20.07 ? C2 ADP 2101 B 1 HETATM 26 N N3 ADP . . . H 4 46.754 65.239 107.659 1 25.78 ? N3 ADP 2101 B 1 HETATM 27 C C4 ADP . . . H 4 47.382 65.546 108.819 1 23.21 ? C4 ADP 2101 B 1 # _model_server_stats.io_time_ms 71 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 276 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 27 #