data_5NUG # _model_server_result.job_id G_FGNMScdL71SpyoigfO2w _model_server_result.datetime_utc '2024-11-22 13:54:34' _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":"F","auth_seq_id":4804}' # _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 . . . F 2 -10.413 35.925 1.801 1 109.88 ? PB ADP 4804 A 1 HETATM 2 O O1B ADP . . . F 2 -10.242 36.054 0.307 1 105.44 ? O1B ADP 4804 A 1 HETATM 3 O O2B ADP . . . F 2 -10.259 34.522 2.332 1 123 ? O2B ADP 4804 A 1 HETATM 4 O O3B ADP . . . F 2 -9.649 36.965 2.578 1 107.48 ? O3B ADP 4804 A 1 HETATM 5 P PA ADP . . . F 2 -12.842 36.81 0.927 1 94.9 ? PA ADP 4804 A 1 HETATM 6 O O1A ADP . . . F 2 -13.219 35.653 0.047 1 96.05 ? O1A ADP 4804 A 1 HETATM 7 O O2A ADP . . . F 2 -12.096 37.967 0.317 1 92.47 ? O2A ADP 4804 A 1 HETATM 8 O O3A ADP . . . F 2 -11.957 36.216 2.111 1 99.84 ? O3A ADP 4804 A 1 HETATM 9 O O5' ADP . . . F 2 -14.158 37.38 1.682 1 97.73 ? O5' ADP 4804 A 1 HETATM 10 C C5' ADP . . . F 2 -15.303 36.531 1.763 1 96.61 ? C5' ADP 4804 A 1 HETATM 11 C C4' ADP . . . F 2 -16.448 37.044 2.628 1 90.68 ? C4' ADP 4804 A 1 HETATM 12 O O4' ADP . . . F 2 -17.047 38.216 2.087 1 88.94 ? O4' ADP 4804 A 1 HETATM 13 C C3' ADP . . . F 2 -17.52 35.959 2.694 1 92.75 ? C3' ADP 4804 A 1 HETATM 14 O O3' ADP . . . F 2 -17.824 35.633 4.052 1 91.13 ? O3' ADP 4804 A 1 HETATM 15 C C2' ADP . . . F 2 -18.715 36.506 1.932 1 99.74 ? C2' ADP 4804 A 1 HETATM 16 O O2' ADP . . . F 2 -19.952 36.387 2.643 1 108.46 ? O2' ADP 4804 A 1 HETATM 17 C C1' ADP . . . F 2 -18.4 37.971 1.693 1 99.62 ? C1' ADP 4804 A 1 HETATM 18 N N9 ADP . . . F 2 -18.433 38.391 0.286 1 109.18 ? N9 ADP 4804 A 1 HETATM 19 C C8 ADP . . . F 2 -18.095 37.707 -0.82 1 121.05 ? C8 ADP 4804 A 1 HETATM 20 N N7 ADP . . . F 2 -18.219 38.475 -1.929 1 123.86 ? N7 ADP 4804 A 1 HETATM 21 C C5 ADP . . . F 2 -18.627 39.678 -1.512 1 122.6 ? C5 ADP 4804 A 1 HETATM 22 C C6 ADP . . . F 2 -18.946 40.973 -2.138 1 132.51 ? C6 ADP 4804 A 1 HETATM 23 N N6 ADP . . . F 2 -18.858 41.137 -3.477 1 143.33 ? N6 ADP 4804 A 1 HETATM 24 N N1 ADP . . . F 2 -19.343 41.977 -1.333 1 131.99 ? N1 ADP 4804 A 1 HETATM 25 C C2 ADP . . . F 2 -19.435 41.827 0.003 1 131.4 ? C2 ADP 4804 A 1 HETATM 26 N N3 ADP . . . F 2 -19.15 40.683 0.635 1 122.33 ? N3 ADP 4804 A 1 HETATM 27 C C4 ADP . . . F 2 -18.752 39.608 -0.058 1 114.27 ? C4 ADP 4804 A 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 50 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #