data_3TNQ # _model_server_result.job_id h4gd17kAiXpQMnaFAVuCrw _model_server_result.datetime_utc '2024-11-20 07:21:05' _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 3tnq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":400}' # _entry.id 3TNQ # _exptl.entry_id 3TNQ _exptl.method 'X-RAY DIFFRACTION' # _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 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 3TNQ _cell.length_a 153.819 _cell.length_b 212.753 _cell.length_c 61.951 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3TNQ _symmetry.cell_setting ? _symmetry.Int_Tables_number 21 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 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 # _struct_asym.details ? _struct_asym.entity_id 4 _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 covale ? covale1 A C PHE 138 B PHE 138 1_555 A N SEP 139 B SEP 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale2 A C SEP 139 B SEP 139 1_555 A N GLU 140 B GLU 140 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale3 A C TRP 196 B TRP 196 1_555 A N TPO 197 B TPO 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale4 A C TPO 197 B TPO 197 1_555 A N LEU 198 B LEU 198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale5 A C VAL 337 B VAL 337 1_555 A N SEP 338 B SEP 338 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale6 A C SEP 338 B SEP 338 1_555 A N ILE 339 B ILE 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale7 B C ALA 111 A ALA 111 1_555 B N SEP 112 A SEP 112 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale8 B C SEP 112 A SEP 112 1_555 B N VAL 113 A VAL 113 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? metalc ? metalc1 A OD1 ASN 171 B ASN 171 1_555 C MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.391 ? metalc ? metalc2 A OD1 ASP 184 B ASP 184 1_555 D MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? metalc ? metalc3 A OD2 ASP 184 B ASP 184 1_555 D MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.475 ? metalc ? metalc4 A OD1 ASP 184 B ASP 184 1_555 C MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.426 ? metalc ? metalc5 E O2B ADP . B ADP 400 1_555 D MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.521 ? metalc ? metalc6 E O2A ADP . B ADP 400 1_555 C MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.411 ? metalc ? metalc7 E O2B ADP . B ADP 400 1_555 C MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.45 ? metalc ? metalc8 D MG MG . B MG 401 1_555 B O3P SEP 112 A SEP 112 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.269 ? # _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 3TNQ _atom_sites.fract_transf_matrix[1][1] 0.006501 _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] 0.0047 _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] 0.016142 _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 3 MG B 1 402 402 MG MG . D 3 MG B 1 401 401 MG MG . E 4 ADP B 1 400 400 ADP ADP . F 5 HOH B 1 351 2 HOH HOH . F 5 HOH B 2 352 3 HOH HOH . F 5 HOH B 3 353 4 HOH HOH . F 5 HOH B 4 354 5 HOH HOH . F 5 HOH B 5 355 6 HOH HOH . F 5 HOH B 6 356 7 HOH HOH . F 5 HOH B 7 357 8 HOH HOH . F 5 HOH B 8 358 10 HOH HOH . F 5 HOH B 9 359 11 HOH HOH . F 5 HOH B 10 360 12 HOH HOH . F 5 HOH B 11 361 13 HOH HOH . G 5 HOH A 1 417 9 HOH HOH . G 5 HOH A 2 418 14 HOH HOH . # 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 4 45.003 -31.897 -39.284 1 50.15 ? PB ADP 400 B 1 HETATM 2 O O1B ADP . . . E 4 44.207 -31.308 -40.434 1 48.13 ? O1B ADP 400 B 1 HETATM 3 O O2B ADP . . . E 4 44.719 -31.184 -37.978 1 47 ? O2B ADP 400 B 1 HETATM 4 O O3B ADP . . . E 4 44.972 -33.417 -39.124 1 33 ? O3B ADP 400 B 1 HETATM 5 P PA ADP . . . E 4 47.708 -31.048 -38.737 1 44.17 ? PA ADP 400 B 1 HETATM 6 O O1A ADP . . . E 4 48.077 -29.616 -38.992 1 48.37 ? O1A ADP 400 B 1 HETATM 7 O O2A ADP . . . E 4 47.447 -31.497 -37.311 1 48.33 ? O2A ADP 400 B 1 HETATM 8 O O3A ADP . . . E 4 46.516 -31.521 -39.721 1 34.36 ? O3A ADP 400 B 1 HETATM 9 O O5' ADP . . . E 4 48.923 -31.945 -39.279 1 37.79 ? O5' ADP 400 B 1 HETATM 10 C C5' ADP . . . E 4 48.776 -33.358 -39.271 1 38.31 ? C5' ADP 400 B 1 HETATM 11 C C4' ADP . . . E 4 50.111 -34.061 -39.113 1 40.88 ? C4' ADP 400 B 1 HETATM 12 O O4' ADP . . . E 4 51.068 -33.589 -40.054 1 40.2 ? O4' ADP 400 B 1 HETATM 13 C C3' ADP . . . E 4 50.747 -33.841 -37.748 1 46.04 ? C3' ADP 400 B 1 HETATM 14 O O3' ADP . . . E 4 50.326 -34.813 -36.785 1 52.78 ? O3' ADP 400 B 1 HETATM 15 C C2' ADP . . . E 4 52.225 -33.997 -38.011 1 42.23 ? C2' ADP 400 B 1 HETATM 16 O O2' ADP . . . E 4 52.616 -35.362 -37.819 1 38.6 ? O2' ADP 400 B 1 HETATM 17 C C1' ADP . . . E 4 52.374 -33.615 -39.47 1 44.16 ? C1' ADP 400 B 1 HETATM 18 N N9 ADP . . . E 4 52.963 -32.255 -39.489 1 44.77 ? N9 ADP 400 B 1 HETATM 19 C C8 ADP . . . E 4 52.279 -31.1 -39.48 1 45.78 ? C8 ADP 400 B 1 HETATM 20 N N7 ADP . . . E 4 53.115 -30.031 -39.493 1 42.3 ? N7 ADP 400 B 1 HETATM 21 C C5 ADP . . . E 4 54.367 -30.505 -39.504 1 40.05 ? C5 ADP 400 B 1 HETATM 22 C C6 ADP . . . E 4 55.715 -29.915 -39.523 1 43.56 ? C6 ADP 400 B 1 HETATM 23 N N6 ADP . . . E 4 55.904 -28.574 -39.527 1 46.39 ? N6 ADP 400 B 1 HETATM 24 N N1 ADP . . . E 4 56.753 -30.768 -39.531 1 47.85 ? N1 ADP 400 B 1 HETATM 25 C C2 ADP . . . E 4 56.59 -32.103 -39.518 1 46.96 ? C2 ADP 400 B 1 HETATM 26 N N3 ADP . . . E 4 55.396 -32.708 -39.5 1 44.46 ? N3 ADP 400 B 1 HETATM 27 C C4 ADP . . . E 4 54.265 -31.969 -39.497 1 44.76 ? C4 ADP 400 B 1 # _model_server_stats.io_time_ms 65 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 27 #