data_8AT1 # _model_server_result.job_id rcl2BDrTTKk7esO0tHekHQ _model_server_result.datetime_utc '2025-01-11 07:50:17' _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 8at1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":155}' # _entry.id 8AT1 # _exptl.entry_id 8AT1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 483.156 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "CYTIDINE-5'-TRIPHOSPHATE" _entity.pdbx_number_of_molecules 2 _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 120 _cell.entry_id 8AT1 _cell.length_a 122.2 _cell.length_b 122.2 _cell.length_c 155.2 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8AT1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 150 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 3 2 1' # _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details dodecameric _pdbx_struct_assembly.oligomeric_count 12 _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,H,I,J,K,L _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # 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] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_655 -y+1,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 122.2 0 0 3 'crystal symmetry operation' 3_665 -x+y+1,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 61.1 105.828304 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 6 I N N ? 6 L N N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 3 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 GLC _pdbx_entity_branch_link.comp_id_2 GLC _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 3 n E GLC 1 E 1 GLC A 312 MAL 3 n E GLC 2 E 2 GLC A 312 MAL 3 n F GLC 1 F 1 GLC C 312 MAL 3 n F GLC 2 F 2 GLC C 312 MAL # 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 E O4 GLC . E GLC 1 1_555 E C1 GLC . E GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.228 sing covale ? covale2 F O4 GLC . F GLC 1 1_555 F C1 GLC . F GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.229 sing metalc ? metalc1 B SG CYS 109 B CYS 109 1_555 H ZN ZN . B ZN 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.353 ? metalc ? metalc2 B SG CYS 114 B CYS 114 1_555 H ZN ZN . B ZN 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? metalc ? metalc3 B SG CYS 138 B CYS 138 1_555 H ZN ZN . B ZN 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.363 ? metalc ? metalc4 B SG CYS 141 B CYS 141 1_555 H ZN ZN . B ZN 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? metalc ? metalc5 D SG CYS 109 D CYS 109 1_555 K ZN ZN . D ZN 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.377 ? metalc ? metalc6 D SG CYS 114 D CYS 114 1_555 K ZN ZN . D ZN 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? metalc ? metalc7 D SG CYS 138 D CYS 138 1_555 K ZN ZN . D ZN 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.318 ? metalc ? metalc8 D SG CYS 141 D CYS 141 1_555 K ZN ZN . D ZN 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? # _chem_comp.formula 'C9 H16 N3 O14 P3' _chem_comp.formula_weight 483.156 _chem_comp.id CTP _chem_comp.mon_nstd_flag . _chem_comp.name "CYTIDINE-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 N1 C2 CTP sing 70 n n N1 C6 CTP sing 71 n n N1 C1' CTP sing 72 n n C2 N3 CTP sing 73 n n C2 O2 CTP doub 74 n n N3 C4 CTP doub 75 n n C4 C5 CTP sing 76 n n C4 N4 CTP sing 77 n n C5 C6 CTP doub 78 n n C5 H5 CTP sing 79 n n C6 H6 CTP sing 80 n n N4 HN41 CTP sing 81 n n N4 HN42 CTP sing 82 n n C1' C2' CTP sing 83 n n C1' O4' CTP sing 84 n n C1' H1' CTP sing 85 n n C2' O2' CTP sing 86 n n C2' C3' CTP sing 87 n n C2' H2' CTP sing 88 n n O2' HO2' CTP sing 89 n n C3' C4' CTP sing 90 n n C3' O3' CTP sing 91 n n C3' H3' CTP sing 92 n n C4' O4' CTP sing 93 n n C4' C5' CTP sing 94 n n C4' H4' CTP sing 95 n n O3' HO3' CTP sing 96 n n C5' O5' CTP sing 97 n n C5' "H5'1" CTP sing 98 n n C5' "H5'2" CTP sing 99 n n O5' PA CTP sing 100 n n PA O1A CTP doub 101 n n PA O2A CTP sing 102 n n PA O3A CTP sing 103 n n O2A HOA2 CTP sing 104 n n O3A PB CTP sing 105 n n PB O1B CTP doub 106 n n PB O2B CTP sing 107 n n PB O3B CTP sing 108 n n O2B HOB2 CTP sing 109 n n O3B PG CTP sing 110 n n PG O1G CTP doub 111 n n PG O2G CTP sing 112 n n PG O3G CTP sing 113 n n O2G HOG2 CTP sing 114 n n O3G HOG3 CTP sing 115 n n # _atom_sites.entry_id 8AT1 _atom_sites.fract_transf_matrix[1][1] 0.008183 _atom_sites.fract_transf_matrix[1][2] 0.004725 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009449 _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] 0.006443 _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 G 4 PCT A 1 311 311 PCT PAM . H 5 ZN B 1 154 109 ZN ZN . I 6 CTP B 1 155 154 CTP CTP . J 4 PCT C 1 311 311 PCT PAM . K 5 ZN D 1 154 109 ZN ZN . L 6 CTP D 1 155 154 CTP CTP . # 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 N N1 CTP . . . I 6 13.394 82.817 26.662 1 54.95 ? N1 CTP 155 B 1 HETATM 2 C C2 CTP . . . I 6 14.187 83.685 27.287 1 54.97 ? C2 CTP 155 B 1 HETATM 3 N N3 CTP . . . I 6 14.576 84.898 26.91 1 54.71 ? N3 CTP 155 B 1 HETATM 4 C C4 CTP . . . I 6 14.126 85.283 25.72 1 54.67 ? C4 CTP 155 B 1 HETATM 5 C C5 CTP . . . I 6 13.277 84.473 24.986 1 54.36 ? C5 CTP 155 B 1 HETATM 6 C C6 CTP . . . I 6 12.944 83.235 25.504 1 54.6 ? C6 CTP 155 B 1 HETATM 7 O O2 CTP . . . I 6 14.63 83.407 28.381 1 55.23 ? O2 CTP 155 B 1 HETATM 8 N N4 CTP . . . I 6 14.53 86.429 25.165 1 55.34 ? N4 CTP 155 B 1 HETATM 9 C C1' CTP . . . I 6 13.209 81.428 27.129 1 55.61 ? C1' CTP 155 B 1 HETATM 10 C C2' CTP . . . I 6 12.08 81.429 28.081 1 56.14 ? C2' CTP 155 B 1 HETATM 11 O O2' CTP . . . I 6 12.691 81.454 29.376 1 55.57 ? O2' CTP 155 B 1 HETATM 12 C C3' CTP . . . I 6 11.283 80.168 27.783 1 56.53 ? C3' CTP 155 B 1 HETATM 13 C C4' CTP . . . I 6 12.011 79.547 26.6 1 57.15 ? C4' CTP 155 B 1 HETATM 14 O O4' CTP . . . I 6 12.888 80.526 26.074 1 56.28 ? O4' CTP 155 B 1 HETATM 15 O O3' CTP . . . I 6 11.344 79.205 28.839 1 56.64 ? O3' CTP 155 B 1 HETATM 16 C C5' CTP . . . I 6 11.055 79.089 25.521 1 58.98 ? C5' CTP 155 B 1 HETATM 17 O O5' CTP . . . I 6 10.686 80.186 24.701 1 61.64 ? O5' CTP 155 B 1 HETATM 18 P PA CTP . . . I 6 9.217 80.892 24.968 1 63.34 ? PA CTP 155 B 1 HETATM 19 O O1A CTP . . . I 6 9.464 82.445 25.11 1 63.75 ? O1A CTP 155 B 1 HETATM 20 O O2A CTP . . . I 6 8.303 80.552 23.721 1 63.63 ? O2A CTP 155 B 1 HETATM 21 O O3A CTP . . . I 6 8.554 80.383 26.392 1 65.62 ? O3A CTP 155 B 1 HETATM 22 P PB CTP . . . I 6 7.46 79.192 26.098 1 68.09 ? PB CTP 155 B 1 HETATM 23 O O1B CTP . . . I 6 6.37 79.676 25.063 1 68.01 ? O1B CTP 155 B 1 HETATM 24 O O2B CTP . . . I 6 6.784 78.826 27.478 1 67.97 ? O2B CTP 155 B 1 HETATM 25 O O3B CTP . . . I 6 8.254 77.894 25.459 1 69.62 ? O3B CTP 155 B 1 HETATM 26 P PG CTP . . . I 6 7.453 76.504 25.815 1 71.05 ? PG CTP 155 B 1 HETATM 27 O O1G CTP . . . I 6 5.902 76.794 25.743 1 70.98 ? O1G CTP 155 B 1 HETATM 28 O O2G CTP . . . I 6 7.891 76.077 27.271 1 71.38 ? O2G CTP 155 B 1 HETATM 29 O O3G CTP . . . I 6 7.874 75.406 24.755 1 71.2 ? O3G CTP 155 B 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 276 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 29 #