data_3J25 # _model_server_result.job_id X78ZsMcnKBAs341uhQ0stw _model_server_result.datetime_utc '2025-03-03 03:48:49' _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 3j25 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":701}' # _entry.id 3J25 # _exptl.entry_id 3J25 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 521.208 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER' _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 3J25 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3J25 _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 monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_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 'C11 H18 N5 O13 P3' _chem_comp.formula_weight 521.208 _chem_comp.id GCP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER' _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 PG O1G GCP doub 83 n n PG O2G GCP sing 84 n n PG O3G GCP sing 85 n n PG C3B GCP sing 86 n n O2G HOG2 GCP sing 87 n n O3G HOG3 GCP sing 88 n n C3B PB GCP sing 89 n n C3B H3B1 GCP sing 90 n n C3B H3B2 GCP sing 91 n n PB O1B GCP doub 92 n n PB O2B GCP sing 93 n n PB O3A GCP sing 94 n n O2B HOB2 GCP sing 95 n n O3A PA GCP sing 96 n n PA O1A GCP doub 97 n n PA O2A GCP sing 98 n n PA O5' GCP sing 99 n n O2A HOA2 GCP sing 100 n n O5' C5' GCP sing 101 n n C5' C4' GCP sing 102 n n C5' "H5'2" GCP sing 103 n n C5' "H5'1" GCP sing 104 n n C4' O4' GCP sing 105 n n C4' C3' GCP sing 106 n n C4' H4' GCP sing 107 n n O4' C1' GCP sing 108 n n C3' O3' GCP sing 109 n n C3' C2' GCP sing 110 n n C3' H3' GCP sing 111 n n O3' HO3' GCP sing 112 n n C2' O2' GCP sing 113 n n C2' C1' GCP sing 114 n n C2' H2' GCP sing 115 n n O2' HO2' GCP sing 116 n n C1' N9 GCP sing 117 n n C1' H1' GCP sing 118 n n N9 C8 GCP sing 119 n y N9 C4 GCP sing 120 n y C8 N7 GCP doub 121 n y C8 H8 GCP sing 122 n n N7 C5 GCP sing 123 n y C5 C6 GCP sing 124 n y C5 C4 GCP doub 125 n y C6 O6 GCP doub 126 n n C6 N1 GCP sing 127 n y N1 C2 GCP sing 128 n y N1 HN1 GCP sing 129 n n C2 N2 GCP sing 130 n n C2 N3 GCP doub 131 n y N2 HN21 GCP sing 132 n n N2 HN22 GCP sing 133 n n N3 C4 GCP sing 134 n y # _atom_sites.entry_id 3J25 _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 # _pdbx_nonpoly_scheme.asym_id B _pdbx_nonpoly_scheme.entity_id 2 _pdbx_nonpoly_scheme.mon_id GCP _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 701 _pdbx_nonpoly_scheme.auth_seq_num 1406 _pdbx_nonpoly_scheme.pdb_mon_id GCP _pdbx_nonpoly_scheme.auth_mon_id GCP _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 P PG GCP . . . B 2 -12.533 44.083 -55.322 1 90.8 ? PG GCP 701 A 1 HETATM 2 O O1G GCP . . . B 2 -13.73 43.298 -55.578 1 89.99 ? O1G GCP 701 A 1 HETATM 3 O O2G GCP . . . B 2 -13.01 45.505 -55.121 1 91.77 ? O2G GCP 701 A 1 HETATM 4 O O3G GCP . . . B 2 -11.754 43.731 -54.102 1 90.66 ? O3G GCP 701 A 1 HETATM 5 C C3B GCP . . . B 2 -11.391 43.994 -56.811 1 92.33 ? C3B GCP 701 A 1 HETATM 6 P PB GCP . . . B 2 -10.64 45.603 -57.265 1 93.54 ? PB GCP 701 A 1 HETATM 7 O O1B GCP . . . B 2 -11.198 46.061 -58.555 1 93.27 ? O1B GCP 701 A 1 HETATM 8 O O2B GCP . . . B 2 -10.866 46.626 -56.149 1 93.54 ? O2B GCP 701 A 1 HETATM 9 O O3A GCP . . . B 2 -9.109 45.391 -57.491 1 94.61 ? O3A GCP 701 A 1 HETATM 10 P PA GCP . . . B 2 -7.965 46.332 -57.052 1 96.14 ? PA GCP 701 A 1 HETATM 11 O O1A GCP . . . B 2 -8.016 47.62 -57.751 1 95.61 ? O1A GCP 701 A 1 HETATM 12 O O2A GCP . . . B 2 -8.075 46.443 -55.58 1 95.81 ? O2A GCP 701 A 1 HETATM 13 O O5' GCP . . . B 2 -6.727 45.493 -57.576 1 99.38 ? O5' GCP 701 A 1 HETATM 14 C C5' GCP . . . B 2 -5.635 45.065 -56.745 1 106.24 ? C5' GCP 701 A 1 HETATM 15 C C4' GCP . . . B 2 -4.475 44.555 -57.602 1 109.66 ? C4' GCP 701 A 1 HETATM 16 O O4' GCP . . . B 2 -4.847 44.372 -59.002 1 110.43 ? O4' GCP 701 A 1 HETATM 17 C C3' GCP . . . B 2 -3.221 45.445 -57.678 1 111.53 ? C3' GCP 701 A 1 HETATM 18 O O3' GCP . . . B 2 -2.4 45.391 -56.493 1 112.46 ? O3' GCP 701 A 1 HETATM 19 C C2' GCP . . . B 2 -2.516 44.939 -58.905 1 112.57 ? C2' GCP 701 A 1 HETATM 20 O O2' GCP . . . B 2 -1.557 43.92 -58.77 1 112.67 ? O2' GCP 701 A 1 HETATM 21 C C1' GCP . . . B 2 -3.708 44.577 -59.826 1 113 ? C1' GCP 701 A 1 HETATM 22 N N9 GCP . . . B 2 -3.967 45.62 -60.869 1 115.33 ? N9 GCP 701 A 1 HETATM 23 C C8 GCP . . . B 2 -4.701 46.771 -60.799 1 116.25 ? C8 GCP 701 A 1 HETATM 24 N N7 GCP . . . B 2 -4.69 47.473 -61.877 1 116.68 ? N7 GCP 701 A 1 HETATM 25 C C5 GCP . . . B 2 -3.977 46.774 -62.728 1 116.68 ? C5 GCP 701 A 1 HETATM 26 C C6 GCP . . . B 2 -3.586 47.039 -64.071 1 116.78 ? C6 GCP 701 A 1 HETATM 27 O O6 GCP . . . B 2 -3.944 48.015 -64.736 1 117.35 ? O6 GCP 701 A 1 HETATM 28 N N1 GCP . . . B 2 -2.774 46.038 -64.724 1 116.84 ? N1 GCP 701 A 1 HETATM 29 C C2 GCP . . . B 2 -2.353 44.924 -63.998 1 116.82 ? C2 GCP 701 A 1 HETATM 30 N N2 GCP . . . B 2 -1.558 44.066 -64.682 1 116.73 ? N2 GCP 701 A 1 HETATM 31 N N3 GCP . . . B 2 -2.658 44.617 -62.738 1 116.82 ? N3 GCP 701 A 1 HETATM 32 C C4 GCP . . . B 2 -3.432 45.631 -62.159 1 116.62 ? C4 GCP 701 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 566 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 32 #