data_5JLH # _model_server_result.job_id 8BzRMLu-zA7ViKWSKRx_vA _model_server_result.datetime_utc '2024-10-18 15:28:53' _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 5jlh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":401}' # _entry.id 5JLH # _exptl.entry_id 5JLH _exptl.method 'ELECTRON MICROSCOPY' # _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 5 _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 5JLH _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5JLH _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 ? _pdbx_struct_assembly.oligomeric_details undecameric _pdbx_struct_assembly.oligomeric_count 11 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U _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 ? _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 L N N ? 4 N N N ? 4 P N N ? 4 R N N ? 4 T 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 L O1B ADP . A ADP 401 1_555 M MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? metalc ? metalc2 L O3B ADP . A ADP 401 1_555 M MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? metalc ? metalc3 N O1B ADP . B ADP 401 1_555 O MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? metalc ? metalc4 N O3B ADP . B ADP 401 1_555 O MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.136 ? metalc ? metalc5 P O1B ADP . C ADP 401 1_555 Q MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.248 ? metalc ? metalc6 P O3B ADP . C ADP 401 1_555 Q MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.136 ? metalc ? metalc7 R O1B ADP . D ADP 401 1_555 S MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.248 ? metalc ? metalc8 R O3B ADP . D ADP 401 1_555 S MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.136 ? metalc ? metalc9 T O1B ADP . E ADP 401 1_555 U MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.248 ? metalc ? metalc10 T O3B ADP . E ADP 401 1_555 U MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? # _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 5JLH _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 L 4 ADP A 1 401 377 ADP ADP . M 5 MG A 1 402 376 MG MG . N 4 ADP B 1 401 377 ADP ADP . O 5 MG B 1 402 376 MG MG . P 4 ADP C 1 401 377 ADP ADP . Q 5 MG C 1 402 376 MG MG . R 4 ADP D 1 401 377 ADP ADP . S 5 MG D 1 402 376 MG MG . T 4 ADP E 1 401 377 ADP ADP . U 5 MG E 1 402 376 MG MG . # 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 . . . N 4 14.91 8.008 55.333 1 165.22 ? PB ADP 401 B 1 HETATM 2 O O1B ADP . . . N 4 13.793 7.913 54.318 1 202.8 ? O1B ADP 401 B 1 HETATM 3 O O2B ADP . . . N 4 14.557 8.817 56.568 1 145.47 ? O2B ADP 401 B 1 HETATM 4 O O3B ADP . . . N 4 16.244 8.227 54.639 1 156.19 ? O3B ADP 401 B 1 HETATM 5 P PA ADP . . . N 4 16.21 6.109 56.856 1 124.1 ? PA ADP 401 B 1 HETATM 6 O O1A ADP . . . N 4 17.335 5.846 55.91 1 106.78 ? O1A ADP 401 B 1 HETATM 7 O O2A ADP . . . N 4 16.322 7.125 57.97 1 145.55 ? O2A ADP 401 B 1 HETATM 8 O O3A ADP . . . N 4 14.977 6.533 55.964 1 146.23 ? O3A ADP 401 B 1 HETATM 9 O O5' ADP . . . N 4 15.643 4.733 57.459 1 162.73 ? O5' ADP 401 B 1 HETATM 10 C C5' ADP . . . N 4 15.916 4.329 58.805 1 187.79 ? C5' ADP 401 B 1 HETATM 11 C C4' ADP . . . N 4 15.15 3.055 59.184 1 185.29 ? C4' ADP 401 B 1 HETATM 12 O O4' ADP . . . N 4 15.764 1.87 58.654 1 177.03 ? O4' ADP 401 B 1 HETATM 13 C C3' ADP . . . N 4 15.076 2.87 60.688 1 182.31 ? C3' ADP 401 B 1 HETATM 14 O O3' ADP . . . N 4 13.889 3.436 61.251 1 178.77 ? O3' ADP 401 B 1 HETATM 15 C C2' ADP . . . N 4 15.182 1.362 60.854 1 174.28 ? C2' ADP 401 B 1 HETATM 16 O O2' ADP . . . N 4 13.902 0.761 60.801 1 157.51 ? O2' ADP 401 B 1 HETATM 17 C C1' ADP . . . N 4 15.947 0.87 59.655 1 155.11 ? C1' ADP 401 B 1 HETATM 18 N N9 ADP . . . N 4 17.379 0.764 59.996 1 157.49 ? N9 ADP 401 B 1 HETATM 19 C C8 ADP . . . N 4 18.194 1.791 60.328 1 161.42 ? C8 ADP 401 B 1 HETATM 20 N N7 ADP . . . N 4 19.446 1.354 60.583 1 166.77 ? N7 ADP 401 B 1 HETATM 21 C C5 ADP . . . N 4 19.45 0.026 60.4 1 167.5 ? C5 ADP 401 B 1 HETATM 22 C C6 ADP . . . N 4 20.476 -1.046 60.502 1 181.66 ? C6 ADP 401 B 1 HETATM 23 N N6 ADP . . . N 4 21.762 -0.798 60.853 1 184.17 ? N6 ADP 401 B 1 HETATM 24 N N1 ADP . . . N 4 20.08 -2.303 60.226 1 179.07 ? N1 ADP 401 B 1 HETATM 25 C C2 ADP . . . N 4 18.815 -2.575 59.879 1 164.85 ? C2 ADP 401 B 1 HETATM 26 N N3 ADP . . . N 4 17.814 -1.672 59.773 1 158.06 ? N3 ADP 401 B 1 HETATM 27 C C4 ADP . . . N 4 18.075 -0.365 60.015 1 157.4 ? C4 ADP 401 B 1 # _model_server_stats.io_time_ms 25 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 57 _model_server_stats.query_time_ms 305 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #