data_5LJV # _model_server_result.job_id TOb9sdRqlhlNDDC9Ws3zGQ _model_server_result.datetime_utc '2024-11-28 15:17:36' _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 5ljv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":402}' # _entry.id 5LJV # _exptl.entry_id 5LJV _exptl.method 'ELECTRON MICROSCOPY' # _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 6 _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 5LJV _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5LJV _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 hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,I,J,K,L,M,N,O,P,Q,R _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 ? 3 H N N ? 3 J N N ? 3 L N N ? 3 N N N ? 3 P N N ? 3 R 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 OE1 GLU 143 A GLU 143 1_555 G MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.605 ? metalc ? metalc2 G MG MG . A MG 401 1_555 H O1B ADP . A ADP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.907 ? metalc ? metalc3 G MG MG . A MG 401 1_555 H O2B ADP . A ADP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.309 ? metalc ? metalc4 B OE1 GLU 143 B GLU 143 1_555 I MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.55 ? metalc ? metalc5 I MG MG . B MG 401 1_555 J O2B ADP . B ADP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.934 ? metalc ? metalc6 I MG MG . B MG 401 1_555 J O1B ADP . B ADP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.288 ? metalc ? metalc7 C OE1 GLU 143 C GLU 143 1_555 K MG MG . C MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.649 ? metalc ? metalc8 K MG MG . C MG 401 1_555 L O1B ADP . C ADP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.952 ? metalc ? metalc9 K MG MG . C MG 401 1_555 L O2B ADP . C ADP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? metalc ? metalc10 D OE1 GLU 143 D GLU 143 1_555 M MG MG . D MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.657 ? metalc ? metalc11 M MG MG . D MG 401 1_555 N O2B ADP . D ADP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? metalc ? metalc12 M MG MG . D MG 401 1_555 N O1B ADP . D ADP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.959 ? metalc ? metalc13 E OE1 GLU 143 E GLU 143 1_555 O MG MG . E MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.566 ? metalc ? metalc14 O MG MG . E MG 401 1_555 P O1B ADP . E ADP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? metalc ? metalc15 O MG MG . E MG 401 1_555 P O2B ADP . E ADP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.975 ? metalc ? metalc16 F OE1 GLU 143 F GLU 143 1_555 Q MG MG . F MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.619 ? metalc ? metalc17 Q MG MG . F MG 401 1_555 R O2B ADP . F ADP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? metalc ? metalc18 Q MG MG . F MG 401 1_555 R O1B ADP . F ADP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.932 ? # _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 5LJV _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 G 2 MG A 1 401 998 MG MG . H 3 ADP A 1 402 999 ADP ADP . I 2 MG B 1 401 998 MG MG . J 3 ADP B 1 402 999 ADP ADP . K 2 MG C 1 401 998 MG MG . L 3 ADP C 1 402 999 ADP ADP . M 2 MG D 1 401 998 MG MG . N 3 ADP D 1 402 999 ADP ADP . O 2 MG E 1 401 998 MG MG . P 3 ADP E 1 402 999 ADP ADP . Q 2 MG F 1 401 998 MG MG . R 3 ADP F 1 402 999 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 . . . N 3 173.985 181.728 242.494 1 66.83 ? PB ADP 402 D 1 HETATM 2 O O1B ADP . . . N 3 175.177 182.272 241.59 1 65.89 ? O1B ADP 402 D 1 HETATM 3 O O2B ADP . . . N 3 172.982 180.71 241.803 1 68.91 ? O2B ADP 402 D 1 HETATM 4 O O3B ADP . . . N 3 174.398 181.138 243.85 1 65.14 ? O3B ADP 402 D 1 HETATM 5 P PA ADP . . . N 3 171.445 182.808 242.686 1 57.9 ? PA ADP 402 D 1 HETATM 6 O O1A ADP . . . N 3 170.828 182.416 241.323 1 57.8 ? O1A ADP 402 D 1 HETATM 7 O O2A ADP . . . N 3 171.046 181.711 243.639 1 65 ? O2A ADP 402 D 1 HETATM 8 O O3A ADP . . . N 3 173.025 183.029 242.731 1 59.13 ? O3A ADP 402 D 1 HETATM 9 O O5' ADP . . . N 3 171.041 184.197 243.299 1 61.25 ? O5' ADP 402 D 1 HETATM 10 C C5' ADP . . . N 3 171.197 184.443 244.65 1 67.67 ? C5' ADP 402 D 1 HETATM 11 C C4' ADP . . . N 3 171.999 185.726 244.762 1 77.41 ? C4' ADP 402 D 1 HETATM 12 O O4' ADP . . . N 3 171.228 186.822 244.375 1 79.61 ? O4' ADP 402 D 1 HETATM 13 C C3' ADP . . . N 3 172.453 186.063 246.192 1 85.71 ? C3' ADP 402 D 1 HETATM 14 O O3' ADP . . . N 3 173.534 186.973 246.166 1 78.73 ? O3' ADP 402 D 1 HETATM 15 C C2' ADP . . . N 3 171.367 186.817 246.827 1 86.95 ? C2' ADP 402 D 1 HETATM 16 O O2' ADP . . . N 3 171.759 187.714 247.881 1 84.72 ? O2' ADP 402 D 1 HETATM 17 C C1' ADP . . . N 3 170.862 187.497 245.548 1 83.3 ? C1' ADP 402 D 1 HETATM 18 N N9 ADP . . . N 3 169.43 187.451 245.733 1 84.72 ? N9 ADP 402 D 1 HETATM 19 C C8 ADP . . . N 3 168.558 186.435 246.039 1 89.1 ? C8 ADP 402 D 1 HETATM 20 N N7 ADP . . . N 3 167.279 186.857 246.176 1 92.81 ? N7 ADP 402 D 1 HETATM 21 C C5 ADP . . . N 3 167.419 188.165 245.951 1 86.75 ? C5 ADP 402 D 1 HETATM 22 C C6 ADP . . . N 3 166.458 189.255 245.906 1 84.03 ? C6 ADP 402 D 1 HETATM 23 N N6 ADP . . . N 3 165.131 188.907 246.145 1 99.92 ? N6 ADP 402 D 1 HETATM 24 N N1 ADP . . . N 3 166.969 190.509 245.629 1 72.96 ? N1 ADP 402 D 1 HETATM 25 C C2 ADP . . . N 3 168.289 190.737 245.391 1 71.98 ? C2 ADP 402 D 1 HETATM 26 N N3 ADP . . . N 3 169.218 189.761 245.371 1 70.49 ? N3 ADP 402 D 1 HETATM 27 C C4 ADP . . . N 3 168.812 188.542 245.675 1 79.72 ? C4 ADP 402 D 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 411 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 27 #