data_1V8J # _model_server_result.job_id IVSyZBJQp6wuvf26KfwKQw _model_server_result.datetime_utc '2024-10-25 20:23:20' _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 1v8j # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":500}' # _entry.id 1V8J # _exptl.entry_id 1V8J _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 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 1V8J _cell.length_a 61.209 _cell.length_b 192.453 _cell.length_c 73.554 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1V8J _symmetry.cell_setting ? _symmetry.Int_Tables_number 21 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 2 2 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _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 3 _struct_asym.id C _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 disulf ? disulf1 A SG CYS 59 A CYS 59 1_555 A SG CYS 101 A CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? metalc ? metalc1 A OG1 THR 169 A THR 169 1_555 B MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.514 ? metalc ? metalc2 C O3B ADP . A ADP 500 1_555 B MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? # _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 1V8J _atom_sites.fract_transf_matrix[1][1] 0.016337 _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] 0.005196 _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] 0.013595 _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 MG A 1 501 501 MG MG2 . C 3 ADP A 1 500 500 ADP ADP . D 4 HOH A 1 601 601 HOH HOH . D 4 HOH A 2 602 602 HOH HOH . D 4 HOH A 3 603 603 HOH HOH . D 4 HOH A 4 604 604 HOH HOH . D 4 HOH A 5 605 605 HOH HOH . D 4 HOH A 6 606 606 HOH HOH . D 4 HOH A 7 607 607 HOH HOH . D 4 HOH A 8 608 608 HOH HOH . D 4 HOH A 9 609 609 HOH HOH . D 4 HOH A 10 610 610 HOH HOH . D 4 HOH A 11 611 611 HOH HOH . D 4 HOH A 12 612 612 HOH HOH . D 4 HOH A 13 613 613 HOH HOH . D 4 HOH A 14 614 614 HOH HOH . D 4 HOH A 15 615 615 HOH HOH . D 4 HOH A 16 616 616 HOH HOH . D 4 HOH A 17 617 617 HOH HOH . D 4 HOH A 18 618 618 HOH HOH . D 4 HOH A 19 619 619 HOH HOH . D 4 HOH A 20 620 620 HOH HOH . D 4 HOH A 21 621 621 HOH HOH . D 4 HOH A 22 622 622 HOH HOH . D 4 HOH A 23 623 623 HOH HOH . D 4 HOH A 24 624 624 HOH HOH . D 4 HOH A 25 625 625 HOH HOH . D 4 HOH A 26 626 626 HOH HOH . D 4 HOH A 27 627 627 HOH HOH . D 4 HOH A 28 628 628 HOH HOH . D 4 HOH A 29 629 629 HOH HOH . D 4 HOH A 30 630 630 HOH HOH . D 4 HOH A 31 631 631 HOH HOH . D 4 HOH A 32 632 632 HOH HOH . D 4 HOH A 33 633 633 HOH HOH . D 4 HOH A 34 634 634 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 . . . C 3 -40.915 79.904 -21.355 1 38.87 ? PB ADP 500 A 1 HETATM 2 O O1B ADP . . . C 3 -40.476 79.975 -22.74 1 37.03 ? O1B ADP 500 A 1 HETATM 3 O O2B ADP . . . C 3 -42.225 80.53 -20.975 1 45.85 ? O2B ADP 500 A 1 HETATM 4 O O3B ADP . . . C 3 -40.735 78.421 -20.896 1 43.21 ? O3B ADP 500 A 1 HETATM 5 P PA ADP . . . C 3 -38.851 80.17 -19.403 1 44.31 ? PA ADP 500 A 1 HETATM 6 O O1A ADP . . . C 3 -39.801 80.026 -18.181 1 34.79 ? O1A ADP 500 A 1 HETATM 7 O O2A ADP . . . C 3 -37.636 80.78 -19.593 1 50.36 ? O2A ADP 500 A 1 HETATM 8 O O3A ADP . . . C 3 -39.696 80.495 -20.815 1 37.19 ? O3A ADP 500 A 1 HETATM 9 O O5' ADP . . . C 3 -39.144 81.826 -18.889 1 32.28 ? O5' ADP 500 A 1 HETATM 10 C C5' ADP . . . C 3 -38.54 83.085 -19.528 1 38.22 ? C5' ADP 500 A 1 HETATM 11 C C4' ADP . . . C 3 -37.377 83.711 -18.743 1 36.47 ? C4' ADP 500 A 1 HETATM 12 O O4' ADP . . . C 3 -37.889 84.62 -17.758 1 45.95 ? O4' ADP 500 A 1 HETATM 13 C C3' ADP . . . C 3 -36.395 82.9 -17.846 1 41.89 ? C3' ADP 500 A 1 HETATM 14 O O3' ADP . . . C 3 -35.095 83.526 -17.948 1 52.41 ? O3' ADP 500 A 1 HETATM 15 C C2' ADP . . . C 3 -36.866 83.065 -16.329 1 45.99 ? C2' ADP 500 A 1 HETATM 16 O O2' ADP . . . C 3 -35.779 83.012 -15.369 1 58.38 ? O2' ADP 500 A 1 HETATM 17 C C1' ADP . . . C 3 -37.575 84.453 -16.332 1 46.77 ? C1' ADP 500 A 1 HETATM 18 N N9 ADP . . . C 3 -38.865 84.456 -15.545 1 46.39 ? N9 ADP 500 A 1 HETATM 19 C C8 ADP . . . C 3 -40.073 84.104 -15.979 1 43.99 ? C8 ADP 500 A 1 HETATM 20 N N7 ADP . . . C 3 -40.98 84.232 -15.091 1 40.08 ? N7 ADP 500 A 1 HETATM 21 C C5 ADP . . . C 3 -40.314 84.78 -14.001 1 44.33 ? C5 ADP 500 A 1 HETATM 22 C C6 ADP . . . C 3 -40.748 85.209 -12.641 1 53.08 ? C6 ADP 500 A 1 HETATM 23 N N6 ADP . . . C 3 -42.056 85.238 -12.249 1 58.4 ? N6 ADP 500 A 1 HETATM 24 N N1 ADP . . . C 3 -39.785 85.694 -11.795 1 62.05 ? N1 ADP 500 A 1 HETATM 25 C C2 ADP . . . C 3 -38.506 85.701 -12.178 1 63.19 ? C2 ADP 500 A 1 HETATM 26 N N3 ADP . . . C 3 -38.027 85.303 -13.383 1 50.9 ? N3 ADP 500 A 1 HETATM 27 C C4 ADP . . . C 3 -38.99 84.872 -14.249 1 41.3 ? C4 ADP 500 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 27 #