data_4JT2 # _model_server_result.job_id UPyc_kgY2S_Wj_W-Qe4lYw _model_server_result.datetime_utc '2024-11-22 00:59:13' _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 4jt2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1001}' # _entry.id 4JT2 # _exptl.entry_id 4JT2 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 483.156 _entity.id 3 _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 90 _cell.entry_id 4JT2 _cell.length_a 45.306 _cell.length_b 66.781 _cell.length_c 119.546 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4JT2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 E 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 covale ? covale1 A C SER 1 A SER 0 1_555 A N MSE 2 A MSE 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale2 A C MSE 2 A MSE 1 1_555 A N LYS 3 A LYS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale3 A C LEU 44 A LEU 43 1_555 A N MSE 45 A MSE 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale4 A C MSE 45 A MSE 44 1_555 A N SER 46 A SER 45 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale5 A C GLN 137 A GLN 136 1_555 A N MSE 138 A MSE 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale6 A C MSE 138 A MSE 137 1_555 A N LYS 139 A LYS 138 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale7 B C SER 1 B SER 0 1_555 B N MSE 2 B MSE 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale8 B C MSE 2 B MSE 1 1_555 B N LYS 3 B LYS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale9 B C LEU 44 B LEU 43 1_555 B N MSE 45 B MSE 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale10 B C MSE 45 B MSE 44 1_555 B N SER 46 B SER 45 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale11 B C GLN 137 B GLN 136 1_555 B N MSE 138 B MSE 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale12 B C MSE 138 B MSE 137 1_555 B N LYS 139 B LYS 138 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? metalc ? metalc1 A OG SER 23 A SER 22 1_555 C MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.194 ? metalc ? metalc2 C MG MG . A MG 201 1_555 D O3G CTP . A CTP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.844 ? metalc ? metalc3 C MG MG . A MG 201 1_555 D O2B CTP . A CTP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.973 ? metalc ? metalc4 C MG MG . A MG 201 1_555 G O HOH . A HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.977 ? metalc ? metalc5 C MG MG . A MG 201 1_555 G O HOH . A HOH 330 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? metalc ? metalc6 C MG MG . A MG 201 1_555 G O HOH . A HOH 366 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.852 ? metalc ? metalc7 B OG SER 23 B SER 22 1_555 F MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? metalc ? metalc8 E O2B CTP . B CTP 1001 1_555 F MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.935 ? metalc ? metalc9 E O3G CTP . B CTP 1001 1_555 F MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.972 ? metalc ? metalc10 F MG MG . B MG 1002 1_555 H O HOH . B HOH 1122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? metalc ? metalc11 F MG MG . B MG 1002 1_555 H O HOH . B HOH 1144 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? metalc ? metalc12 F MG MG . B MG 1002 1_555 H O HOH . B HOH 1146 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? # _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 4JT2 _atom_sites.fract_transf_matrix[1][1] 0.022072 _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] 0.014974 _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] 0.008365 _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 2 MG A 1 201 1002 MG MG . D 3 CTP A 1 202 1001 CTP CTP . E 3 CTP B 1 1001 1001 CTP CTP . F 2 MG B 1 1002 1002 MG MG . G 4 HOH A 1 301 2 HOH HOH . G 4 HOH A 2 302 5 HOH HOH . G 4 HOH A 3 303 6 HOH HOH . G 4 HOH A 4 304 9 HOH HOH . G 4 HOH A 5 305 11 HOH HOH . G 4 HOH A 6 306 12 HOH HOH . G 4 HOH A 7 307 13 HOH HOH . G 4 HOH A 8 308 14 HOH HOH . G 4 HOH A 9 309 15 HOH HOH . G 4 HOH A 10 310 17 HOH HOH . G 4 HOH A 11 311 18 HOH HOH . G 4 HOH A 12 312 19 HOH HOH . G 4 HOH A 13 313 22 HOH HOH . G 4 HOH A 14 314 24 HOH HOH . G 4 HOH A 15 315 25 HOH HOH . G 4 HOH A 16 316 26 HOH HOH . G 4 HOH A 17 317 27 HOH HOH . G 4 HOH A 18 318 28 HOH HOH . G 4 HOH A 19 319 29 HOH HOH . G 4 HOH A 20 320 30 HOH HOH . G 4 HOH A 21 321 35 HOH HOH . G 4 HOH A 22 322 39 HOH HOH . G 4 HOH A 23 323 40 HOH HOH . G 4 HOH A 24 324 41 HOH HOH . G 4 HOH A 25 325 42 HOH HOH . G 4 HOH A 26 326 43 HOH HOH . G 4 HOH A 27 327 47 HOH HOH . G 4 HOH A 28 328 49 HOH HOH . G 4 HOH A 29 329 50 HOH HOH . G 4 HOH A 30 330 51 HOH HOH . G 4 HOH A 31 331 52 HOH HOH . G 4 HOH A 32 332 54 HOH HOH . G 4 HOH A 33 333 55 HOH HOH . G 4 HOH A 34 334 56 HOH HOH . G 4 HOH A 35 335 58 HOH HOH . G 4 HOH A 36 336 62 HOH HOH . G 4 HOH A 37 337 63 HOH HOH . G 4 HOH A 38 338 66 HOH HOH . G 4 HOH A 39 339 67 HOH HOH . G 4 HOH A 40 340 69 HOH HOH . G 4 HOH A 41 341 71 HOH HOH . G 4 HOH A 42 342 76 HOH HOH . G 4 HOH A 43 343 77 HOH HOH . G 4 HOH A 44 344 80 HOH HOH . G 4 HOH A 45 345 81 HOH HOH . G 4 HOH A 46 346 82 HOH HOH . G 4 HOH A 47 347 83 HOH HOH . G 4 HOH A 48 348 86 HOH HOH . G 4 HOH A 49 349 88 HOH HOH . G 4 HOH A 50 350 91 HOH HOH . G 4 HOH A 51 351 94 HOH HOH . G 4 HOH A 52 352 97 HOH HOH . G 4 HOH A 53 353 102 HOH HOH . G 4 HOH A 54 354 103 HOH HOH . G 4 HOH A 55 355 105 HOH HOH . G 4 HOH A 56 356 107 HOH HOH . G 4 HOH A 57 357 109 HOH HOH . G 4 HOH A 58 358 110 HOH HOH . G 4 HOH A 59 359 112 HOH HOH . G 4 HOH A 60 360 116 HOH HOH . G 4 HOH A 61 361 117 HOH HOH . G 4 HOH A 62 362 121 HOH HOH . G 4 HOH A 63 363 122 HOH HOH . G 4 HOH A 64 364 123 HOH HOH . G 4 HOH A 65 365 125 HOH HOH . G 4 HOH A 66 366 126 HOH HOH . H 4 HOH B 1 1101 1 HOH HOH . H 4 HOH B 2 1102 3 HOH HOH . H 4 HOH B 3 1103 4 HOH HOH . H 4 HOH B 4 1104 7 HOH HOH . H 4 HOH B 5 1105 8 HOH HOH . H 4 HOH B 6 1106 10 HOH HOH . H 4 HOH B 7 1107 16 HOH HOH . H 4 HOH B 8 1108 20 HOH HOH . H 4 HOH B 9 1109 21 HOH HOH . H 4 HOH B 10 1110 23 HOH HOH . H 4 HOH B 11 1111 31 HOH HOH . H 4 HOH B 12 1112 32 HOH HOH . H 4 HOH B 13 1113 33 HOH HOH . H 4 HOH B 14 1114 34 HOH HOH . H 4 HOH B 15 1115 36 HOH HOH . H 4 HOH B 16 1116 37 HOH HOH . H 4 HOH B 17 1117 38 HOH HOH . H 4 HOH B 18 1118 44 HOH HOH . H 4 HOH B 19 1119 45 HOH HOH . H 4 HOH B 20 1120 46 HOH HOH . H 4 HOH B 21 1121 48 HOH HOH . H 4 HOH B 22 1122 53 HOH HOH . H 4 HOH B 23 1123 57 HOH HOH . H 4 HOH B 24 1124 59 HOH HOH . H 4 HOH B 25 1125 60 HOH HOH . H 4 HOH B 26 1126 61 HOH HOH . H 4 HOH B 27 1127 64 HOH HOH . H 4 HOH B 28 1128 65 HOH HOH . H 4 HOH B 29 1129 68 HOH HOH . H 4 HOH B 30 1130 70 HOH HOH . H 4 HOH B 31 1131 72 HOH HOH . H 4 HOH B 32 1132 73 HOH HOH . H 4 HOH B 33 1133 74 HOH HOH . H 4 HOH B 34 1134 75 HOH HOH . H 4 HOH B 35 1135 78 HOH HOH . H 4 HOH B 36 1136 79 HOH HOH . H 4 HOH B 37 1137 84 HOH HOH . H 4 HOH B 38 1138 85 HOH HOH . H 4 HOH B 39 1139 87 HOH HOH . H 4 HOH B 40 1140 89 HOH HOH . H 4 HOH B 41 1141 90 HOH HOH . H 4 HOH B 42 1142 92 HOH HOH . H 4 HOH B 43 1143 93 HOH HOH . H 4 HOH B 44 1144 95 HOH HOH . H 4 HOH B 45 1145 96 HOH HOH . H 4 HOH B 46 1146 98 HOH HOH . H 4 HOH B 47 1147 99 HOH HOH . H 4 HOH B 48 1148 100 HOH HOH . H 4 HOH B 49 1149 101 HOH HOH . H 4 HOH B 50 1150 104 HOH HOH . H 4 HOH B 51 1151 106 HOH HOH . H 4 HOH B 52 1152 108 HOH HOH . H 4 HOH B 53 1153 111 HOH HOH . H 4 HOH B 54 1154 113 HOH HOH . H 4 HOH B 55 1155 114 HOH HOH . H 4 HOH B 56 1156 115 HOH HOH . H 4 HOH B 57 1157 118 HOH HOH . H 4 HOH B 58 1158 119 HOH HOH . H 4 HOH B 59 1159 120 HOH HOH . H 4 HOH B 60 1160 124 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 3 14.499 48.124 53.127 1 37.07 ? N1 CTP 1001 B 1 HETATM 2 C C2 CTP . . . E 3 14.129 49.08 54.091 1 29.95 ? C2 CTP 1001 B 1 HETATM 3 N N3 CTP . . . E 3 14.793 49.145 55.261 1 29.42 ? N3 CTP 1001 B 1 HETATM 4 C C4 CTP . . . E 3 15.815 48.29 55.518 1 36.84 ? C4 CTP 1001 B 1 HETATM 5 C C5 CTP . . . E 3 16.188 47.338 54.567 1 35.46 ? C5 CTP 1001 B 1 HETATM 6 C C6 CTP . . . E 3 15.506 47.276 53.359 1 35.24 ? C6 CTP 1001 B 1 HETATM 7 O O2 CTP . . . E 3 13.185 49.868 53.852 1 34.76 ? O2 CTP 1001 B 1 HETATM 8 N N4 CTP . . . E 3 16.476 48.365 56.704 1 27.13 ? N4 CTP 1001 B 1 HETATM 9 C C1' CTP . . . E 3 13.767 48.101 51.867 1 38.19 ? C1' CTP 1001 B 1 HETATM 10 C C2' CTP . . . E 3 14.53 49.016 50.92 1 43.44 ? C2' CTP 1001 B 1 HETATM 11 O O2' CTP . . . E 3 13.855 50.271 50.803 1 56.23 ? O2' CTP 1001 B 1 HETATM 12 C C3' CTP . . . E 3 14.548 48.291 49.595 1 40.6 ? C3' CTP 1001 B 1 HETATM 13 C C4' CTP . . . E 3 13.903 46.939 49.861 1 36.64 ? C4' CTP 1001 B 1 HETATM 14 O O4' CTP . . . E 3 13.737 46.801 51.272 1 33.67 ? O4' CTP 1001 B 1 HETATM 15 O O3' CTP . . . E 3 13.797 49.018 48.615 1 46.56 ? O3' CTP 1001 B 1 HETATM 16 C C5' CTP . . . E 3 14.785 45.818 49.337 1 41.8 ? C5' CTP 1001 B 1 HETATM 17 O O5' CTP . . . E 3 15.774 45.45 50.303 1 37.2 ? O5' CTP 1001 B 1 HETATM 18 P PA CTP . . . E 3 17.062 44.631 49.794 1 31.18 ? PA CTP 1001 B 1 HETATM 19 O O1A CTP . . . E 3 18.251 44.966 50.656 1 33.86 ? O1A CTP 1001 B 1 HETATM 20 O O2A CTP . . . E 3 17.19 44.775 48.298 1 23.44 ? O2A CTP 1001 B 1 HETATM 21 O O3A CTP . . . E 3 16.551 43.143 50.134 1 24.57 ? O3A CTP 1001 B 1 HETATM 22 P PB CTP . . . E 3 17.36 41.852 49.637 1 20.5 ? PB CTP 1001 B 1 HETATM 23 O O1B CTP . . . E 3 17.465 40.928 50.826 1 23.49 ? O1B CTP 1001 B 1 HETATM 24 O O2B CTP . . . E 3 18.621 42.322 48.958 1 27.25 ? O2B CTP 1001 B 1 HETATM 25 O O3B CTP . . . E 3 16.345 41.202 48.555 1 37.74 ? O3B CTP 1001 B 1 HETATM 26 P PG CTP . . . E 3 16.793 40.266 47.302 1 27.78 ? PG CTP 1001 B 1 HETATM 27 O O1G CTP . . . E 3 17.093 38.897 47.866 1 32.98 ? O1G CTP 1001 B 1 HETATM 28 O O2G CTP . . . E 3 15.566 40.299 46.429 1 22.91 ? O2G CTP 1001 B 1 HETATM 29 O O3G CTP . . . E 3 18.002 40.956 46.701 1 27.52 ? O3G CTP 1001 B 1 # _model_server_stats.io_time_ms 49 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 305 _model_server_stats.encode_time_ms 14 _model_server_stats.element_count 29 #