data_3JBZ # _model_server_result.job_id cFg3ZtYAcRYugS9ccNXYBg _model_server_result.datetime_utc '2025-03-09 01:48:43' _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 3jbz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":2601}' # _entry.id 3JBZ # _exptl.entry_id 3JBZ _exptl.method 'ELECTRON MICROSCOPY' # _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 3JBZ _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3JBZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1' # _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 959 A ASN 2343 1_555 C MG MG . A MG 2602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.426 ? metalc ? metalc2 A OD1 ASP 973 A ASP 2357 1_555 D MG MG . A MG 2603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? metalc ? metalc3 A OD2 ASP 973 A ASP 2357 1_555 D MG MG . A MG 2603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.967 ? metalc ? metalc4 B O1A ADP . A ADP 2601 1_555 C MG MG . A MG 2602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? metalc ? metalc5 B O3B ADP . A ADP 2601 1_555 C MG MG . A MG 2602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.525 ? metalc ? metalc6 B O3B ADP . A ADP 2601 1_555 E MG MGF . A MGF 2604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.591 ? # _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 3JBZ _atom_sites.fract_transf_matrix[1][1] 0.007174 _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] 0.006127 _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] 0.004812 _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 2601 2601 ADP ADP . C 3 MG A 1 2602 2602 MG MG . D 3 MG A 1 2603 2603 MG MG . E 4 MGF A 1 2604 2604 MGF MGF . # 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 -7.562 -32.435 -39.074 1 81.87 ? PB ADP 2601 A 1 HETATM 2 O O1B ADP . . . B 2 -7.334 -31.044 -39.641 1 78.57 ? O1B ADP 2601 A 1 HETATM 3 O O2B ADP . . . B 2 -8.989 -32.947 -39.2 1 81.51 ? O2B ADP 2601 A 1 HETATM 4 O O3B ADP . . . B 2 -6.941 -32.566 -37.701 1 78.5 ? O3B ADP 2601 A 1 HETATM 5 P PA ADP . . . B 2 -6.571 -35.074 -39.876 1 81.14 ? PA ADP 2601 A 1 HETATM 6 O O1A ADP . . . B 2 -7.414 -35.545 -38.699 1 79.59 ? O1A ADP 2601 A 1 HETATM 7 O O2A ADP . . . B 2 -5.097 -35.44 -39.908 1 78.98 ? O2A ADP 2601 A 1 HETATM 8 O O3A ADP . . . B 2 -6.688 -33.449 -40.012 1 82.45 ? O3A ADP 2601 A 1 HETATM 9 O O5' ADP . . . B 2 -7.246 -35.592 -41.259 1 76.62 ? O5' ADP 2601 A 1 HETATM 10 C C5' ADP . . . B 2 -8.526 -36.218 -41.277 1 73 ? C5' ADP 2601 A 1 HETATM 11 C C4' ADP . . . B 2 -8.36 -37.731 -41.383 1 71.37 ? C4' ADP 2601 A 1 HETATM 12 O O4' ADP . . . B 2 -7.24 -38.112 -42.193 1 70.2 ? O4' ADP 2601 A 1 HETATM 13 C C3' ADP . . . B 2 -8.099 -38.436 -40.058 1 70.58 ? C3' ADP 2601 A 1 HETATM 14 O O3' ADP . . . B 2 -9.284 -38.569 -39.268 1 70.68 ? O3' ADP 2601 A 1 HETATM 15 C C2' ADP . . . B 2 -7.483 -39.759 -40.494 1 69 ? C2' ADP 2601 A 1 HETATM 16 O O2' ADP . . . B 2 -8.462 -40.729 -40.877 1 67.54 ? O2' ADP 2601 A 1 HETATM 17 C C1' ADP . . . B 2 -6.732 -39.394 -41.762 1 68.85 ? C1' ADP 2601 A 1 HETATM 18 N N9 ADP . . . B 2 -5.251 -39.378 -41.539 1 67.81 ? N9 ADP 2601 A 1 HETATM 19 C C8 ADP . . . B 2 -4.511 -38.291 -41.21 1 67.14 ? C8 ADP 2601 A 1 HETATM 20 N N7 ADP . . . B 2 -3.189 -38.592 -41.098 1 66.22 ? N7 ADP 2601 A 1 HETATM 21 C C5 ADP . . . B 2 -3.06 -39.909 -41.358 1 66.14 ? C5 ADP 2601 A 1 HETATM 22 C C6 ADP . . . B 2 -1.939 -40.882 -41.412 1 65.29 ? C6 ADP 2601 A 1 HETATM 23 N N6 ADP . . . B 2 -0.677 -40.464 -41.15 1 64.77 ? N6 ADP 2601 A 1 HETATM 24 N N1 ADP . . . B 2 -2.216 -42.178 -41.725 1 64.48 ? N1 ADP 2601 A 1 HETATM 25 C C2 ADP . . . B 2 -3.471 -42.588 -41.984 1 64.31 ? C2 ADP 2601 A 1 HETATM 26 N N3 ADP . . . B 2 -4.54 -41.757 -41.949 1 65.44 ? N3 ADP 2601 A 1 HETATM 27 C C4 ADP . . . B 2 -4.413 -40.429 -41.651 1 66.74 ? C4 ADP 2601 A 1 # _model_server_stats.io_time_ms 56 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 323 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #