data_5KBX # _model_server_result.job_id hVm4cQdJS6vz6pvZyJDf9Q _model_server_result.datetime_utc '2024-12-18 23:05:47' _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 5kbx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":201}' # _entry.id 5KBX # _exptl.entry_id 5KBX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _entity.pdbx_number_of_molecules 3 _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 5KBX _cell.length_a 71.696 _cell.length_b 71.696 _cell.length_c 176.389 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5KBX _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall 'P 4nw 2abw' _symmetry.space_group_name_H-M 'P 43 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 C N N ? 3 E N N ? 3 F 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 B C PHE 58 B PHE 552 1_555 B N MSE 59 B MSE 553 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale2 B C MSE 59 B MSE 553 1_555 B N ASP 60 B ASP 554 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale3 B C GLN 121 B GLN 615 1_555 B N MSE 122 B MSE 616 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale4 B C MSE 122 B MSE 616 1_555 B N ASP 123 B ASP 617 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale5 B C CYS 154 B CYS 648 1_555 B N MSE 155 B MSE 649 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale6 B C MSE 155 B MSE 649 1_555 B N GLN 156 B GLN 650 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? # _chem_comp.formula 'C3 H8 O3' _chem_comp.formula_weight 92.094 _chem_comp.id GOL _chem_comp.mon_nstd_flag . _chem_comp.name GLYCEROL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms GLYCERIN;PROPANE-1,2,3-TRIOL # 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 C1 O1 GOL sing 129 n n C1 C2 GOL sing 130 n n C1 H11 GOL sing 131 n n C1 H12 GOL sing 132 n n O1 HO1 GOL sing 133 n n C2 O2 GOL sing 134 n n C2 C3 GOL sing 135 n n C2 H2 GOL sing 136 n n O2 HO2 GOL sing 137 n n C3 O3 GOL sing 138 n n C3 H31 GOL sing 139 n n C3 H32 GOL sing 140 n n O3 HO3 GOL sing 141 n n # _atom_sites.entry_id 5KBX _atom_sites.fract_transf_matrix[1][1] 0.013948 _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] 0.013948 _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] 0.005669 _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 GOL A 1 201 3 GOL GOL . D 4 PO4 A 1 202 1 PO4 PO4 . E 3 GOL B 1 801 1 GOL GOL . F 3 GOL B 1 802 2 GOL GOL . G 4 PO4 B 1 803 2 PO4 PO4 . H 5 HOH A 1 301 30 HOH HOH . H 5 HOH A 2 302 6 HOH HOH . H 5 HOH A 3 303 21 HOH HOH . H 5 HOH A 4 304 4 HOH HOH . H 5 HOH A 5 305 32 HOH HOH . H 5 HOH A 6 306 15 HOH HOH . H 5 HOH A 7 307 12 HOH HOH . H 5 HOH A 8 308 14 HOH HOH . H 5 HOH A 9 309 22 HOH HOH . H 5 HOH A 10 310 28 HOH HOH . H 5 HOH A 11 311 20 HOH HOH . I 5 HOH B 1 901 13 HOH HOH . I 5 HOH B 2 902 7 HOH HOH . I 5 HOH B 3 903 10 HOH HOH . I 5 HOH B 4 904 1 HOH HOH . I 5 HOH B 5 905 24 HOH HOH . I 5 HOH B 6 906 2 HOH HOH . I 5 HOH B 7 907 9 HOH HOH . I 5 HOH B 8 908 26 HOH HOH . I 5 HOH B 9 909 3 HOH HOH . I 5 HOH B 10 910 23 HOH HOH . I 5 HOH B 11 911 16 HOH HOH . I 5 HOH B 12 912 31 HOH HOH . I 5 HOH B 13 913 8 HOH HOH . I 5 HOH B 14 914 11 HOH HOH . I 5 HOH B 15 915 18 HOH HOH . I 5 HOH B 16 916 25 HOH HOH . I 5 HOH B 17 917 5 HOH HOH . I 5 HOH B 18 918 19 HOH HOH . I 5 HOH B 19 919 29 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 C1 GOL . . . C 3 47.611 56.023 64.06 1 51.02 ? C1 GOL 201 A 1 HETATM 2 O O1 GOL . . . C 3 48.512 56.454 63.088 1 50.37 ? O1 GOL 201 A 1 HETATM 3 C C2 GOL . . . C 3 47.876 56.877 65.321 1 63.99 ? C2 GOL 201 A 1 HETATM 4 O O2 GOL . . . C 3 48.232 58.177 64.997 1 68.48 ? O2 GOL 201 A 1 HETATM 5 C C3 GOL . . . C 3 46.557 56.818 66.128 1 58.96 ? C3 GOL 201 A 1 HETATM 6 O O3 GOL . . . C 3 46.369 55.488 66.499 1 63.2 ? O3 GOL 201 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 242 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 6 #