data_1TUM # _model_server_result.job_id K7YMqZv1HYEnz1hjsEeeyw _model_server_result.datetime_utc '2024-11-13 16:35:54' _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 1tum # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":130}' # _entry.id 1TUM # _exptl.entry_id 1TUM _exptl.method 'SOLUTION NMR' # _entity.details ? _entity.formula_weight 505.208 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER' _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 1TUM _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1TUM _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 ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_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 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 3 _struct_asym.id C _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 A O GLY 38 A GLY 38 1_555 B MG MG . A MG 132 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.465 ? metalc ? metalc2 A OE2 GLU 56 A GLU 56 1_555 B MG MG . A MG 132 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.447 ? metalc ? metalc3 A OE2 GLU 57 A GLU 57 1_555 B MG MG . A MG 132 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.434 ? metalc ? metalc4 A OE1 GLU 98 A GLU 98 1_555 B MG MG . A MG 132 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.434 ? metalc ? metalc5 C O1G APC . A APC 130 1_555 D CO CON . A CON 131 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? metalc ? metalc6 C O1B APC . A APC 130 1_555 D CO CON . A CON 131 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? metalc ? metalc7 B MG MG . A MG 132 1_555 E O HOH . A HOH 133 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? metalc ? metalc8 B MG MG . A MG 132 1_555 E O HOH . A HOH 134 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.114 ? # _chem_comp.formula 'C11 H18 N5 O12 P3' _chem_comp.formula_weight 505.208 _chem_comp.id APC _chem_comp.mon_nstd_flag . _chem_comp.name 'DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE" # 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 PG O1G APC doub 13 n n PG O2G APC sing 14 n n PG O3G APC sing 15 n n PG O3B APC sing 16 n n O2G HOG2 APC sing 17 n n O3G HOG3 APC sing 18 n n PB O1B APC doub 19 n n PB O2B APC sing 20 n n PB O3B APC sing 21 n n PB C3A APC sing 22 n n O2B HOB2 APC sing 23 n n PA O1A APC doub 24 n n PA O2A APC sing 25 n n PA C3A APC sing 26 n n PA O5' APC sing 27 n n O2A HOA2 APC sing 28 n n C3A H3A1 APC sing 29 n n C3A H3A2 APC sing 30 n n O5' C5' APC sing 31 n n C5' C4' APC sing 32 n n C5' "H5'1" APC sing 33 n n C5' "H5'2" APC sing 34 n n C4' O4' APC sing 35 n n C4' C3' APC sing 36 n n C4' H4' APC sing 37 n n O4' C1' APC sing 38 n n C3' O3' APC sing 39 n n C3' C2' APC sing 40 n n C3' H3' APC sing 41 n n O3' HO3' APC sing 42 n n C2' O2' APC sing 43 n n C2' C1' APC sing 44 n n C2' H2' APC sing 45 n n O2' HO2' APC sing 46 n n C1' N9 APC sing 47 n n C1' H1' APC sing 48 n n N9 C8 APC sing 49 n y N9 C4 APC sing 50 n y C8 N7 APC doub 51 n y C8 H8 APC sing 52 n n N7 C5 APC sing 53 n y C5 C6 APC sing 54 n y C5 C4 APC doub 55 n y C6 N6 APC sing 56 n n C6 N1 APC doub 57 n y N6 HN61 APC sing 58 n n N6 HN62 APC sing 59 n n N1 C2 APC sing 60 n y C2 N3 APC doub 61 n y C2 H2 APC sing 62 n n N3 C4 APC sing 63 n y # _atom_sites.entry_id 1TUM _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 B 2 MG A 1 132 132 MG MO2 . C 3 APC A 1 130 130 APC APC . D 4 CON A 1 131 131 CON CON . E 5 HOH A 1 133 132 HOH MO2 . E 5 HOH A 2 134 132 HOH MO2 . # 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 PG APC . . . C 3 7.768 -0.402 8.551 1 0 ? PG APC 130 A 1 HETATM 2 O O1G APC . . . C 3 7.66 -0.011 10.107 1 0 ? O1G APC 130 A 1 HETATM 3 O O2G APC . . . C 3 7.42 -1.823 8.337 1 0 ? O2G APC 130 A 1 HETATM 4 O O3G APC . . . C 3 6.819 0.537 7.65 1 0 ? O3G APC 130 A 1 HETATM 5 P PB APC . . . C 3 10.443 0.812 8.526 1 0 ? PB APC 130 A 1 HETATM 6 O O1B APC . . . C 3 10.493 0.775 10.136 1 0 ? O1B APC 130 A 1 HETATM 7 O O2B APC . . . C 3 11.719 0.291 7.985 1 0 ? O2B APC 130 A 1 HETATM 8 O O3B APC . . . C 3 9.248 -0.122 7.982 1 0 ? O3B APC 130 A 1 HETATM 9 P PA APC . . . C 3 11.514 2.952 8.221 1 0 ? PA APC 130 A 1 HETATM 10 O O1A APC . . . C 3 12.422 2.562 7.12 1 0 ? O1A APC 130 A 1 HETATM 11 O O2A APC . . . C 3 11.981 2.768 9.613 1 0 ? O2A APC 130 A 1 HETATM 12 C C3A APC . . . C 3 10.24 2.205 8.067 1 0 ? C3A APC 130 A 1 HETATM 13 O O5' APC . . . C 3 11.217 4.522 8.037 1 0 ? O5' APC 130 A 1 HETATM 14 C C5' APC . . . C 3 10.088 4.968 7.287 1 0 ? C5' APC 130 A 1 HETATM 15 C C4' APC . . . C 3 9.169 5.837 8.141 1 0 ? C4' APC 130 A 1 HETATM 16 O O4' APC . . . C 3 8.566 6.898 7.374 1 0 ? O4' APC 130 A 1 HETATM 17 C C3' APC . . . C 3 8.049 5.005 8.722 1 0 ? C3' APC 130 A 1 HETATM 18 O O3' APC . . . C 3 8.311 4.663 10.086 1 0 ? O3' APC 130 A 1 HETATM 19 C C2' APC . . . C 3 6.803 5.84 8.597 1 0 ? C2' APC 130 A 1 HETATM 20 O O2' APC . . . C 3 6.341 6.27 9.878 1 0 ? O2' APC 130 A 1 HETATM 21 C C1' APC . . . C 3 7.172 7.028 7.726 1 0 ? C1' APC 130 A 1 HETATM 22 N N9 APC . . . C 3 6.31 7.044 6.533 1 0 ? N9 APC 130 A 1 HETATM 23 C C8 APC . . . C 3 6.104 6.075 5.608 1 0 ? C8 APC 130 A 1 HETATM 24 N N7 APC . . . C 3 5.211 6.302 4.703 1 0 ? N7 APC 130 A 1 HETATM 25 C C5 APC . . . C 3 4.766 7.578 5.05 1 0 ? C5 APC 130 A 1 HETATM 26 C C6 APC . . . C 3 3.807 8.432 4.493 1 0 ? C6 APC 130 A 1 HETATM 27 N N6 APC . . . C 3 3.087 8.12 3.416 1 0 ? N6 APC 130 A 1 HETATM 28 N N1 APC . . . C 3 3.627 9.625 5.081 1 0 ? N1 APC 130 A 1 HETATM 29 C C2 APC . . . C 3 4.342 9.965 6.153 1 0 ? C2 APC 130 A 1 HETATM 30 N N3 APC . . . C 3 5.267 9.233 6.768 1 0 ? N3 APC 130 A 1 HETATM 31 C C4 APC . . . C 3 5.434 8.041 6.16 1 0 ? C4 APC 130 A 1 HETATM 32 H HOG3 APC . . . C 3 6.162 -0.03 7.239 1 0 ? HOG3 APC 130 A 1 HETATM 33 H H3A1 APC . . . C 3 9.931 2.203 7.02 1 0 ? H3A1 APC 130 A 1 HETATM 34 H H3A2 APC . . . C 3 9.465 2.68 8.67 1 0 ? H3A2 APC 130 A 1 HETATM 35 H "H5'1" APC . . . C 3 9.531 4.101 6.931 1 0 ? "H5'1" APC 130 A 1 HETATM 36 H "H5'2" APC . . . C 3 10.438 5.54 6.433 1 0 ? "H5'2" APC 130 A 1 HETATM 37 H H4' APC . . . C 3 9.749 6.271 8.953 1 0 ? H4' APC 130 A 1 HETATM 38 H H3' APC . . . C 3 7.937 4.101 8.121 1 0 ? H3' APC 130 A 1 HETATM 39 H HO3' APC . . . C 3 8.112 5.383 10.689 1 0 ? HO3' APC 130 A 1 HETATM 40 H H2' APC . . . C 3 6.024 5.256 8.101 1 0 ? H2' APC 130 A 1 HETATM 41 H HO2' APC . . . C 3 5.39 6.146 9.889 1 0 ? HO2' APC 130 A 1 HETATM 42 H H1' APC . . . C 3 7.023 7.95 8.288 1 0 ? H1' APC 130 A 1 HETATM 43 H H8 APC . . . C 3 6.685 5.144 5.616 1 0 ? H8 APC 130 A 1 HETATM 44 H HN61 APC . . . C 3 3.219 7.229 2.96 1 0 ? HN61 APC 130 A 1 HETATM 45 H HN62 APC . . . C 3 2.408 8.776 3.057 1 0 ? HN62 APC 130 A 1 HETATM 46 H H2 APC . . . C 3 4.164 10.96 6.553 1 0 ? H2 APC 130 A 1 # _model_server_stats.io_time_ms 64 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 62 _model_server_stats.query_time_ms 4548 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 46 #