data_1KNJ # _model_server_result.job_id FovEn0OU0_S3R29Sts6jvg _model_server_result.datetime_utc '2024-11-25 15:29:38' _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":"D","auth_seq_id":301}' # _entry.id 1KNJ # _exptl.entry_id 1KNJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 278.091 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE' _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 4 _struct_asym.id D _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 'C5 H12 O9 P2' _chem_comp.formula_weight 278.091 _chem_comp.id CDI _chem_comp.mon_nstd_flag . _chem_comp.name '2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE' _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 C4 C3 CDI sing 106 n n C4 O2 CDI sing 107 n n C4 HC41 CDI sing 108 n n C4 HC42 CDI sing 109 n n C3 OB4 CDI sing 110 n n C3 C2 CDI sing 111 n n C3 C5 CDI sing 112 n n OB4 PB CDI sing 113 n n PB OB2 CDI sing 114 n n PB OB3 CDI doub 115 n n PB OB1 CDI sing 116 n n OB2 HB2O CDI sing 117 n n PA OA3 CDI sing 118 n n PA OA1 CDI sing 119 n n PA OA2 CDI doub 120 n n PA OB1 CDI sing 121 n n OA3 C1 CDI sing 122 n n OA1 HA1O CDI sing 123 n n C1 C2 CDI sing 124 n n C1 HC11 CDI sing 125 n n C1 HC12 CDI sing 126 n n C2 O1 CDI sing 127 n n C2 HC2 CDI sing 128 n n O1 HO1 CDI sing 129 n n C5 HC51 CDI sing 130 n n C5 HC52 CDI sing 131 n n C5 HC53 CDI sing 132 n n O2 HO2 CDI sing 133 n n # _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 C C4 CDI . . . D 4 14.233 33.256 5.18 1 85.67 ? C4 CDI 301 A 1 HETATM 2 C C3 CDI . . . D 4 15.755 33.158 5.105 1 84.61 ? C3 CDI 301 A 1 HETATM 3 O OB4 CDI . . . D 4 16.227 32.177 4.189 1 85.25 ? OB4 CDI 301 A 1 HETATM 4 P PB CDI . . . D 4 15.75 30.852 4.258 1 84.01 ? PB CDI 301 A 1 HETATM 5 O OB2 CDI . . . D 4 14.378 30.666 3.944 1 83.43 ? OB2 CDI 301 A 1 HETATM 6 O OB3 CDI . . . D 4 16.289 30.269 3.053 1 83.78 ? OB3 CDI 301 A 1 HETATM 7 P PA CDI . . . D 4 15.622 30.009 6.498 1 85.27 ? PA CDI 301 A 1 HETATM 8 O OA3 CDI . . . D 4 16.239 30.785 7.497 1 85.33 ? OA3 CDI 301 A 1 HETATM 9 O OA1 CDI . . . D 4 15.819 28.699 7.049 1 85.55 ? OA1 CDI 301 A 1 HETATM 10 O OA2 CDI . . . D 4 14.205 30.018 6.472 1 85.03 ? OA2 CDI 301 A 1 HETATM 11 C C1 CDI . . . D 4 15.817 32.131 7.564 1 86.18 ? C1 CDI 301 A 1 HETATM 12 C C2 CDI . . . D 4 16.424 33.015 6.481 1 85.35 ? C2 CDI 301 A 1 HETATM 13 O O1 CDI . . . D 4 17.806 32.676 6.314 1 83.99 ? O1 CDI 301 A 1 HETATM 14 C C5 CDI . . . D 4 16.265 34.488 4.494 1 84.56 ? C5 CDI 301 A 1 HETATM 15 O O2 CDI . . . D 4 13.662 33.328 3.87 1 85.21 ? O2 CDI 301 A 1 HETATM 16 O OB1 CDI . . . D 4 16.295 30.02 5.259 1 84.59 ? OB1 CDI 301 A 1 # _model_server_stats.io_time_ms 63 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 16 #