data_5U03 # _model_server_result.job_id n_EBx5E6VccmOYW0y48iXw _model_server_result.datetime_utc '2024-10-28 14:26:55' _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 5u03 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":601}' # _entry.id 5U03 # _exptl.entry_id 5U03 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 507.181 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-TRIPHOSPHATE" _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? hexadecameric 16 'representative helical assembly' 1 ? tetrameric 4 'helical asymmetric unit' 2 ? tetrameric 4 'helical asymmetric unit, std helical frame' 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I,J,K,L 1 (1-4) A,B,C,D,E,F,G,H,I,J,K,L 2 3 A,B,C,D,E,F,G,H,I,J,K,L 3 H # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] H 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 1 'helical symmetry operation' ? ? -0.518027 0.855364 0 -0.855364 -0.518027 0 0 0 1 0 0 -208.2 2 'helical symmetry operation' ? ? 0.490904 0.871214 0 -0.871214 0.490904 0 0 0 1 0 0 -104.1 3 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 4 'helical symmetry operation' ? ? 0.490904 -0.871214 0 0.871214 0.490904 0 0 0 1 0 0 104.1 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 E N N ? 2 G N N ? 2 I N N ? 2 K 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 disulf ? disulf1 A SG CYS 218 A CYS 218 1_555 A SG CYS 243 A CYS 243 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? disulf ? disulf2 B SG CYS 218 B CYS 218 1_555 B SG CYS 243 B CYS 243 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? disulf ? disulf3 C SG CYS 218 C CYS 218 1_555 C SG CYS 243 C CYS 243 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? disulf ? disulf4 D SG CYS 218 D CYS 218 1_555 D SG CYS 243 D CYS 243 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? # _chem_comp.formula 'C10 H16 N5 O13 P3' _chem_comp.formula_weight 507.181 _chem_comp.id ATP _chem_comp.mon_nstd_flag . _chem_comp.name "ADENOSINE-5'-TRIPHOSPHATE" _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 PG O1G ATP doub 70 n n PG O2G ATP sing 71 n n PG O3G ATP sing 72 n n PG O3B ATP sing 73 n n O2G HOG2 ATP sing 74 n n O3G HOG3 ATP sing 75 n n PB O1B ATP doub 76 n n PB O2B ATP sing 77 n n PB O3B ATP sing 78 n n PB O3A ATP sing 79 n n O2B HOB2 ATP sing 80 n n PA O1A ATP doub 81 n n PA O2A ATP sing 82 n n PA O3A ATP sing 83 n n PA O5' ATP sing 84 n n O2A HOA2 ATP sing 85 n n O5' C5' ATP sing 86 n n C5' C4' ATP sing 87 n n C5' "H5'1" ATP sing 88 n n C5' "H5'2" ATP sing 89 n n C4' O4' ATP sing 90 n n C4' C3' ATP sing 91 n n C4' H4' ATP sing 92 n n O4' C1' ATP sing 93 n n C3' O3' ATP sing 94 n n C3' C2' ATP sing 95 n n C3' H3' ATP sing 96 n n O3' HO3' ATP sing 97 n n C2' O2' ATP sing 98 n n C2' C1' ATP sing 99 n n C2' H2' ATP sing 100 n n O2' HO2' ATP sing 101 n n C1' N9 ATP sing 102 n n C1' H1' ATP sing 103 n n N9 C8 ATP sing 104 n y N9 C4 ATP sing 105 n y C8 N7 ATP doub 106 n y C8 H8 ATP sing 107 n n N7 C5 ATP sing 108 n y C5 C6 ATP sing 109 n y C5 C4 ATP doub 110 n y C6 N6 ATP sing 111 n n C6 N1 ATP doub 112 n y N6 HN61 ATP sing 113 n n N6 HN62 ATP sing 114 n n N1 C2 ATP sing 115 n y C2 N3 ATP doub 116 n y C2 H2 ATP sing 117 n n N3 C4 ATP sing 118 n y # _atom_sites.entry_id 5U03 _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 E 2 ATP A 1 601 602 ATP ATP . F 3 UTP A 1 602 603 UTP UTP . G 2 ATP B 1 601 602 ATP ATP . H 3 UTP B 1 602 603 UTP UTP . I 2 ATP C 1 601 602 ATP ATP . J 3 UTP C 1 602 603 UTP UTP . K 2 ATP D 1 601 602 ATP ATP . L 3 UTP D 1 602 603 UTP UTP . # 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 ATP . . . I 2 -16.277 2.425 40.958 1 146.53 ? PG ATP 601 C 1 HETATM 2 O O1G ATP . . . I 2 -16.368 1.262 39.948 1 145.94 ? O1G ATP 601 C 1 HETATM 3 O O2G ATP . . . I 2 -16.531 1.857 42.376 1 146.99 ? O2G ATP 601 C 1 HETATM 4 O O3G ATP . . . I 2 -17.22 3.53 40.6 1 147.01 ? O3G ATP 601 C 1 HETATM 5 P PB ATP . . . I 2 -14.256 4.712 41.272 1 143.93 ? PB ATP 601 C 1 HETATM 6 O O1B ATP . . . I 2 -12.814 5.039 40.776 1 144.88 ? O1B ATP 601 C 1 HETATM 7 O O2B ATP . . . I 2 -15.2 5.776 40.776 1 143.72 ? O2B ATP 601 C 1 HETATM 8 O O3B ATP . . . I 2 -14.566 2.98 40.901 1 145.5 ? O3B ATP 601 C 1 HETATM 9 P PA ATP . . . I 2 -15.318 4.742 43.966 1 140.31 ? PA ATP 601 C 1 HETATM 10 O O1A ATP . . . I 2 -16.282 3.649 43.705 1 141.75 ? O1A ATP 601 C 1 HETATM 11 O O2A ATP . . . I 2 -16.05 6.056 43.983 1 139.91 ? O2A ATP 601 C 1 HETATM 12 O O3A ATP . . . I 2 -14.201 4.785 42.833 1 141.73 ? O3A ATP 601 C 1 HETATM 13 O O5' ATP . . . I 2 -14.473 4.648 45.337 1 138.64 ? O5' ATP 601 C 1 HETATM 14 C C5' ATP . . . I 2 -13.611 3.516 45.597 1 136.79 ? C5' ATP 601 C 1 HETATM 15 C C4' ATP . . . I 2 -13.216 3.512 47.052 1 135.25 ? C4' ATP 601 C 1 HETATM 16 O O4' ATP . . . I 2 -12.123 4.431 47.263 1 134.62 ? O4' ATP 601 C 1 HETATM 17 C C3' ATP . . . I 2 -14.311 3.887 48.054 1 135.09 ? C3' ATP 601 C 1 HETATM 18 O O3' ATP . . . I 2 -14.355 2.946 49.121 1 136.64 ? O3' ATP 601 C 1 HETATM 19 C C2' ATP . . . I 2 -13.913 5.298 48.505 1 134.68 ? C2' ATP 601 C 1 HETATM 20 O O2' ATP . . . I 2 -14.297 5.584 49.846 1 135.43 ? O2' ATP 601 C 1 HETATM 21 C C1' ATP . . . I 2 -12.396 5.234 48.389 1 135.03 ? C1' ATP 601 C 1 HETATM 22 N N9 ATP . . . I 2 -11.74 6.529 48.212 1 135.24 ? N9 ATP 601 C 1 HETATM 23 C C8 ATP . . . I 2 -11.618 7.247 47.051 1 134.23 ? C8 ATP 601 C 1 HETATM 24 N N7 ATP . . . I 2 -10.906 8.342 47.168 1 134.01 ? N7 ATP 601 C 1 HETATM 25 C C5 ATP . . . I 2 -10.544 8.356 48.505 1 134.72 ? C5 ATP 601 C 1 HETATM 26 C C6 ATP . . . I 2 -9.808 9.271 49.28 1 135.74 ? C6 ATP 601 C 1 HETATM 27 N N6 ATP . . . I 2 -9.287 10.402 48.795 1 136.79 ? N6 ATP 601 C 1 HETATM 28 N N1 ATP . . . I 2 -9.649 8.998 50.595 1 136.2 ? N1 ATP 601 C 1 HETATM 29 C C2 ATP . . . I 2 -10.207 7.891 51.096 1 135.97 ? C2 ATP 601 C 1 HETATM 30 N N3 ATP . . . I 2 -10.927 6.958 50.467 1 135.41 ? N3 ATP 601 C 1 HETATM 31 C C4 ATP . . . I 2 -11.058 7.246 49.163 1 135.19 ? C4 ATP 601 C 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 29 _model_server_stats.query_time_ms 264 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 31 #