data_1KNJ # _model_server_result.job_id AVf64ZkrMCyP9IC8_kmObw _model_server_result.datetime_utc '2024-10-18 22:18:55' _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 1knj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":201}' # _entry.id 1KNJ # _exptl.entry_id 1KNJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 323.197 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "CYTIDINE-5'-MONOPHOSPHATE" _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 1KNJ _cell.length_a 144.254 _cell.length_b 144.254 _cell.length_c 144.254 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1KNJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 199 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 21 3' # _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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' 5_555 z,x,y 0 0 1 1 0 0 0 1 0 0 0 0 3 'crystal symmetry operation' 9_555 y,z,x 0 1 0 0 0 1 1 0 0 0 0 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 covale ? covale1 A C MSE 1 A MSE 1 1_555 A N ARG 2 A ARG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale2 A C LYS 104 A LYS 104 1_555 A N MSE 105 A MSE 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale3 A C MSE 105 A MSE 105 1_555 A N LEU 106 A LEU 106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale4 A C GLN 111 A GLN 111 1_555 A N MSE 112 A MSE 112 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? covale ? covale5 A C MSE 112 A MSE 112 1_555 A N ARG 113 A ARG 113 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale6 A C HIS 123 A HIS 123 1_555 A N MSE 124 A MSE 124 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale7 A C MSE 124 A MSE 124 1_555 A N ASP 125 A ASP 125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? metalc ? metalc1 A OD1 ASP 8 A ASP 8 1_555 B MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.487 ? metalc ? metalc2 A OD2 ASP 8 A ASP 8 1_555 B MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? # _chem_comp.formula 'C9 H14 N3 O8 P' _chem_comp.formula_weight 323.197 _chem_comp.id C5P _chem_comp.mon_nstd_flag . _chem_comp.name "CYTIDINE-5'-MONOPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 1KNJ _atom_sites.fract_transf_matrix[1][1] 0.006932 _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] 0.006932 _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] 0.006932 _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 MN A 1 401 1 MN MN . C 3 C5P A 1 201 1 C5P C5P . D 4 CDI A 1 301 1 CDI PBB . E 5 HOH A 1 402 1 HOH HOH . E 5 HOH A 2 403 2 HOH HOH . E 5 HOH A 3 404 3 HOH HOH . E 5 HOH A 4 405 4 HOH HOH . E 5 HOH A 5 406 5 HOH HOH . E 5 HOH A 6 407 6 HOH HOH . E 5 HOH A 7 408 7 HOH HOH . E 5 HOH A 8 409 8 HOH HOH . E 5 HOH A 9 410 9 HOH HOH . E 5 HOH A 10 411 10 HOH HOH . E 5 HOH A 11 412 11 HOH HOH . E 5 HOH A 12 413 12 HOH HOH . E 5 HOH A 13 414 13 HOH HOH . E 5 HOH A 14 415 14 HOH HOH . E 5 HOH A 15 416 15 HOH HOH . E 5 HOH A 16 417 16 HOH HOH . E 5 HOH A 17 418 17 HOH HOH . E 5 HOH A 18 419 18 HOH HOH . E 5 HOH A 19 420 19 HOH HOH . E 5 HOH A 20 421 20 HOH HOH . E 5 HOH A 21 422 21 HOH HOH . E 5 HOH A 22 423 22 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 O O3P C5P . . . C 3 13.428 28.991 9.534 1 98.58 ? O3P C5P 201 A 1 HETATM 2 P P C5P . . . C 3 11.993 28.876 9.161 1 98.07 ? P C5P 201 A 1 HETATM 3 O O1P C5P . . . C 3 11.666 28.999 7.719 1 97.51 ? O1P C5P 201 A 1 HETATM 4 O O2P C5P . . . C 3 11.448 27.52 9.708 1 97.51 ? O2P C5P 201 A 1 HETATM 5 O O5' C5P . . . C 3 11.194 30.008 9.988 1 96.04 ? O5' C5P 201 A 1 HETATM 6 C C5' C5P . . . C 3 11.497 31.404 9.69 1 90.13 ? C5' C5P 201 A 1 HETATM 7 C C4' C5P . . . C 3 10.718 32.388 10.539 1 85.38 ? C4' C5P 201 A 1 HETATM 8 O O4' C5P . . . C 3 9.324 32.029 10.795 1 81.8 ? O4' C5P 201 A 1 HETATM 9 C C3' C5P . . . C 3 11.354 32.75 11.892 1 84.35 ? C3' C5P 201 A 1 HETATM 10 O O3' C5P . . . C 3 11.452 34.122 12.096 1 86.71 ? O3' C5P 201 A 1 HETATM 11 C C2' C5P . . . C 3 10.514 32.049 12.929 1 82.93 ? C2' C5P 201 A 1 HETATM 12 O O2' C5P . . . C 3 10.447 32.739 14.161 1 84.43 ? O2' C5P 201 A 1 HETATM 13 C C1' C5P . . . C 3 9.149 31.889 12.244 1 80.85 ? C1' C5P 201 A 1 HETATM 14 N N1 C5P . . . C 3 8.488 30.661 12.684 1 76.65 ? N1 C5P 201 A 1 HETATM 15 C C2 C5P . . . C 3 7.304 30.811 13.484 1 72.93 ? C2 C5P 201 A 1 HETATM 16 N N3 C5P . . . C 3 6.6 29.744 13.947 1 72.02 ? N3 C5P 201 A 1 HETATM 17 C C4 C5P . . . C 3 6.985 28.447 13.696 1 72.51 ? C4 C5P 201 A 1 HETATM 18 C C5 C5P . . . C 3 8.131 28.254 12.928 1 72.42 ? C5 C5P 201 A 1 HETATM 19 C C6 C5P . . . C 3 8.883 29.252 12.428 1 74.23 ? C6 C5P 201 A 1 HETATM 20 O O2 C5P . . . C 3 6.868 32.048 13.774 1 70.6 ? O2 C5P 201 A 1 HETATM 21 N N4 C5P . . . C 3 6.234 27.433 14.194 1 72.93 ? N4 C5P 201 A 1 # _model_server_stats.io_time_ms 41 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 360 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 21 #