data_5V9Z # _model_server_result.job_id JbRWq0GX4e-HUbO1lC7MbA _model_server_result.datetime_utc '2024-12-04 20:06:15' _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 5v9z # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":101}' # _entry.id 5V9Z # _exptl.entry_id 5V9Z _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.309 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-O-[(S)-hydroxy(4-methyl-1H-imidazol-5-yl)phosphoryl]guanosine" _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 5V9Z _cell.length_a 45.275 _cell.length_b 45.275 _cell.length_c 154.573 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5V9Z _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 43 21 2' # _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 _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 3 _struct_asym.id C _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 O3' G 7 A G 7 1_555 A P LCC 8 A LCC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.656 ? covale ? covale2 A O3' LCC 8 A LCC 8 1_555 A P LCC 9 A LCC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.68 ? covale ? covale3 A O3' LCC 9 A LCC 9 1_555 A P G 10 A G 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.658 ? hydrog WATSON-CRICK hydrog1 A N1 G 2 A G 2 1_555 B N3 C 7 B C 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N2 G 2 A G 2 1_555 B O2 C 7 B C 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O6 G 2 A G 2 1_555 B N4 C 7 B C 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N1 A 3 A A 3 1_555 B N3 U 6 B U 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N6 A 3 A A 3 1_555 B O4 U 6 B U 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A N1 G 4 A G 4 1_555 B N3 C 5 B C 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N2 G 4 A G 4 1_555 B O2 C 5 B C 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A O6 G 4 A G 4 1_555 B N4 C 5 B C 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A N1 G 5 A G 5 1_555 B N3 C 4 B C 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N2 G 5 A G 5 1_555 B O2 C 4 B C 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A O6 G 5 A G 5 1_555 B N4 C 4 B C 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A N3 U 6 A U 6 1_555 B N1 A 3 B A 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A O4 U 6 A U 6 1_555 B N6 A 3 B A 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A N1 G 7 A G 7 1_555 B N3 C 2 B C 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A N2 G 7 A G 7 1_555 B O2 C 2 B C 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A O6 G 7 A G 7 1_555 B N4 C 2 B C 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A N1 G 10 A G 10 1_555 A N3 C 25 A C 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A N2 G 10 A G 10 1_555 A O2 C 25 A C 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 A O6 G 10 A G 10 1_555 A N4 C 25 A C 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 A N1 A 11 A A 11 1_555 A N3 U 24 A U 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 A N6 A 11 A A 11 1_555 A O4 U 24 A U 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 A N1 G 12 A G 12 1_555 A N3 C 23 A C 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 A N2 G 12 A G 12 1_555 A O2 C 23 A C 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 A O6 G 12 A G 12 1_555 A N4 C 23 A C 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 A N3 C 13 A C 13 1_555 A N1 G 22 A G 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 A N4 C 13 A C 13 1_555 A O6 G 22 A G 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 A O2 C 13 A C 13 1_555 A N2 G 22 A G 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 A N1 G 14 A G 14 1_555 A N3 C 21 A C 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 A N2 G 14 A G 14 1_555 A O2 C 21 A C 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 A O6 G 14 A G 14 1_555 A N4 C 21 A C 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 A N3 C 15 A C 15 1_555 A N1 G 20 A G 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 A N4 C 15 A C 15 1_555 A O6 G 20 A G 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 A O2 C 15 A C 15 1_555 A N2 G 20 A G 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_11_PAIR hydrog34 A N2 G 16 A G 16 1_555 A N7 A 19 A A 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_11_PAIR hydrog35 A N3 G 16 A G 16 1_555 A N6 A 19 A A 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C14 H18 N7 O7 P' _chem_comp.formula_weight 427.309 _chem_comp.id 8OS _chem_comp.mon_nstd_flag n _chem_comp.name "5'-O-[(S)-hydroxy(4-methyl-1H-imidazol-5-yl)phosphoryl]guanosine" _chem_comp.type 'rna linking' _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 C14 C13 8OS sing 1 n n O7 P1 8OS doub 2 n n C13 N7 8OS sing 3 n y C13 C11 8OS doub 4 n y C10 C9 8OS sing 5 n n C10 O5 8OS sing 6 n n N7 C12 8OS doub 7 n y O4 C8 8OS sing 8 n n P1 C11 8OS sing 9 n n P1 O5 8OS sing 10 n n P1 O6 8OS sing 11 n n C11 N6 8OS sing 12 n y C9 C8 8OS sing 13 n n C9 O2 8OS sing 14 n n C8 C7 8OS sing 15 n n C12 N6 8OS sing 16 n y O2 C6 8OS sing 17 n n O3 C7 8OS sing 18 n n C7 C6 8OS sing 19 n n C6 N5 8OS sing 20 n n C5 N5 8OS sing 21 n y C5 N4 8OS doub 22 n y N5 C3 8OS sing 23 n y N4 C4 8OS sing 24 n y C3 N3 8OS sing 25 n n C3 C4 8OS doub 26 n y N3 C2 8OS doub 27 n n C4 C1 8OS sing 28 n n C2 N2 8OS sing 29 n n C2 N1 8OS sing 30 n n C1 N1 8OS sing 31 n n C1 O1 8OS doub 32 n n N1 H1 8OS sing 33 n n N2 H2 8OS sing 34 n n N2 H3 8OS sing 35 n n C5 H4 8OS sing 36 n n C6 H5 8OS sing 37 n n C7 H6 8OS sing 38 n n O3 H7 8OS sing 39 n n C8 H8 8OS sing 40 n n O4 H9 8OS sing 41 n n C9 H10 8OS sing 42 n n C10 H11 8OS sing 43 n n C10 H12 8OS sing 44 n n O6 H13 8OS sing 45 n n N6 H14 8OS sing 46 n n C12 H15 8OS sing 47 n n C14 H17 8OS sing 48 n n C14 H18 8OS sing 49 n n C14 H19 8OS sing 50 n n # _atom_sites.entry_id 5V9Z _atom_sites.fract_transf_matrix[1][1] 0.022087 _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] 0.022087 _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] 0.006469 _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 8OS A 1 101 1 8OS rG . D 4 HOH A 1 201 10 HOH HOH . D 4 HOH A 2 202 4 HOH HOH . D 4 HOH A 3 203 2 HOH HOH . D 4 HOH A 4 204 8 HOH HOH . D 4 HOH A 5 205 5 HOH HOH . D 4 HOH A 6 206 9 HOH HOH . D 4 HOH A 7 207 3 HOH HOH . E 4 HOH B 1 101 11 HOH HOH . E 4 HOH B 2 102 14 HOH HOH . E 4 HOH B 3 103 12 HOH HOH . E 4 HOH B 4 104 13 HOH HOH . E 4 HOH B 5 105 1 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 O O1 8OS . . . C 3 -4.4 30.186 140.656 1 65.84 ? O1 8OS 101 A 1 HETATM 2 C C1 8OS . . . C 3 -4.3 29.274 139.852 1 70.41 ? C1 8OS 101 A 1 HETATM 3 N N1 8OS . . . C 3 -4.899 28.088 140.194 1 73.44 ? N1 8OS 101 A 1 HETATM 4 C C2 8OS . . . C 3 -4.817 27.003 139.324 1 69.75 ? C2 8OS 101 A 1 HETATM 5 N N2 8OS . . . C 3 -5.38 25.837 139.632 1 69.72 ? N2 8OS 101 A 1 HETATM 6 N N3 8OS . . . C 3 -4.158 27.154 138.185 1 64.88 ? N3 8OS 101 A 1 HETATM 7 C C3 8OS . . . C 3 -3.599 28.323 137.862 1 71.07 ? C3 8OS 101 A 1 HETATM 8 C C4 8OS . . . C 3 -3.655 29.388 138.673 1 74.82 ? C4 8OS 101 A 1 HETATM 9 N N4 8OS . . . C 3 -2.978 30.384 138.077 1 69.08 ? N4 8OS 101 A 1 HETATM 10 C C5 8OS . . . C 3 -2.532 29.912 136.919 1 67.42 ? C5 8OS 101 A 1 HETATM 11 N N5 8OS . . . C 3 -2.904 28.64 136.785 1 69.16 ? N5 8OS 101 A 1 HETATM 12 C C6 8OS . . . C 3 -2.725 27.62 135.671 1 68.57 ? C6 8OS 101 A 1 HETATM 13 O O2 8OS . . . C 3 -1.712 27.945 134.688 1 66.72 ? O2 8OS 101 A 1 HETATM 14 C C7 8OS . . . C 3 -4.043 27.554 134.84 1 66.01 ? C7 8OS 101 A 1 HETATM 15 O O3 8OS . . . C 3 -4.171 26.384 134.053 1 62.96 ? O3 8OS 101 A 1 HETATM 16 C C8 8OS . . . C 3 -3.821 28.693 133.937 1 69.37 ? C8 8OS 101 A 1 HETATM 17 O O4 8OS . . . C 3 -4.719 28.63 132.855 1 68.49 ? O4 8OS 101 A 1 HETATM 18 C C9 8OS . . . C 3 -2.404 28.364 133.493 1 69.5 ? C9 8OS 101 A 1 HETATM 19 C C10 8OS . . . C 3 -1.654 29.55 132.897 1 78.36 ? C10 8OS 101 A 1 HETATM 20 O O5 8OS . . . C 3 -2.222 30.85 133.155 1 77.55 ? O5 8OS 101 A 1 HETATM 21 P P1 8OS . . . C 3 -1.293 32.112 132.691 1 83.43 ? P1 8OS 101 A 1 HETATM 22 O O6 8OS . . . C 3 -1.355 33.312 134.105 1 74.48 ? O6 8OS 101 A 1 HETATM 23 O O7 8OS . . . C 3 0.34 31.581 132.658 1 77.41 ? O7 8OS 101 A 1 HETATM 24 C C11 8OS . . . C 3 -1.732 33.118 131.117 1 94.22 ? C11 8OS 101 A 1 HETATM 25 N N6 8OS . . . C 3 -2.956 33.438 130.715 1 99.73 ? N6 8OS 101 A 1 HETATM 26 C C12 8OS . . . C 3 -2.866 33.923 129.469 1 83.58 ? C12 8OS 101 A 1 HETATM 27 N N7 8OS . . . C 3 -1.603 33.904 129.087 1 88.73 ? N7 8OS 101 A 1 HETATM 28 C C13 8OS . . . C 3 -0.874 33.398 130.137 1 91.18 ? C13 8OS 101 A 1 HETATM 29 C C14 8OS . . . C 3 0.63 33.177 130.146 1 88.45 ? C14 8OS 101 A 1 # _model_server_stats.io_time_ms 5 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 234 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 29 #