data_2BE9 # _model_server_result.job_id yPXvv4wEIgIp1tMmwm7pcw _model_server_result.datetime_utc '2024-11-05 00:28:31' _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 2be9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":401}' # _entry.id 2BE9 # _exptl.entry_id 2BE9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 483.156 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "CYTIDINE-5'-TRIPHOSPHATE" _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 120 _cell.entry_id 2BE9 _cell.length_a 131.932 _cell.length_b 131.932 _cell.length_c 139.132 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2BE9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 182 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63 2 2' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4,5,6 # 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 1 131.932 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 65.966 114.256464 0 4 'crystal symmetry operation' 10_665 -y+1,-x+1,-z+1/2 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 65.966 114.256464 69.566 5 'crystal symmetry operation' 11_655 -x+y+1,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 131.932 0 69.566 6 'crystal symmetry operation' 12_555 x,x-y,-z+1/2 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 0 0 69.566 # _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 B SG CYS 117 B CYS 113 1_555 C ZN ZN . B ZN 1113 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.231 ? metalc ? metalc2 B SG CYS 122 B CYS 118 1_555 C ZN ZN . B ZN 1113 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.25 ? metalc ? metalc3 B SG CYS 146 B CYS 142 1_555 C ZN ZN . B ZN 1113 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.124 ? metalc ? metalc4 B SG CYS 149 B CYS 145 1_555 C ZN ZN . B ZN 1113 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? # _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 2BE9 _atom_sites.fract_transf_matrix[1][1] 0.00758 _atom_sites.fract_transf_matrix[1][2] 0.004376 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008752 _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] 0.007187 _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 ZN B 1 1113 113 ZN ZN2 . D 4 SO4 B 1 1114 1 SO4 SO4 . E 5 CTP B 1 401 1 CTP CTP . F 6 HOH A 1 300 2 HOH HOH . F 6 HOH A 2 301 4 HOH HOH . F 6 HOH A 3 302 5 HOH HOH . F 6 HOH A 4 303 6 HOH HOH . F 6 HOH A 5 304 9 HOH HOH . F 6 HOH A 6 305 10 HOH HOH . F 6 HOH A 7 306 14 HOH HOH . F 6 HOH A 8 307 15 HOH HOH . F 6 HOH A 9 308 20 HOH HOH . F 6 HOH A 10 309 21 HOH HOH . F 6 HOH A 11 310 22 HOH HOH . F 6 HOH A 12 311 23 HOH HOH . F 6 HOH A 13 312 25 HOH HOH . F 6 HOH A 14 313 26 HOH HOH . F 6 HOH A 15 314 28 HOH HOH . F 6 HOH A 16 315 35 HOH HOH . F 6 HOH A 17 316 37 HOH HOH . F 6 HOH A 18 317 38 HOH HOH . F 6 HOH A 19 318 39 HOH HOH . F 6 HOH A 20 319 40 HOH HOH . F 6 HOH A 21 320 43 HOH HOH . F 6 HOH A 22 321 46 HOH HOH . F 6 HOH A 23 322 50 HOH HOH . F 6 HOH A 24 323 55 HOH HOH . F 6 HOH A 25 324 56 HOH HOH . F 6 HOH A 26 325 61 HOH HOH . F 6 HOH A 27 326 64 HOH HOH . F 6 HOH A 28 327 66 HOH HOH . F 6 HOH A 29 328 70 HOH HOH . F 6 HOH A 30 329 79 HOH HOH . F 6 HOH A 31 330 84 HOH HOH . F 6 HOH A 32 331 89 HOH HOH . F 6 HOH A 33 332 90 HOH HOH . F 6 HOH A 34 333 94 HOH HOH . F 6 HOH A 35 334 95 HOH HOH . F 6 HOH A 36 335 97 HOH HOH . F 6 HOH A 37 336 108 HOH HOH . F 6 HOH A 38 337 119 HOH HOH . F 6 HOH A 39 338 127 HOH HOH . F 6 HOH A 40 339 137 HOH HOH . F 6 HOH A 41 340 152 HOH HOH . F 6 HOH A 42 341 159 HOH HOH . F 6 HOH A 43 342 197 HOH HOH . F 6 HOH A 44 343 200 HOH HOH . F 6 HOH A 45 344 202 HOH HOH . F 6 HOH A 46 345 304 HOH HOH . F 6 HOH A 47 346 305 HOH HOH . F 6 HOH A 48 347 306 HOH HOH . F 6 HOH A 49 348 307 HOH HOH . F 6 HOH A 50 349 309 HOH HOH . F 6 HOH A 51 350 350 HOH HOH . F 6 HOH A 52 351 351 HOH HOH . F 6 HOH A 53 352 352 HOH HOH . F 6 HOH A 54 353 353 HOH HOH . F 6 HOH A 55 354 357 HOH HOH . F 6 HOH A 56 355 358 HOH HOH . F 6 HOH A 57 356 359 HOH HOH . G 6 HOH B 1 1115 3 HOH HOH . G 6 HOH B 2 1116 7 HOH HOH . G 6 HOH B 3 1117 8 HOH HOH . G 6 HOH B 4 1118 24 HOH HOH . G 6 HOH B 5 1119 47 HOH HOH . G 6 HOH B 6 1120 58 HOH HOH . G 6 HOH B 7 1121 102 HOH HOH . G 6 HOH B 8 1122 112 HOH HOH . G 6 HOH B 9 1123 113 HOH HOH . G 6 HOH B 10 1124 115 HOH HOH . G 6 HOH B 11 1125 123 HOH HOH . G 6 HOH B 12 1126 124 HOH HOH . G 6 HOH B 13 1127 131 HOH HOH . G 6 HOH B 14 1128 143 HOH HOH . G 6 HOH B 15 1129 162 HOH HOH . G 6 HOH B 16 1130 218 HOH HOH . G 6 HOH B 17 1131 300 HOH HOH . G 6 HOH B 18 1132 302 HOH HOH . G 6 HOH B 19 1133 355 HOH HOH . G 6 HOH B 20 1134 356 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 N N1 CTP . . . E 5 125.324 65.093 43.426 1 68.52 ? N1 CTP 401 B 1 HETATM 2 C C2 CTP . . . E 5 124.509 66.214 43.403 1 68.74 ? C2 CTP 401 B 1 HETATM 3 N N3 CTP . . . E 5 124.708 67.234 44.319 1 68.78 ? N3 CTP 401 B 1 HETATM 4 C C4 CTP . . . E 5 125.754 67.156 45.218 1 68.89 ? C4 CTP 401 B 1 HETATM 5 C C5 CTP . . . E 5 126.557 66.02 45.255 1 68.72 ? C5 CTP 401 B 1 HETATM 6 C C6 CTP . . . E 5 126.423 65.076 44.244 1 68.29 ? C6 CTP 401 B 1 HETATM 7 O O2 CTP . . . E 5 123.61 66.32 42.572 1 68.06 ? O2 CTP 401 B 1 HETATM 8 N N4 CTP . . . E 5 125.988 68.167 46.04 1 68.68 ? N4 CTP 401 B 1 HETATM 9 C C1' CTP . . . E 5 124.983 63.935 42.566 1 69.5 ? C1' CTP 401 B 1 HETATM 10 C C2' CTP . . . E 5 126.095 63.625 41.571 1 69.42 ? C2' CTP 401 B 1 HETATM 11 O O2' CTP . . . E 5 125.732 64.102 40.3 1 69.88 ? O2' CTP 401 B 1 HETATM 12 C C3' CTP . . . E 5 126.208 62.11 41.625 1 69.94 ? C3' CTP 401 B 1 HETATM 13 C C4' CTP . . . E 5 125.733 61.776 43.023 1 70.54 ? C4' CTP 401 B 1 HETATM 14 O O4' CTP . . . E 5 124.756 62.746 43.321 1 70.18 ? O4' CTP 401 B 1 HETATM 15 O O3' CTP . . . E 5 125.328 61.513 40.695 1 68.55 ? O3' CTP 401 B 1 HETATM 16 C C5' CTP . . . E 5 126.81 62.065 44.045 1 72.49 ? C5' CTP 401 B 1 HETATM 17 O O5' CTP . . . E 5 127.657 60.976 44.26 1 74.37 ? O5' CTP 401 B 1 HETATM 18 P PA CTP . . . E 5 129.182 61.358 44.536 1 75.52 ? PA CTP 401 B 1 HETATM 19 O O1A CTP . . . E 5 129.297 62.861 44.661 1 76.21 ? O1A CTP 401 B 1 HETATM 20 O O2A CTP . . . E 5 129.721 60.634 45.747 1 74.29 ? O2A CTP 401 B 1 HETATM 21 O O3A CTP . . . E 5 129.851 60.924 43.145 1 77.05 ? O3A CTP 401 B 1 HETATM 22 P PB CTP . . . E 5 130.261 59.389 42.914 1 79.43 ? PB CTP 401 B 1 HETATM 23 O O1B CTP . . . E 5 131.313 59.03 43.943 1 79.8 ? O1B CTP 401 B 1 HETATM 24 O O2B CTP . . . E 5 130.738 59.158 41.495 1 79.9 ? O2B CTP 401 B 1 HETATM 25 O O3B CTP . . . E 5 128.918 58.531 43.202 1 79.91 ? O3B CTP 401 B 1 HETATM 26 P PG CTP . . . E 5 128.856 56.915 43.094 1 79.54 ? PG CTP 401 B 1 HETATM 27 O O1G CTP . . . E 5 130.154 56.338 43.622 1 80.2 ? O1G CTP 401 B 1 HETATM 28 O O2G CTP . . . E 5 128.669 56.499 41.649 1 78.88 ? O2G CTP 401 B 1 HETATM 29 O O3G CTP . . . E 5 127.726 56.394 43.964 1 79.71 ? O3G CTP 401 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 29 #