data_5NUG # _model_server_result.job_id m3AGKBPBQ060y-GD80359g _model_server_result.datetime_utc '2024-11-22 13:51:58' _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 5nug # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":4801}' # _entry.id 5NUG # _exptl.entry_id 5NUG _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 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 5NUG _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5NUG _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,G 1 1 B,H,I,J,K,L 2 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 F N N ? 2 G N N ? 2 H N N ? 2 K N N ? 2 L 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 OG SER 2231 A SER 2231 1_555 E MG MG . A MG 4803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.881 ? metalc ? metalc2 A OE2 GLU 2344 A GLU 2344 1_555 E MG MG . A MG 4803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.275 ? metalc ? metalc3 D O1G ATP . A ATP 4802 1_555 E MG MG . A MG 4803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.583 ? metalc ? metalc4 D O3G ATP . A ATP 4802 1_555 E MG MG . A MG 4803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.818 ? metalc ? metalc5 D O2B ATP . A ATP 4802 1_555 E MG MG . A MG 4803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.729 ? metalc ? metalc6 D O3B ATP . A ATP 4802 1_555 E MG MG . A MG 4803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.726 ? metalc ? metalc7 B OG SER 2231 B SER 2231 1_555 J MG MG . B MG 4803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.881 ? metalc ? metalc8 B OE2 GLU 2344 B GLU 2344 1_555 J MG MG . B MG 4803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.275 ? metalc ? metalc9 I O1G ATP . B ATP 4802 1_555 J MG MG . B MG 4803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.583 ? metalc ? metalc10 I O3G ATP . B ATP 4802 1_555 J MG MG . B MG 4803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.818 ? metalc ? metalc11 I O2B ATP . B ATP 4802 1_555 J MG MG . B MG 4803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.729 ? metalc ? metalc12 I O3B ATP . B ATP 4802 1_555 J MG MG . B MG 4803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.726 ? # _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 5NUG _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 C 2 ADP A 1 4801 4801 ADP ADP . D 3 ATP A 1 4802 4803 ATP ATP . E 4 MG A 1 4803 4804 MG MG . F 2 ADP A 1 4804 4805 ADP ADP . G 2 ADP A 1 4805 4806 ADP ADP . H 2 ADP B 1 4801 4801 ADP ADP . I 3 ATP B 1 4802 4803 ATP ATP . J 4 MG B 1 4803 4804 MG MG . K 2 ADP B 1 4804 4805 ADP ADP . L 2 ADP B 1 4805 4806 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 . . . H 2 -40.337 -34.843 -8.164 1 96.58 ? PB ADP 4801 B 1 HETATM 2 O O1B ADP . . . H 2 -39.838 -33.563 -8.798 1 92.84 ? O1B ADP 4801 B 1 HETATM 3 O O2B ADP . . . H 2 -41.422 -34.608 -7.144 1 95.62 ? O2B ADP 4801 B 1 HETATM 4 O O3B ADP . . . H 2 -39.218 -35.739 -7.699 1 100.2 ? O3B ADP 4801 B 1 HETATM 5 P PA ADP . . . H 2 -42.129 -35.066 -10.272 1 85.84 ? PA ADP 4801 B 1 HETATM 6 O O1A ADP . . . H 2 -41.393 -34.077 -11.142 1 85.09 ? O1A ADP 4801 B 1 HETATM 7 O O2A ADP . . . H 2 -43.26 -34.576 -9.396 1 85.46 ? O2A ADP 4801 B 1 HETATM 8 O O3A ADP . . . H 2 -41.043 -35.752 -9.306 1 89.31 ? O3A ADP 4801 B 1 HETATM 9 O O5' ADP . . . H 2 -42.766 -36.168 -11.263 1 81.23 ? O5' ADP 4801 B 1 HETATM 10 C C5' ADP . . . H 2 -42.072 -36.975 -12.214 1 77.42 ? C5' ADP 4801 B 1 HETATM 11 C C4' ADP . . . H 2 -42.417 -36.688 -13.695 1 73.92 ? C4' ADP 4801 B 1 HETATM 12 O O4' ADP . . . H 2 -43.418 -37.618 -14.133 1 72.57 ? O4' ADP 4801 B 1 HETATM 13 C C3' ADP . . . H 2 -42.919 -35.286 -14.057 1 70.11 ? C3' ADP 4801 B 1 HETATM 14 O O3' ADP . . . H 2 -42.043 -34.651 -14.999 1 67.33 ? O3' ADP 4801 B 1 HETATM 15 C C2' ADP . . . H 2 -44.302 -35.47 -14.648 1 68.29 ? C2' ADP 4801 B 1 HETATM 16 O O2' ADP . . . H 2 -44.392 -34.906 -15.957 1 65.6 ? O2' ADP 4801 B 1 HETATM 17 C C1' ADP . . . H 2 -44.56 -36.964 -14.687 1 72.6 ? C1' ADP 4801 B 1 HETATM 18 N N9 ADP . . . H 2 -45.78 -37.253 -13.903 1 79.28 ? N9 ADP 4801 B 1 HETATM 19 C C8 ADP . . . H 2 -45.816 -37.443 -12.581 1 84.81 ? C8 ADP 4801 B 1 HETATM 20 N N7 ADP . . . H 2 -47.075 -37.688 -12.14 1 87.25 ? N7 ADP 4801 B 1 HETATM 21 C C5 ADP . . . H 2 -47.876 -37.648 -13.2 1 85.81 ? C5 ADP 4801 B 1 HETATM 22 C C6 ADP . . . H 2 -49.328 -37.795 -13.422 1 86.86 ? C6 ADP 4801 B 1 HETATM 23 N N6 ADP . . . H 2 -50.134 -38.058 -12.373 1 87.77 ? N6 ADP 4801 B 1 HETATM 24 N N1 ADP . . . H 2 -49.793 -37.664 -14.689 1 89.87 ? N1 ADP 4801 B 1 HETATM 25 C C2 ADP . . . H 2 -48.956 -37.404 -15.726 1 94.28 ? C2 ADP 4801 B 1 HETATM 26 N N3 ADP . . . H 2 -47.617 -37.249 -15.579 1 92.66 ? N3 ADP 4801 B 1 HETATM 27 C C4 ADP . . . H 2 -47.022 -37.355 -14.364 1 85.43 ? C4 ADP 4801 B 1 # _model_server_stats.io_time_ms 26 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 63 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #