data_2X5Z # _model_server_result.job_id 6kaZsaHWGi8ThxJh91fcNw _model_server_result.datetime_utc '2025-06-25 13:02:45' _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 2x5z # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":601}' # _entry.id 2X5Z # _exptl.entry_id 2X5Z _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 605.341 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE" _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 2X5Z _cell.length_a 84.227 _cell.length_b 96.035 _cell.length_c 217.122 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2X5Z _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 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 _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 ? 2 C N N ? 2 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 metalc ? metalc1 A OD2 ASP 109 A ASP 109 1_555 D MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.348 ? metalc ? metalc2 A OD1 ASP 260 A ASP 260 1_555 D MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.187 ? metalc ? metalc3 C O2A GDD . A GDD 601 1_555 D MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.835 ? metalc ? metalc4 C O3B GDD . A GDD 601 1_555 D MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.96 ? metalc ? metalc5 D MG MG . A MG 602 1_555 F O HOH . A HOH 2016 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.509 ? metalc ? metalc6 D MG MG . A MG 602 1_555 F O HOH . A HOH 2023 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? # _chem_comp.formula 'C16 H25 N5 O16 P2' _chem_comp.formula_weight 605.341 _chem_comp.id GDD _chem_comp.mon_nstd_flag . _chem_comp.name "GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE" _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 N2 C2 GDD sing 83 n n N2 H2N1 GDD sing 84 n n N2 H2N2 GDD sing 85 n n C2 N1 GDD sing 86 n n C2 N3 GDD doub 87 n n N1 C6 GDD sing 88 n n N1 H1 GDD sing 89 n n N3 C4 GDD sing 90 n n C4 C5 GDD doub 91 n y C4 N9 GDD sing 92 n y C5 C6 GDD sing 93 n n C5 N7 GDD sing 94 n y C6 O6 GDD doub 95 n n N7 C8 GDD doub 96 n y C8 N9 GDD sing 97 n y C8 H8 GDD sing 98 n n N9 C1' GDD sing 99 n n C1' C2' GDD sing 100 n n C1' O4' GDD sing 101 n n C1' H1' GDD sing 102 n n C2' O2' GDD sing 103 n n C2' C3' GDD sing 104 n n C2' H2' GDD sing 105 n n O2' HA GDD sing 106 n n C3' O3' GDD sing 107 n n C3' C4' GDD sing 108 n n C3' H3' GDD sing 109 n n O3' HB GDD sing 110 n n C4' O4' GDD sing 111 n n C4' C5' GDD sing 112 n n C4' H4' GDD sing 113 n n C5' O5' GDD sing 114 n n C5' "H5'1" GDD sing 115 n n C5' "H5'2" GDD sing 116 n n O5' PA GDD sing 117 n n PA O1A GDD doub 118 n n PA O2A GDD sing 119 n n PA O3A GDD sing 120 n n O2A HO2A GDD sing 121 n n O3A PB GDD sing 122 n n PB O2B GDD sing 123 n n PB O3B GDD doub 124 n n PB O1B GDD sing 125 n n O2B HO2B GDD sing 126 n n O1B C11 GDD sing 127 n n C11 O51 GDD sing 128 n n C11 C21 GDD sing 129 n n C11 H11 GDD sing 130 n n O51 C51 GDD sing 131 n n C51 C61 GDD sing 132 n n C51 C41 GDD sing 133 n n C51 H51 GDD sing 134 n n C61 O6A GDD sing 135 n n C61 H611 GDD sing 136 n n C61 H612 GDD sing 137 n n O6A H6A GDD sing 138 n n C21 O21 GDD sing 139 n n C21 C31 GDD sing 140 n n C21 H21 GDD sing 141 n n O21 HC GDD sing 142 n n C31 O31 GDD sing 143 n n C31 C41 GDD sing 144 n n C31 H31 GDD sing 145 n n O31 HD GDD sing 146 n n C41 O41 GDD sing 147 n n C41 H41 GDD sing 148 n n O41 HE GDD sing 149 n n # _atom_sites.entry_id 2X5Z _atom_sites.fract_transf_matrix[1][1] 0.011873 _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] 0.010413 _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] 0.004606 _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 GDD A 1 601 601 GDD GDD . D 3 MG A 1 602 602 MG MG . E 2 GDD B 1 601 601 GDD GDD . F 4 HOH A 1 2001 2001 HOH HOH . F 4 HOH A 2 2002 2002 HOH HOH . F 4 HOH A 3 2003 2003 HOH HOH . F 4 HOH A 4 2004 2004 HOH HOH . F 4 HOH A 5 2005 2005 HOH HOH . F 4 HOH A 6 2006 2006 HOH HOH . F 4 HOH A 7 2007 2007 HOH HOH . F 4 HOH A 8 2008 2008 HOH HOH . F 4 HOH A 9 2009 2009 HOH HOH . F 4 HOH A 10 2010 2010 HOH HOH . F 4 HOH A 11 2011 2011 HOH HOH . F 4 HOH A 12 2012 2012 HOH HOH . F 4 HOH A 13 2013 2013 HOH HOH . F 4 HOH A 14 2014 2014 HOH HOH . F 4 HOH A 15 2015 2015 HOH HOH . F 4 HOH A 16 2016 2016 HOH HOH . F 4 HOH A 17 2017 2017 HOH HOH . F 4 HOH A 18 2018 2018 HOH HOH . F 4 HOH A 19 2019 2019 HOH HOH . F 4 HOH A 20 2020 2020 HOH HOH . F 4 HOH A 21 2021 2021 HOH HOH . F 4 HOH A 22 2022 2022 HOH HOH . F 4 HOH A 23 2023 2023 HOH HOH . G 4 HOH B 1 2001 2001 HOH HOH . G 4 HOH B 2 2002 2002 HOH HOH . G 4 HOH B 3 2003 2003 HOH HOH . G 4 HOH B 4 2004 2004 HOH HOH . G 4 HOH B 5 2005 2005 HOH HOH . G 4 HOH B 6 2006 2006 HOH HOH . G 4 HOH B 7 2007 2007 HOH HOH . G 4 HOH B 8 2008 2008 HOH HOH . G 4 HOH B 9 2009 2009 HOH HOH . G 4 HOH B 10 2010 2010 HOH HOH . G 4 HOH B 11 2011 2011 HOH HOH . G 4 HOH B 12 2012 2012 HOH HOH . G 4 HOH B 13 2013 2013 HOH HOH . G 4 HOH B 14 2014 2014 HOH HOH . G 4 HOH B 15 2015 2015 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 N2 GDD . . . C 2 18.102 12.044 4.174 1 29.6 ? N2 GDD 601 A 1 HETATM 2 C C2 GDD . . . C 2 18.157 10.858 4.791 1 28.82 ? C2 GDD 601 A 1 HETATM 3 N N1 GDD . . . C 2 17.937 9.74 4.077 1 27.1 ? N1 GDD 601 A 1 HETATM 4 N N3 GDD . . . C 2 18.435 10.81 6.119 1 30.29 ? N3 GDD 601 A 1 HETATM 5 C C4 GDD . . . C 2 18.467 9.608 6.737 1 29.48 ? C4 GDD 601 A 1 HETATM 6 C C5 GDD . . . C 2 18.239 8.445 6.008 1 25 ? C5 GDD 601 A 1 HETATM 7 C C6 GDD . . . C 2 17.975 8.52 4.663 1 26.1 ? C6 GDD 601 A 1 HETATM 8 O O6 GDD . . . C 2 17.738 7.395 3.924 1 27.57 ? O6 GDD 601 A 1 HETATM 9 N N7 GDD . . . C 2 18.372 7.442 6.859 1 22.47 ? N7 GDD 601 A 1 HETATM 10 C C8 GDD . . . C 2 18.641 7.922 8.09 1 25.37 ? C8 GDD 601 A 1 HETATM 11 N N9 GDD . . . C 2 18.695 9.264 8.008 1 28.86 ? N9 GDD 601 A 1 HETATM 12 C C1' GDD . . . C 2 18.997 10.209 9.089 1 25.82 ? C1' GDD 601 A 1 HETATM 13 C C2' GDD . . . C 2 18.075 10.048 10.283 1 24.94 ? C2' GDD 601 A 1 HETATM 14 O O2' GDD . . . C 2 16.941 10.9 10.118 1 23.69 ? O2' GDD 601 A 1 HETATM 15 C C3' GDD . . . C 2 18.938 10.461 11.449 1 23.52 ? C3' GDD 601 A 1 HETATM 16 O O3' GDD . . . C 2 18.757 11.865 11.558 1 25.18 ? O3' GDD 601 A 1 HETATM 17 C C4' GDD . . . C 2 20.36 10.153 11.005 1 26.39 ? C4' GDD 601 A 1 HETATM 18 O O4' GDD . . . C 2 20.304 9.931 9.588 1 28.28 ? O4' GDD 601 A 1 HETATM 19 C C5' GDD . . . C 2 20.954 8.9 11.61 1 24.6 ? C5' GDD 601 A 1 HETATM 20 O O5' GDD . . . C 2 20.031 7.873 11.266 1 25.26 ? O5' GDD 601 A 1 HETATM 21 P PA GDD . . . C 2 19.691 6.734 12.356 1 25.01 ? PA GDD 601 A 1 HETATM 22 O O1A GDD . . . C 2 18.907 5.834 11.454 1 23.45 ? O1A GDD 601 A 1 HETATM 23 O O2A GDD . . . C 2 19.261 7.194 13.748 1 22.22 ? O2A GDD 601 A 1 HETATM 24 O O3A GDD . . . C 2 21.188 6.262 12.522 1 28.09 ? O3A GDD 601 A 1 HETATM 25 P PB GDD . . . C 2 21.567 5.328 13.72 1 29.04 ? PB GDD 601 A 1 HETATM 26 O O2B GDD . . . C 2 21.306 3.926 13.291 1 32.68 ? O2B GDD 601 A 1 HETATM 27 O O3B GDD . . . C 2 20.97 5.975 14.936 1 29 ? O3B GDD 601 A 1 HETATM 28 O O1B GDD . . . C 2 23.193 5.365 13.724 1 30.41 ? O1B GDD 601 A 1 HETATM 29 C C11 GDD . . . C 2 23.965 6.575 13.593 1 28.99 ? C11 GDD 601 A 1 HETATM 30 O O51 GDD . . . C 2 23.842 7.438 14.706 1 27.51 ? O51 GDD 601 A 1 HETATM 31 C C51 GDD . . . C 2 24.202 6.83 15.95 1 29.83 ? C51 GDD 601 A 1 HETATM 32 C C61 GDD . . . C 2 23.914 7.726 17.15 1 30.39 ? C61 GDD 601 A 1 HETATM 33 O O6A GDD . . . C 2 23.003 8.794 16.816 1 35.38 ? O6A GDD 601 A 1 HETATM 34 C C21 GDD . . . C 2 25.437 6.237 13.466 1 29.81 ? C21 GDD 601 A 1 HETATM 35 O O21 GDD . . . C 2 26.135 7.434 13.193 1 30.37 ? O21 GDD 601 A 1 HETATM 36 C C31 GDD . . . C 2 25.994 5.614 14.731 1 30.4 ? C31 GDD 601 A 1 HETATM 37 O O31 GDD . . . C 2 27.402 5.455 14.616 1 27.72 ? O31 GDD 601 A 1 HETATM 38 C C41 GDD . . . C 2 25.676 6.502 15.909 1 30.77 ? C41 GDD 601 A 1 HETATM 39 O O41 GDD . . . C 2 26.06 5.828 17.101 1 33.08 ? O41 GDD 601 A 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 553 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 39 #