data_4R8Q # _model_server_result.job_id Zab-xAotTp84HqnvDcB-Qg _model_server_result.datetime_utc '2025-07-08 00:24:18' _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 4r8q # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1501}' # _entry.id 4R8Q # _exptl.entry_id 4R8Q _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 90 _cell.entry_id 4R8Q _cell.length_a 108.768 _cell.length_b 147.632 _cell.length_c 47.196 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4R8Q _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _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 _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 # 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 202 A ASN 922 1_555 C MG MG . A MG 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? metalc ? metalc2 A OD2 ASP 226 A ASP 946 1_555 C MG MG . A MG 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.121 ? metalc ? metalc3 A OD1 ASP 226 A ASP 946 1_555 D MG MG . A MG 1503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? metalc ? metalc4 A OD2 ASP 226 A ASP 946 1_555 D MG MG . A MG 1503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? metalc ? metalc5 B O1B ADP . A ADP 1501 1_555 C MG MG . A MG 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.943 ? metalc ? metalc6 B O2A ADP . A ADP 1501 1_555 C MG MG . A MG 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? metalc ? metalc7 B O3B ADP . A ADP 1501 1_555 D MG MG . A MG 1503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? metalc ? metalc8 C MG MG . A MG 1502 1_555 E O HOH . A HOH 1601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? metalc ? metalc9 C MG MG . A MG 1502 1_555 E O HOH . A HOH 1602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc10 D MG MG . A MG 1503 1_555 E O HOH . A HOH 1603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? metalc ? metalc11 D MG MG . A MG 1503 1_555 E O HOH . A HOH 1604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? metalc ? metalc12 D MG MG . A MG 1503 1_555 E O HOH . A HOH 1605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? # _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 4R8Q _atom_sites.fract_transf_matrix[1][1] 0.009194 _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] 0.006774 _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] 0.021188 _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 1501 1501 ADP ADP . C 3 MG A 1 1502 1502 MG MG . D 3 MG A 1 1503 1503 MG MG . E 4 HOH A 1 1601 1601 HOH HOH . E 4 HOH A 2 1602 1602 HOH HOH . E 4 HOH A 3 1603 1603 HOH HOH . E 4 HOH A 4 1604 1604 HOH HOH . E 4 HOH A 5 1605 1605 HOH HOH . E 4 HOH A 6 1606 1 HOH HOH . E 4 HOH A 7 1607 2 HOH HOH . E 4 HOH A 8 1608 3 HOH HOH . E 4 HOH A 9 1609 4 HOH HOH . E 4 HOH A 10 1610 5 HOH HOH . E 4 HOH A 11 1611 6 HOH HOH . E 4 HOH A 12 1612 7 HOH HOH . E 4 HOH A 13 1613 8 HOH HOH . E 4 HOH A 14 1614 9 HOH HOH . E 4 HOH A 15 1615 10 HOH HOH . E 4 HOH A 16 1616 11 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 -24.793 23.88 -20.818 1 27.71 ? PB ADP 1501 A 1 HETATM 2 O O1B ADP . . . B 2 -26.227 23.705 -20.383 1 28.81 ? O1B ADP 1501 A 1 HETATM 3 O O2B ADP . . . B 2 -24.616 24.643 -22.106 1 27.7 ? O2B ADP 1501 A 1 HETATM 4 O O3B ADP . . . B 2 -23.871 24.327 -19.708 1 31.11 ? O3B ADP 1501 A 1 HETATM 5 P PA ADP . . . B 2 -25.027 21.052 -20.668 1 18.82 ? PA ADP 1501 A 1 HETATM 6 O O1A ADP . . . B 2 -24.035 20.2 -19.914 1 22.88 ? O1A ADP 1501 A 1 HETATM 7 O O2A ADP . . . B 2 -26.341 21.449 -20.033 1 19.09 ? O2A ADP 1501 A 1 HETATM 8 O O3A ADP . . . B 2 -24.274 22.391 -21.166 1 24.57 ? O3A ADP 1501 A 1 HETATM 9 O O5' ADP . . . B 2 -25.344 20.321 -22.064 1 25.69 ? O5' ADP 1501 A 1 HETATM 10 C C5' ADP . . . B 2 -26.319 20.868 -22.947 1 25.44 ? C5' ADP 1501 A 1 HETATM 11 C C4' ADP . . . B 2 -27.297 19.791 -23.391 1 24.44 ? C4' ADP 1501 A 1 HETATM 12 O O4' ADP . . . B 2 -26.616 18.605 -23.812 1 28.27 ? O4' ADP 1501 A 1 HETATM 13 C C3' ADP . . . B 2 -28.224 19.36 -22.265 1 25.77 ? C3' ADP 1501 A 1 HETATM 14 O O3' ADP . . . B 2 -29.374 20.206 -22.165 1 30.31 ? O3' ADP 1501 A 1 HETATM 15 C C2' ADP . . . B 2 -28.563 17.927 -22.621 1 25.84 ? C2' ADP 1501 A 1 HETATM 16 O O2' ADP . . . B 2 -29.731 17.849 -23.446 1 26.8 ? O2' ADP 1501 A 1 HETATM 17 C C1' ADP . . . B 2 -27.359 17.447 -23.41 1 27.69 ? C1' ADP 1501 A 1 HETATM 18 N N9 ADP . . . B 2 -26.513 16.592 -22.544 1 30.25 ? N9 ADP 1501 A 1 HETATM 19 C C8 ADP . . . B 2 -25.713 17.037 -21.553 1 26.94 ? C8 ADP 1501 A 1 HETATM 20 N N7 ADP . . . B 2 -25.075 16.004 -20.952 1 25.49 ? N7 ADP 1501 A 1 HETATM 21 C C5 ADP . . . B 2 -25.468 14.874 -21.56 1 27.76 ? C5 ADP 1501 A 1 HETATM 22 C C6 ADP . . . B 2 -25.179 13.432 -21.415 1 30.35 ? C6 ADP 1501 A 1 HETATM 23 N N6 ADP . . . B 2 -24.317 12.99 -20.473 1 29.31 ? N6 ADP 1501 A 1 HETATM 24 N N1 ADP . . . B 2 -25.805 12.577 -22.252 1 33.46 ? N1 ADP 1501 A 1 HETATM 25 C C2 ADP . . . B 2 -26.665 13.002 -23.194 1 30.66 ? C2 ADP 1501 A 1 HETATM 26 N N3 ADP . . . B 2 -26.969 14.297 -23.375 1 29.81 ? N3 ADP 1501 A 1 HETATM 27 C C4 ADP . . . B 2 -26.419 15.264 -22.607 1 30.11 ? C4 ADP 1501 A 1 HETATM 28 H "H5'1" ADP . . . B 2 -25.824 21.295 -23.821 1 30.53 ? "H5'1" ADP 1501 A 1 HETATM 29 H "H5'2" ADP . . . B 2 -26.862 21.67 -22.442 1 30.53 ? "H5'2" ADP 1501 A 1 HETATM 30 H H4' ADP . . . B 2 -27.905 20.185 -24.217 1 29.33 ? H4' ADP 1501 A 1 HETATM 31 H H3' ADP . . . B 2 -27.664 19.37 -21.319 1 30.93 ? H3' ADP 1501 A 1 HETATM 32 H HO3' ADP . . . B 2 -29.937 19.901 -21.44 1 36.37 ? HO3' ADP 1501 A 1 HETATM 33 H H2' ADP . . . B 2 -28.678 17.328 -21.707 1 31.01 ? H2' ADP 1501 A 1 HETATM 34 H HO2' ADP . . . B 2 -30.489 18.211 -22.967 1 32.16 ? HO2' ADP 1501 A 1 HETATM 35 H H1' ADP . . . B 2 -27.7 16.885 -24.29 1 33.22 ? H1' ADP 1501 A 1 HETATM 36 H H8 ADP . . . B 2 -25.594 18.077 -21.279 1 32.33 ? H8 ADP 1501 A 1 HETATM 37 H HN61 ADP . . . B 2 -23.861 13.648 -19.857 1 35.17 ? HN61 ADP 1501 A 1 HETATM 38 H HN62 ADP . . . B 2 -24.128 12.001 -20.386 1 35.17 ? HN62 ADP 1501 A 1 HETATM 39 H H2 ADP . . . B 2 -27.134 12.266 -23.836 1 36.79 ? H2 ADP 1501 A 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 310 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 39 #