data_6L5Q # _model_server_result.job_id rAy2d182iwCbhMOXBJQw1w _model_server_result.datetime_utc '2024-10-19 11:37:32' _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 6l5q # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 6L5Q # _exptl.entry_id 6L5Q _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 566.302 _entity.id 2 _entity.src_method man _entity.type non-polymer _entity.pdbx_description "GALACTOSE-URIDINE-5'-DIPHOSPHATE" _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 6L5Q _cell.length_a 85.827 _cell.length_b 139.278 _cell.length_c 73.822 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6L5Q _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B _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 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C15 H24 N2 O17 P2' _chem_comp.formula_weight 566.302 _chem_comp.id GDU _chem_comp.mon_nstd_flag . _chem_comp.name "GALACTOSE-URIDINE-5'-DIPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms UDP-D-GALACTOPYRANOSE # 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 GDU sing 83 n n N1 C6 GDU sing 84 n n N1 C1D GDU sing 85 n n C2 N3 GDU sing 86 n n C2 O2 GDU doub 87 n n N3 C4 GDU sing 88 n n N3 HN3 GDU sing 89 n n C4 C5 GDU sing 90 n n C4 O4 GDU doub 91 n n C5 C6 GDU doub 92 n n C5 H5 GDU sing 93 n n C6 H6 GDU sing 94 n n C1D C2D GDU sing 95 n n C1D O4D GDU sing 96 n n C1D H1D GDU sing 97 n n C2D O2D GDU sing 98 n n C2D C3D GDU sing 99 n n C2D H2D GDU sing 100 n n O2D HO2' GDU sing 101 n n C3D C4D GDU sing 102 n n C3D O3D GDU sing 103 n n C3D H3D GDU sing 104 n n C4D O4D GDU sing 105 n n C4D C5D GDU sing 106 n n C4D H4D GDU sing 107 n n O3D HO3' GDU sing 108 n n C5D O5D GDU sing 109 n n C5D "H5'1" GDU sing 110 n n C5D "H5'2" GDU sing 111 n n O5D PA GDU sing 112 n n PA O1A GDU doub 113 n n PA O2A GDU sing 114 n n PA O3A GDU sing 115 n n O2A HOA2 GDU sing 116 n n O3A PB GDU sing 117 n n PB O1B GDU doub 118 n n PB O2B GDU sing 119 n n PB O3B GDU sing 120 n n O2B HOB2 GDU sing 121 n n O3B C1' GDU sing 122 n n C1' C2' GDU sing 123 n n C1' O5' GDU sing 124 n n C1' H1' GDU sing 125 n n C2' C3' GDU sing 126 n n C2' O2' GDU sing 127 n n C2' H2' GDU sing 128 n n C3' C4' GDU sing 129 n n C3' O3' GDU sing 130 n n C3' H3' GDU sing 131 n n C4' C5' GDU sing 132 n n C4' O4' GDU sing 133 n n C4' H4' GDU sing 134 n n C5' C6' GDU sing 135 n n C5' O5' GDU sing 136 n n C5' H5' GDU sing 137 n n C6' O6' GDU sing 138 n n C6' "H6'1" GDU sing 139 n n C6' "H6'2" GDU sing 140 n n O2' HO2A GDU sing 141 n n O3' HO3A GDU sing 142 n n O4' HO4' GDU sing 143 n n O6' HO6' GDU sing 144 n n # _atom_sites.entry_id 6L5Q _atom_sites.fract_transf_matrix[1][1] 0.011651 _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] 0.00718 _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] 0.013546 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # _pdbx_nonpoly_scheme.asym_id B _pdbx_nonpoly_scheme.entity_id 2 _pdbx_nonpoly_scheme.mon_id GDU _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 501 _pdbx_nonpoly_scheme.auth_seq_num 501 _pdbx_nonpoly_scheme.pdb_mon_id GDU _pdbx_nonpoly_scheme.auth_mon_id GDU _pdbx_nonpoly_scheme.pdb_ins_code . # 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 GDU . . . B 2 -17.791 -16.434 -21.052 1 32.3 ? N1 GDU 501 A 1 HETATM 2 C C2 GDU . . . B 2 -16.854 -16.415 -22.068 1 34.02 ? C2 GDU 501 A 1 HETATM 3 N N3 GDU . . . B 2 -17.177 -15.613 -23.133 1 34.58 ? N3 GDU 501 A 1 HETATM 4 C C4 GDU . . . B 2 -18.313 -14.84 -23.279 1 33.34 ? C4 GDU 501 A 1 HETATM 5 C C5 GDU . . . B 2 -19.232 -14.911 -22.18 1 33.39 ? C5 GDU 501 A 1 HETATM 6 C C6 GDU . . . B 2 -18.944 -15.69 -21.127 1 32.86 ? C6 GDU 501 A 1 HETATM 7 O O2 GDU . . . B 2 -15.82 -17.068 -22.029 1 35.91 ? O2 GDU 501 A 1 HETATM 8 O O4 GDU . . . B 2 -18.46 -14.17 -24.301 1 31.78 ? O4 GDU 501 A 1 HETATM 9 C C1D GDU . . . B 2 -17.5 -17.287 -19.885 1 33.07 ? C1D GDU 501 A 1 HETATM 10 C C2D GDU . . . B 2 -17.152 -16.502 -18.621 1 33.83 ? C2D GDU 501 A 1 HETATM 11 O O2D GDU . . . B 2 -15.788 -16.136 -18.609 1 29.44 ? O2D GDU 501 A 1 HETATM 12 C C3D GDU . . . B 2 -17.558 -17.531 -17.561 1 36.83 ? C3D GDU 501 A 1 HETATM 13 C C4D GDU . . . B 2 -18.89 -18.019 -18.151 1 35.63 ? C4D GDU 501 A 1 HETATM 14 O O4D GDU . . . B 2 -18.644 -18.058 -19.581 1 34.61 ? O4D GDU 501 A 1 HETATM 15 O O3D GDU . . . B 2 -16.615 -18.594 -17.518 1 39.07 ? O3D GDU 501 A 1 HETATM 16 C C5D GDU . . . B 2 -20.081 -17.135 -17.877 1 35.03 ? C5D GDU 501 A 1 HETATM 17 O O5D GDU . . . B 2 -20.435 -17.244 -16.476 1 36.13 ? O5D GDU 501 A 1 HETATM 18 P PA GDU . . . B 2 -21.072 -15.978 -15.728 1 38.01 ? PA GDU 501 A 1 HETATM 19 O O1A GDU . . . B 2 -21.33 -16.336 -14.302 1 34.76 ? O1A GDU 501 A 1 HETATM 20 O O2A GDU . . . B 2 -20.233 -14.773 -15.996 1 41.21 ? O2A GDU 501 A 1 HETATM 21 O O3A GDU . . . B 2 -22.476 -15.8 -16.488 1 46.25 ? O3A GDU 501 A 1 HETATM 22 P PB GDU . . . B 2 -23.829 -16.663 -16.524 1 53.23 ? PB GDU 501 A 1 HETATM 23 O O1B GDU . . . B 2 -24.938 -15.833 -17.084 1 52.23 ? O1B GDU 501 A 1 HETATM 24 O O2B GDU . . . B 2 -23.558 -17.978 -17.178 1 53.56 ? O2B GDU 501 A 1 HETATM 25 O O3B GDU . . . B 2 -24.048 -16.856 -14.946 1 59.76 ? O3B GDU 501 A 1 HETATM 26 C C1' GDU . . . B 2 -25.174 -17.43 -14.337 1 64.63 ? C1' GDU 501 A 1 HETATM 27 C C2' GDU . . . B 2 -25.557 -16.536 -13.169 1 68.17 ? C2' GDU 501 A 1 HETATM 28 C C3' GDU . . . B 2 -24.396 -16.466 -12.191 1 68.35 ? C3' GDU 501 A 1 HETATM 29 C C4' GDU . . . B 2 -24.002 -17.86 -11.735 1 66.14 ? C4' GDU 501 A 1 HETATM 30 C C5' GDU . . . B 2 -23.749 -18.765 -12.94 1 64.33 ? C5' GDU 501 A 1 HETATM 31 C C6' GDU . . . B 2 -23.561 -20.208 -12.542 1 62.23 ? C6' GDU 501 A 1 HETATM 32 O O2' GDU . . . B 2 -25.915 -15.241 -13.646 1 69.66 ? O2' GDU 501 A 1 HETATM 33 O O3' GDU . . . B 2 -24.739 -15.655 -11.067 1 69.15 ? O3' GDU 501 A 1 HETATM 34 O O4' GDU . . . B 2 -25.043 -18.425 -10.943 1 67.09 ? O4' GDU 501 A 1 HETATM 35 O O5' GDU . . . B 2 -24.868 -18.728 -13.859 1 64.87 ? O5' GDU 501 A 1 HETATM 36 O O6' GDU . . . B 2 -24.693 -20.685 -11.819 1 61.67 ? O6' GDU 501 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 255 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 36 #