data_7D72 # _model_server_result.job_id gtWf0vKgl8rip0SZlNnuiQ _model_server_result.datetime_utc '2024-11-22 22:57:59' _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 7d72 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Z","auth_seq_id":401}' # _entry.id 7D72 # _exptl.entry_id 7D72 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 605.341 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE" _entity.pdbx_number_of_molecules 12 _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 7D72 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7D72 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dodecameric _pdbx_struct_assembly.oligomeric_count 12 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA _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 ? _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 M N N ? 3 N N N ? 3 O N N ? 3 P N N ? 3 Q N N ? 3 R N N ? 3 S N N ? 3 U N N ? 3 W N N ? 3 Y N N ? 3 Z N N ? 3 AA 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 disulf ? disulf1 G SG CYS 289 E CYS 289 1_555 G SG CYS 306 E CYS 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf2 I SG CYS 289 G CYS 289 1_555 I SG CYS 306 G CYS 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf3 K SG CYS 289 J CYS 289 1_555 K SG CYS 306 J CYS 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf4 L SG CYS 289 L CYS 289 1_555 L SG CYS 306 L CYS 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? metalc ? metalc1 G OD1 ASP 110 E ASP 110 1_555 T MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? metalc ? metalc2 G OD1 ASP 218 E ASP 218 1_555 T MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.82 ? metalc ? metalc3 S O2A GDD . E GDD 401 1_555 T MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.45 ? metalc ? metalc4 S O3B GDD . E GDD 401 1_555 T MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? metalc ? metalc5 T MG MG . E MG 402 1_555 BA O HOH . E HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.645 ? metalc ? metalc6 T MG MG . E MG 402 1_555 BA O HOH . E HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? metalc ? metalc7 H OD1 ASP 110 F ASP 110 1_555 V MG MG . F MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.281 ? metalc ? metalc8 U O2A GDD . F GDD 401 1_555 V MG MG . F MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? metalc ? metalc9 U O3B GDD . F GDD 401 1_555 V MG MG . F MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? metalc ? metalc10 V MG MG . F MG 402 1_555 CA O HOH . F HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? metalc ? metalc11 V MG MG . F MG 402 1_555 CA O HOH . F HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.689 ? metalc ? metalc12 I OD1 ASP 218 G ASP 218 1_555 X MG MG . G MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.413 ? metalc ? metalc13 X MG MG . G MG 402 1_555 DA O HOH . G HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.271 ? metalc ? metalc14 X MG MG . G MG 402 1_555 DA O HOH . G HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.262 ? # _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 7D72 _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 M 3 GDD K 1 401 401 GDD GDD . N 3 GDD I 1 401 401 GDD GDD . O 3 GDD A 1 501 501 GDD GDD . P 3 GDD B 1 501 501 GDD GDD . Q 3 GDD C 1 501 501 GDD GDD . R 3 GDD D 1 501 501 GDD GDD . S 3 GDD E 1 401 401 GDD GDD . T 4 MG E 1 402 402 MG MG . U 3 GDD F 1 401 401 GDD GDD . V 4 MG F 1 402 402 MG MG . W 3 GDD G 1 401 401 GDD GDD . X 4 MG G 1 402 402 MG MG . Y 3 GDD H 1 401 401 GDD GDD . Z 3 GDD J 1 401 401 GDD GDD . AA 3 GDD L 1 401 401 GDD GDD . BA 5 HOH E 1 501 404 HOH HOH . BA 5 HOH E 2 502 403 HOH HOH . CA 5 HOH F 1 501 403 HOH HOH . CA 5 HOH F 2 502 404 HOH HOH . DA 5 HOH G 1 501 404 HOH HOH . DA 5 HOH G 2 502 403 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 . . . Z 3 142.767 59.504 127.066 1 118.17 ? N2 GDD 401 J 1 HETATM 2 C C2 GDD . . . Z 3 142.053 60.654 127.266 1 118.17 ? C2 GDD 401 J 1 HETATM 3 N N1 GDD . . . Z 3 142.674 61.826 126.954 1 118.17 ? N1 GDD 401 J 1 HETATM 4 N N3 GDD . . . Z 3 140.834 60.512 127.737 1 118.17 ? N3 GDD 401 J 1 HETATM 5 C C4 GDD . . . Z 3 140.117 61.614 127.938 1 118.17 ? C4 GDD 401 J 1 HETATM 6 C C5 GDD . . . Z 3 140.641 62.867 127.66 1 118.17 ? C5 GDD 401 J 1 HETATM 7 C C6 GDD . . . Z 3 141.951 62.943 127.157 1 118.17 ? C6 GDD 401 J 1 HETATM 8 O O6 GDD . . . Z 3 142.44 64.028 126.901 1 118.17 ? O6 GDD 401 J 1 HETATM 9 N N7 GDD . . . Z 3 139.698 63.795 127.957 1 118.17 ? N7 GDD 401 J 1 HETATM 10 C C8 GDD . . . Z 3 138.603 63.17 128.415 1 118.17 ? C8 GDD 401 J 1 HETATM 11 N N9 GDD . . . Z 3 138.863 61.838 128.407 1 118.17 ? N9 GDD 401 J 1 HETATM 12 C C1' GDD . . . Z 3 137.811 60.929 128.855 1 118.17 ? C1' GDD 401 J 1 HETATM 13 C C2' GDD . . . Z 3 137.469 61.162 130.336 1 118.17 ? C2' GDD 401 J 1 HETATM 14 O O2' GDD . . . Z 3 138.052 60.133 131.126 1 118.17 ? O2' GDD 401 J 1 HETATM 15 C C3' GDD . . . Z 3 135.955 60.97 130.382 1 118.17 ? C3' GDD 401 J 1 HETATM 16 O O3' GDD . . . Z 3 135.691 59.623 130.769 1 118.17 ? O3' GDD 401 J 1 HETATM 17 C C4' GDD . . . Z 3 135.495 61.204 128.931 1 118.17 ? C4' GDD 401 J 1 HETATM 18 O O4' GDD . . . Z 3 136.659 61.187 128.086 1 118.17 ? O4' GDD 401 J 1 HETATM 19 C C5' GDD . . . Z 3 134.818 62.564 128.78 1 118.17 ? C5' GDD 401 J 1 HETATM 20 O O5' GDD . . . Z 3 135.631 63.562 129.384 1 118.17 ? O5' GDD 401 J 1 HETATM 21 P PA GDD . . . Z 3 134.905 64.799 130.102 1 118.17 ? PA GDD 401 J 1 HETATM 22 O O1A GDD . . . Z 3 135.77 65.995 130.014 1 118.17 ? O1A GDD 401 J 1 HETATM 23 O O2A GDD . . . Z 3 134.617 64.436 131.643 1 118.17 ? O2A GDD 401 J 1 HETATM 24 O O3A GDD . . . Z 3 133.507 65.113 129.386 1 118.17 ? O3A GDD 401 J 1 HETATM 25 P PB GDD . . . Z 3 132.157 65.709 130.003 1 118.17 ? PB GDD 401 J 1 HETATM 26 O O2B GDD . . . Z 3 132.332 67.265 130.347 1 118.17 ? O2B GDD 401 J 1 HETATM 27 O O3B GDD . . . Z 3 131.788 64.927 131.195 1 118.17 ? O3B GDD 401 J 1 HETATM 28 O O1B GDD . . . Z 3 131.073 65.534 128.841 1 118.17 ? O1B GDD 401 J 1 HETATM 29 C C11 GDD . . . Z 3 131.113 64.341 128.076 1 118.17 ? C11 GDD 401 J 1 HETATM 30 O O51 GDD . . . Z 3 130.396 63.29 128.728 1 118.17 ? O51 GDD 401 J 1 HETATM 31 C C51 GDD . . . Z 3 128.994 63.536 128.873 1 118.17 ? C51 GDD 401 J 1 HETATM 32 C C61 GDD . . . Z 3 128.299 62.348 129.518 1 118.17 ? C61 GDD 401 J 1 HETATM 33 O O6A GDD . . . Z 3 128.985 62.043 130.728 1 118.17 ? O6A GDD 401 J 1 HETATM 34 C C21 GDD . . . Z 3 130.536 64.648 126.701 1 118.17 ? C21 GDD 401 J 1 HETATM 35 O O21 GDD . . . Z 3 130.699 63.467 125.935 1 118.17 ? O21 GDD 401 J 1 HETATM 36 C C31 GDD . . . Z 3 129.035 64.902 126.792 1 118.17 ? C31 GDD 401 J 1 HETATM 37 O O31 GDD . . . Z 3 128.505 64.989 125.473 1 118.17 ? O31 GDD 401 J 1 HETATM 38 C C41 GDD . . . Z 3 128.333 63.758 127.523 1 118.17 ? C41 GDD 401 J 1 HETATM 39 O O41 GDD . . . Z 3 126.971 64.082 127.748 1 118.17 ? O41 GDD 401 J 1 # _model_server_stats.io_time_ms 125 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 46 _model_server_stats.query_time_ms 264 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 39 #