data_1NYI # _model_server_result.job_id wIIN7PaGKnCQqgSn8U2uwQ _model_server_result.datetime_utc '2025-02-27 08:12:20' _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 1nyi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":500}' # _entry.id 1NYI # _exptl.entry_id 1NYI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 363.221 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-MONOPHOSPHATE" _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 120 _cell.entry_id 1NYI _cell.length_a 65.639 _cell.length_b 65.639 _cell.length_c 137.475 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1NYI _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 A P G 1 A G 11 1_555 D O5' 5GP . A 5GP 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.579 ? metalc ? metalc1 A O4 U 10 A U 20 1_555 G CO CO . B CO 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.229 ? metalc ? metalc2 G CO CO . B CO 4 1_555 B O2' U 18 B U 119 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.784 ? hydrog WATSON-CRICK hydrog1 A N1 G 1 A G 11 1_555 B N3 C 24 B C 125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N2 G 1 A G 11 1_555 B O2 C 24 B C 125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O6 G 1 A G 11 1_555 B N4 C 24 B C 125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N3 U 2 A U 12 1_555 B N1 A 23 B A 124 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A O4 U 2 A U 12 1_555 B N6 A 23 B A 124 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A N1 G 3 A G 13 1_555 B N3 C 22 B C 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N2 G 3 A G 13 1_555 B O2 C 22 B C 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A O6 G 3 A G 13 1_555 B N4 C 22 B C 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A N1 G 4 A G 14 1_555 B N3 C 21 B C 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N2 G 4 A G 14 1_555 B O2 C 21 B C 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A O6 G 4 A G 14 1_555 B N4 C 21 B C 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A N3 U 5 A U 15 1_555 B N1 A 20 B A 121 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A O4 U 5 A U 15 1_555 B N6 A 20 B A 121 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'C-C MISPAIR' hydrog14 A N3 C 6 A C 16 1_555 B N4 C 19 B C 120 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'U-A PAIR' hydrog15 A O2 U 10 A U 20 1_555 B N6 A 6 B A 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_11_PAIR hydrog16 A N2 G 11 A G 21 1_555 B N7 A 5 B A 106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_11_PAIR hydrog17 A N3 G 11 A G 21 1_555 B N6 A 5 B A 106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_11_PAIR hydrog18 A N6 A 12 A A 22 1_555 B N3 G 4 B G 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_11_PAIR hydrog19 A N7 A 12 A A 22 1_555 B N2 G 4 B G 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 A N1 G 13 A G 23 1_555 B N3 C 3 B C 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 A N2 G 13 A G 23 1_555 B O2 C 3 B C 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 A O6 G 13 A G 23 1_555 B N4 C 3 B C 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 A N1 G 14 A G 24 1_555 B N3 C 2 B C 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 A N2 G 14 A G 24 1_555 B O2 C 2 B C 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 A O6 G 14 A G 24 1_555 B N4 C 2 B C 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 A N3 C 15 A C 25 1_555 B N1 G 1 B G 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 A N4 C 15 A C 25 1_555 B O6 G 1 B G 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 A O2 C 15 A C 25 1_555 B N2 G 1 B G 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'A-U PAIR' hydrog29 B N6 A 7 B A 108 1_555 B O4 U 18 B U 119 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 B N3 C 8 B C 109 1_555 B N1 G 17 B G 118 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 B N4 C 8 B C 109 1_555 B O6 G 17 B G 118 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 B O2 C 8 B C 109 1_555 B N2 G 17 B G 118 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 B N3 U 9 B U 110 1_555 B N1 A 16 B A 117 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog34 B O4 U 9 B U 110 1_555 B N6 A 16 B A 117 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog35 B N3 C 10 B C 111 1_555 B N1 G 15 B G 116 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog36 B N4 C 10 B C 111 1_555 B O6 G 15 B G 116 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog37 B O2 C 10 B C 111 1_555 B N2 G 15 B G 116 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'G-A MISPAIR' hydrog38 B N2 G 11 B G 112 1_555 B N7 A 14 B A 115 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C10 H14 N5 O8 P' _chem_comp.formula_weight 363.221 _chem_comp.id 5GP _chem_comp.mon_nstd_flag . _chem_comp.name "GUANOSINE-5'-MONOPHOSPHATE" _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 P O1P 5GP doub 1 n n P O2P 5GP sing 2 n n P O3P 5GP sing 3 n n P O5' 5GP sing 4 n n O2P HOP2 5GP sing 5 n n O3P HOP3 5GP sing 6 n n O5' C5' 5GP sing 7 n n C5' C4' 5GP sing 8 n n C5' "H5'1" 5GP sing 9 n n C5' "H5'2" 5GP sing 10 n n C4' O4' 5GP sing 11 n n C4' C3' 5GP sing 12 n n C4' H4' 5GP sing 13 n n O4' C1' 5GP sing 14 n n C3' O3' 5GP sing 15 n n C3' C2' 5GP sing 16 n n C3' H3' 5GP sing 17 n n O3' HO3' 5GP sing 18 n n C2' O2' 5GP sing 19 n n C2' C1' 5GP sing 20 n n C2' H2' 5GP sing 21 n n O2' HO2' 5GP sing 22 n n C1' N9 5GP sing 23 n n C1' H1' 5GP sing 24 n n N9 C8 5GP sing 25 n y N9 C4 5GP sing 26 n y C8 N7 5GP doub 27 n y C8 H8 5GP sing 28 n n N7 C5 5GP sing 29 n y C5 C6 5GP sing 30 n n C5 C4 5GP doub 31 n y C6 O6 5GP doub 32 n n C6 N1 5GP sing 33 n n N1 C2 5GP sing 34 n n N1 HN1 5GP sing 35 n n C2 N2 5GP sing 36 n n C2 N3 5GP doub 37 n n N2 HN21 5GP sing 38 n n N2 HN22 5GP sing 39 n n N3 C4 5GP sing 40 n n # _atom_sites.entry_id 1NYI _atom_sites.fract_transf_matrix[1][1] 0.015235 _atom_sites.fract_transf_matrix[1][2] 0.008796 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017592 _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] 0.007274 _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 CO A 1 2 2 CO CO . D 4 5GP A 1 500 500 5GP GUA . E 3 CO B 1 1 1 CO CO . F 3 CO B 1 3 3 CO CO . G 3 CO B 1 4 4 CO CO . # 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 O O5' 5GP . . . D 4 25.352 -0.486 42.912 1 52.49 ? O5' 5GP 500 A 1 HETATM 2 C C5' 5GP . . . D 4 26.171 -0.178 44.04 1 53.02 ? C5' 5GP 500 A 1 HETATM 3 C C4' 5GP . . . D 4 27.243 -1.228 44.231 1 52.41 ? C4' 5GP 500 A 1 HETATM 4 O O4' 5GP . . . D 4 26.719 -2.288 45.076 1 51.64 ? O4' 5GP 500 A 1 HETATM 5 C C3' 5GP . . . D 4 27.644 -1.899 42.922 1 52.96 ? C3' 5GP 500 A 1 HETATM 6 O O3' 5GP . . . D 4 28.73 -1.216 42.294 1 54.07 ? O3' 5GP 500 A 1 HETATM 7 C C2' 5GP . . . D 4 27.994 -3.314 43.378 1 52.74 ? C2' 5GP 500 A 1 HETATM 8 O O2' 5GP . . . D 4 29.285 -3.409 43.961 1 54.16 ? O2' 5GP 500 A 1 HETATM 9 C C1' 5GP . . . D 4 26.92 -3.544 44.439 1 51.18 ? C1' 5GP 500 A 1 HETATM 10 N N9 5GP . . . D 4 25.636 -4.14 44.003 1 48.62 ? N9 5GP 500 A 1 HETATM 11 C C8 5GP . . . D 4 24.451 -3.49 43.736 1 47.17 ? C8 5GP 500 A 1 HETATM 12 N N7 5GP . . . D 4 23.473 -4.287 43.404 1 46.59 ? N7 5GP 500 A 1 HETATM 13 C C5 5GP . . . D 4 24.031 -5.558 43.452 1 46.82 ? C5 5GP 500 A 1 HETATM 14 C C6 5GP . . . D 4 23.446 -6.83 43.199 1 46.5 ? C6 5GP 500 A 1 HETATM 15 O O6 5GP . . . D 4 22.285 -7.091 42.859 1 46.19 ? O6 5GP 500 A 1 HETATM 16 N N1 5GP . . . D 4 24.354 -7.875 43.368 1 45.89 ? N1 5GP 500 A 1 HETATM 17 C C2 5GP . . . D 4 25.664 -7.707 43.746 1 45.67 ? C2 5GP 500 A 1 HETATM 18 N N2 5GP . . . D 4 26.379 -8.828 43.852 1 45.34 ? N2 5GP 500 A 1 HETATM 19 N N3 5GP . . . D 4 26.23 -6.53 43.997 1 46.06 ? N3 5GP 500 A 1 HETATM 20 C C4 5GP . . . D 4 25.361 -5.491 43.828 1 47.46 ? C4 5GP 500 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 310 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 20 #