data_7NGA # _model_server_result.job_id I_ZmXppkZ77T-aFy3Xg0uw _model_server_result.datetime_utc '2024-10-18 11:31:37' _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 7nga # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1102}' # _entry.id 7NGA # _exptl.entry_id 7NGA _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 5 _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 7NGA _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7NGA _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 trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 ? _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 5 _struct_asym.id E _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 C SG CYS 907 A CYS 907 1_555 D ZN ZN . A ZN 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? metalc ? metalc2 C SG CYS 910 A CYS 910 1_555 D ZN ZN . A ZN 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.322 ? metalc ? metalc3 C SG CYS 962 A CYS 962 1_555 D ZN ZN . A ZN 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.332 ? metalc ? metalc4 C SG CYS 964 A CYS 964 1_555 D ZN ZN . A ZN 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? hydrog WATSON-CRICK hydrog1 A N3 U 1 Y U 1 1_555 B N1 A 15 X A 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A O4 U 1 Y U 1 1_555 B N6 A 15 X A 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A N3 C 2 Y C 2 1_555 B N1 G 14 X G 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N4 C 2 Y C 2 1_555 B O6 G 14 X G 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A O2 C 2 Y C 2 1_555 B N2 G 14 X G 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A N3 C 3 Y C 3 1_555 B N1 G 13 X G 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N4 C 3 Y C 3 1_555 B O6 G 13 X G 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A O2 C 3 Y C 3 1_555 B N2 G 13 X G 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A N1 A 4 Y A 4 1_555 B N3 U 12 X U 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N6 A 4 Y A 4 1_555 B O4 U 12 X U 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A N3 U 5 Y U 5 1_555 B N1 A 11 X A 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A O4 U 5 Y U 5 1_555 B N6 A 11 X A 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N1 G 6 Y G 6 1_555 B N3 C 10 X C 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A N2 G 6 Y G 6 1_555 B O2 C 10 X C 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A O6 G 6 Y G 6 1_555 B N4 C 10 X C 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A N3 C 7 Y C 7 1_555 B N1 G 9 X G 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A N4 C 7 Y C 7 1_555 B O6 G 9 X G 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A O2 C 7 Y C 7 1_555 B N2 G 9 X G 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 A N1 G 8 Y G 8 1_555 B N3 C 8 X C 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 A N2 G 8 Y G 8 1_555 B O2 C 8 X C 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 A O6 G 8 Y G 8 1_555 B N4 C 8 X C 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 A N3 C 9 Y C 9 1_555 B N1 G 7 X G 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 A N4 C 9 Y C 9 1_555 B O6 G 7 X G 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 A O2 C 9 Y C 9 1_555 B N2 G 7 X G 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 A N1 A 10 Y A 10 1_555 B N3 U 6 X U 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 A N6 A 10 Y A 10 1_555 B O4 U 6 X U 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 A N3 U 11 Y U 11 1_555 B N1 A 5 X A 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 A O4 U 11 Y U 11 1_555 B N6 A 5 X A 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 A N1 G 12 Y G 12 1_555 B N3 C 4 X C 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 A N2 G 12 Y G 12 1_555 B O2 C 4 X C 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 A O6 G 12 Y G 12 1_555 B N4 C 4 X C 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 A N1 A 13 Y A 13 1_555 B N3 U 3 X U 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 A N6 A 13 Y A 13 1_555 B O4 U 3 X U 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog34 A N3 C 14 Y C 14 1_555 B N1 G 2 X G 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog35 A N4 C 14 Y C 14 1_555 B O6 G 2 X G 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog36 A O2 C 14 Y C 14 1_555 B N2 G 2 X G 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog37 A N1 G 15 Y G 15 1_555 B N3 C 1 X C 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog38 A N2 G 15 Y G 15 1_555 B O2 C 1 X C 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog39 A O6 G 15 Y G 15 1_555 B N4 C 1 X C 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _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 40 n n PB O2B ADP sing 41 n n PB O3B ADP sing 42 n n PB O3A ADP sing 43 n n O2B HOB2 ADP sing 44 n n O3B HOB3 ADP sing 45 n n PA O1A ADP doub 46 n n PA O2A ADP sing 47 n n PA O3A ADP sing 48 n n PA O5' ADP sing 49 n n O2A HOA2 ADP sing 50 n n O5' C5' ADP sing 51 n n C5' C4' ADP sing 52 n n C5' "H5'1" ADP sing 53 n n C5' "H5'2" ADP sing 54 n n C4' O4' ADP sing 55 n n C4' C3' ADP sing 56 n n C4' H4' ADP sing 57 n n O4' C1' ADP sing 58 n n C3' O3' ADP sing 59 n n C3' C2' ADP sing 60 n n C3' H3' ADP sing 61 n n O3' HO3' ADP sing 62 n n C2' O2' ADP sing 63 n n C2' C1' ADP sing 64 n n C2' H2' ADP sing 65 n n O2' HO2' ADP sing 66 n n C1' N9 ADP sing 67 n n C1' H1' ADP sing 68 n n N9 C8 ADP sing 69 n y N9 C4 ADP sing 70 n y C8 N7 ADP doub 71 n y C8 H8 ADP sing 72 n n N7 C5 ADP sing 73 n y C5 C6 ADP sing 74 n y C5 C4 ADP doub 75 n y C6 N6 ADP sing 76 n n C6 N1 ADP doub 77 n y N6 HN61 ADP sing 78 n n N6 HN62 ADP sing 79 n n N1 C2 ADP sing 80 n y C2 N3 ADP doub 81 n y C2 H2 ADP sing 82 n n N3 C4 ADP sing 83 n y # _atom_sites.entry_id 7NGA _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 D 4 ZN A 1 1101 1101 ZN ZN . E 5 ADP A 1 1102 1201 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 . . . E 5 95.109 134.229 118.891 1 148.82 ? PB ADP 1102 A 1 HETATM 2 O O1B ADP . . . E 5 95.89 134.89 117.78 1 148.82 ? O1B ADP 1102 A 1 HETATM 3 O O2B ADP . . . E 5 93.774 133.659 118.474 1 148.82 ? O2B ADP 1102 A 1 HETATM 4 O O3B ADP . . . E 5 95.921 133.327 119.789 1 148.82 ? O3B ADP 1102 A 1 HETATM 5 P PA ADP . . . E 5 94.103 135.103 121.306 1 148.82 ? PA ADP 1102 A 1 HETATM 6 O O1A ADP . . . E 5 93.75 133.635 121.327 1 148.82 ? O1A ADP 1102 A 1 HETATM 7 O O2A ADP . . . E 5 95.029 135.651 122.363 1 148.82 ? O2A ADP 1102 A 1 HETATM 8 O O3A ADP . . . E 5 94.707 135.443 119.859 1 148.82 ? O3A ADP 1102 A 1 HETATM 9 O O5' ADP . . . E 5 92.745 135.96 121.279 1 148.82 ? O5' ADP 1102 A 1 HETATM 10 C C5' ADP . . . E 5 91.774 135.824 122.309 1 148.82 ? C5' ADP 1102 A 1 HETATM 11 C C4' ADP . . . E 5 90.727 136.918 122.15 1 148.82 ? C4' ADP 1102 A 1 HETATM 12 O O4' ADP . . . E 5 89.67 136.51 121.277 1 148.82 ? O4' ADP 1102 A 1 HETATM 13 C C3' ADP . . . E 5 90.085 137.28 123.475 1 148.82 ? C3' ADP 1102 A 1 HETATM 14 O O3' ADP . . . E 5 90.634 138.509 123.954 1 148.82 ? O3' ADP 1102 A 1 HETATM 15 C C2' ADP . . . E 5 88.603 137.406 123.19 1 148.82 ? C2' ADP 1102 A 1 HETATM 16 O O2' ADP . . . E 5 88.137 138.737 123.422 1 148.82 ? O2' ADP 1102 A 1 HETATM 17 C C1' ADP . . . E 5 88.429 137.055 121.727 1 148.82 ? C1' ADP 1102 A 1 HETATM 18 N N9 ADP . . . E 5 87.334 136.07 121.578 1 148.82 ? N9 ADP 1102 A 1 HETATM 19 C C8 ADP . . . E 5 87.494 134.764 121.308 1 148.82 ? C8 ADP 1102 A 1 HETATM 20 N N7 ADP . . . E 5 86.289 134.142 121.234 1 148.82 ? N7 ADP 1102 A 1 HETATM 21 C C5 ADP . . . E 5 85.337 135.061 121.457 1 148.82 ? C5 ADP 1102 A 1 HETATM 22 C C6 ADP . . . E 5 83.86 135.072 121.521 1 148.82 ? C6 ADP 1102 A 1 HETATM 23 N N6 ADP . . . E 5 83.136 133.945 121.324 1 148.82 ? N6 ADP 1102 A 1 HETATM 24 N N1 ADP . . . E 5 83.257 136.251 121.78 1 148.82 ? N1 ADP 1102 A 1 HETATM 25 C C2 ADP . . . E 5 83.954 137.386 121.98 1 148.82 ? C2 ADP 1102 A 1 HETATM 26 N N3 ADP . . . E 5 85.297 137.44 121.935 1 148.82 ? N3 ADP 1102 A 1 HETATM 27 C C4 ADP . . . E 5 86.032 136.334 121.682 1 148.82 ? C4 ADP 1102 A 1 HETATM 28 H "H5'1" ADP . . . E 5 92.26 135.906 123.283 1 148.82 ? "H5'1" ADP 1102 A 1 HETATM 29 H "H5'2" ADP . . . E 5 91.3 134.843 122.242 1 148.82 ? "H5'2" ADP 1102 A 1 HETATM 30 H H4' ADP . . . E 5 91.219 137.812 121.747 1 148.82 ? H4' ADP 1102 A 1 HETATM 31 H H3' ADP . . . E 5 90.254 136.469 124.197 1 148.82 ? H3' ADP 1102 A 1 HETATM 32 H HO3' ADP . . . E 5 90.374 138.634 124.875 1 148.82 ? HO3' ADP 1102 A 1 HETATM 33 H H2' ADP . . . E 5 88.047 136.683 123.803 1 148.82 ? H2' ADP 1102 A 1 HETATM 34 H HO2' ADP . . . E 5 88.192 138.934 124.365 1 148.82 ? HO2' ADP 1102 A 1 HETATM 35 H H1' ADP . . . E 5 88.191 137.972 121.172 1 148.82 ? H1' ADP 1102 A 1 HETATM 36 H H8 ADP . . . E 5 88.452 134.278 121.173 1 148.82 ? H8 ADP 1102 A 1 HETATM 37 H HN61 ADP . . . E 5 82.129 133.974 121.371 1 148.82 ? HN61 ADP 1102 A 1 HETATM 38 H HN62 ADP . . . E 5 83.604 133.074 121.131 1 148.82 ? HN62 ADP 1102 A 1 HETATM 39 H H2 ADP . . . E 5 83.407 138.299 122.184 1 148.82 ? H2 ADP 1102 A 1 # _model_server_stats.io_time_ms 70 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 311 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 39 #