data_5V0J # _model_server_result.job_id sh6HtWF6gDt3MIFM8Q0Yzg _model_server_result.datetime_utc '2024-12-04 20:07:53' _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 5v0j # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":102}' # _entry.id 5V0J # _exptl.entry_id 5V0J _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.309 _entity.id 2 _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 4 _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 5V0J _cell.length_a 43.388 _cell.length_b 43.388 _cell.length_c 253.851 _cell.Z_PDB 36 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5V0J _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 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,F,G,H,I _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 D N N ? 2 F N N ? 2 G 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 covale ? covale1 A O3' LCC 1 A LCC 1 1_555 A P LCC 2 A LCC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.675 ? covale ? covale2 A O3' LCC 2 A LCC 2 1_555 A P LCA 3 A LCA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.558 ? covale ? covale3 A O3' LCA 3 A LCA 3 1_555 A P LCG 4 A LCG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.705 ? covale ? covale4 A O3' LCG 4 A LCG 4 1_555 A P A 5 A A 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.601 ? covale ? covale5 B O3' LCC 1 B LCC 1 1_555 B P LCC 2 B LCC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.671 ? covale ? covale6 B O3' LCC 2 B LCC 2 1_555 B P LCA 3 B LCA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.702 ? covale ? covale7 B O3' LCA 3 B LCA 3 1_555 B P LCG 4 B LCG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.627 ? covale ? covale8 B O3' LCG 4 B LCG 4 1_555 B P A 5 B A 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.627 ? metalc ? metalc1 C O3 8OS . A 8OS 101 1_555 E MG MG . B MG 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.736 ? metalc ? metalc2 C O4 8OS . A 8OS 101 1_555 E MG MG . B MG 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? metalc ? metalc3 C O3 8OS . A 8OS 101 1_555 E MG MG . B MG 101 2_445 ? ? ? ? ? ? ? ? ? ? ? ? 2.729 ? metalc ? metalc4 C O4 8OS . A 8OS 101 1_555 E MG MG . B MG 101 2_445 ? ? ? ? ? ? ? ? ? ? ? ? 2.441 ? hydrog WATSON-CRICK hydrog1 A N1 LCA 3 A LCA 3 1_555 B N3 U 14 B U 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N6 LCA 3 A LCA 3 1_555 B O4 U 14 B U 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A N1 LCG 4 A LCG 4 1_555 B N3 C 13 B C 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N2 LCG 4 A LCG 4 1_555 B O2 C 13 B C 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A O6 LCG 4 A LCG 4 1_555 B N4 C 13 B C 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A N1 A 5 A A 5 1_555 B N3 U 12 B U 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N6 A 5 A A 5 1_555 B O4 U 12 B U 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N3 C 6 A C 6 1_555 B N1 G 11 B G 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A N4 C 6 A C 6 1_555 B O6 G 11 B G 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A O2 C 6 A C 6 1_555 B N2 G 11 B G 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A N3 U 7 A U 7 1_555 B N1 A 10 B A 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A O4 U 7 A U 7 1_555 B N6 A 10 B A 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N3 U 8 A U 8 1_555 B N1 A 9 B A 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A O4 U 8 A U 8 1_555 B N6 A 9 B A 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A N1 A 9 A A 9 1_555 B N3 U 8 B U 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A N6 A 9 A A 9 1_555 B O4 U 8 B U 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A N1 A 10 A A 10 1_555 B N3 U 7 B U 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A N6 A 10 A A 10 1_555 B O4 U 7 B U 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 A N1 G 11 A G 11 1_555 B N3 C 6 B C 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 A N2 G 11 A G 11 1_555 B O2 C 6 B C 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 A O6 G 11 A G 11 1_555 B N4 C 6 B C 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 A N3 U 12 A U 12 1_555 B N1 A 5 B A 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 A O4 U 12 A U 12 1_555 B N6 A 5 B A 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 A N3 C 13 A C 13 1_555 B N1 LCG 4 B LCG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 A N4 C 13 A C 13 1_555 B O6 LCG 4 B LCG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 A O2 C 13 A C 13 1_555 B N2 LCG 4 B LCG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 A N3 U 14 A U 14 1_555 B N1 LCA 3 B LCA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 A O4 U 14 A U 14 1_555 B N6 LCA 3 B LCA 3 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 5V0J _atom_sites.fract_transf_matrix[1][1] 0.023048 _atom_sites.fract_transf_matrix[1][2] 0.013307 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.026613 _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] 0.003939 _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 8OS A 1 101 3 8OS rG . D 2 8OS A 1 102 4 8OS rG . E 3 MG B 1 101 1 MG MG . F 2 8OS B 1 102 1 8OS rG . G 2 8OS B 1 103 2 8OS rG . H 4 HOH A 1 201 13 HOH HOH . H 4 HOH A 2 202 26 HOH HOH . H 4 HOH A 3 203 53 HOH HOH . H 4 HOH A 4 204 21 HOH HOH . H 4 HOH A 5 205 27 HOH HOH . H 4 HOH A 6 206 35 HOH HOH . H 4 HOH A 7 207 17 HOH HOH . H 4 HOH A 8 208 1 HOH HOH . H 4 HOH A 9 209 40 HOH HOH . H 4 HOH A 10 210 10 HOH HOH . H 4 HOH A 11 211 25 HOH HOH . H 4 HOH A 12 212 2 HOH HOH . H 4 HOH A 13 213 12 HOH HOH . H 4 HOH A 14 214 28 HOH HOH . H 4 HOH A 15 215 24 HOH HOH . H 4 HOH A 16 216 51 HOH HOH . H 4 HOH A 17 217 55 HOH HOH . H 4 HOH A 18 218 14 HOH HOH . H 4 HOH A 19 219 22 HOH HOH . H 4 HOH A 20 220 20 HOH HOH . H 4 HOH A 21 221 23 HOH HOH . H 4 HOH A 22 222 54 HOH HOH . H 4 HOH A 23 223 9 HOH HOH . H 4 HOH A 24 224 29 HOH HOH . H 4 HOH A 25 225 45 HOH HOH . H 4 HOH A 26 226 5 HOH HOH . H 4 HOH A 27 227 42 HOH HOH . I 4 HOH B 1 201 36 HOH HOH . I 4 HOH B 2 202 39 HOH HOH . I 4 HOH B 3 203 19 HOH HOH . I 4 HOH B 4 204 32 HOH HOH . I 4 HOH B 5 205 49 HOH HOH . I 4 HOH B 6 206 30 HOH HOH . I 4 HOH B 7 207 11 HOH HOH . I 4 HOH B 8 208 41 HOH HOH . I 4 HOH B 9 209 8 HOH HOH . I 4 HOH B 10 210 18 HOH HOH . I 4 HOH B 11 211 15 HOH HOH . I 4 HOH B 12 212 60 HOH HOH . I 4 HOH B 13 213 6 HOH HOH . I 4 HOH B 14 214 37 HOH HOH . I 4 HOH B 15 215 31 HOH HOH . I 4 HOH B 16 216 56 HOH HOH . I 4 HOH B 17 217 48 HOH HOH . I 4 HOH B 18 218 38 HOH HOH . I 4 HOH B 19 219 7 HOH HOH . I 4 HOH B 20 220 4 HOH HOH . I 4 HOH B 21 221 16 HOH HOH . I 4 HOH B 22 222 43 HOH HOH . I 4 HOH B 23 223 33 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 . . . D 2 -5.39 -25.334 0.256 1 57.84 ? O1 8OS 102 A 1 HETATM 2 C C1 8OS . . . D 2 -6.562 -25.007 0.46 1 48.65 ? C1 8OS 102 A 1 HETATM 3 N N1 8OS . . . D 2 -7.597 -25.876 0.931 1 51.28 ? N1 8OS 102 A 1 HETATM 4 C C2 8OS . . . D 2 -8.933 -25.393 1.091 1 45.54 ? C2 8OS 102 A 1 HETATM 5 N N2 8OS . . . D 2 -9.98 -26.125 1.522 1 45.9 ? N2 8OS 102 A 1 HETATM 6 N N3 8OS . . . D 2 -9.136 -24.099 0.842 1 41.14 ? N3 8OS 102 A 1 HETATM 7 C C3 8OS . . . D 2 -8.108 -23.302 0.435 1 42.76 ? C3 8OS 102 A 1 HETATM 8 C C4 8OS . . . D 2 -6.868 -23.769 0.246 1 41.3 ? C4 8OS 102 A 1 HETATM 9 N N4 8OS . . . D 2 -6.068 -22.805 -0.165 1 48.11 ? N4 8OS 102 A 1 HETATM 10 C C5 8OS . . . D 2 -6.833 -21.708 -0.23 1 44.93 ? C5 8OS 102 A 1 HETATM 11 N N5 8OS . . . D 2 -8.076 -21.995 0.142 1 50.04 ? N5 8OS 102 A 1 HETATM 12 C C6 8OS . . . D 2 -9.171 -20.865 0.069 1 82.36 ? C6 8OS 102 A 1 HETATM 13 O O2 8OS . . . D 2 -8.636 -19.455 -0.101 1 93.3 ? O2 8OS 102 A 1 HETATM 14 C C7 8OS . . . D 2 -10.222 -20.807 1.205 1 97.65 ? C7 8OS 102 A 1 HETATM 15 O O3 8OS . . . D 2 -11.526 -21.095 0.703 1 120.9 ? O3 8OS 102 A 1 HETATM 16 C C8 8OS . . . D 2 -10.131 -19.344 1.835 1 105.33 ? C8 8OS 102 A 1 HETATM 17 O O4 8OS . . . D 2 -11.416 -18.701 2.013 1 103.76 ? O4 8OS 102 A 1 HETATM 18 C C9 8OS . . . D 2 -9.261 -18.5 0.873 1 106.11 ? C9 8OS 102 A 1 HETATM 19 C C10 8OS . . . D 2 -8.384 -17.459 1.656 1 113.33 ? C10 8OS 102 A 1 HETATM 20 O O5 8OS . . . D 2 -6.972 -17.702 1.515 1 125.37 ? O5 8OS 102 A 1 HETATM 21 P P1 8OS . . . D 2 -5.974 -16.774 0.603 1 135.52 ? P1 8OS 102 A 1 HETATM 22 O O6 8OS . . . D 2 -4.579 -17.383 1.067 1 119.41 ? O6 8OS 102 A 1 HETATM 23 O O7 8OS . . . D 2 -6.002 -15.366 1.065 1 142.11 ? O7 8OS 102 A 1 HETATM 24 C C11 8OS . . . D 2 -6.365 -17.12 -1.2 1 141.32 ? C11 8OS 102 A 1 HETATM 25 N N6 8OS . . . D 2 -6.549 -18.33 -1.746 1 139.94 ? N6 8OS 102 A 1 HETATM 26 C C12 8OS . . . D 2 -6.816 -18.153 -3.043 1 137.93 ? C12 8OS 102 A 1 HETATM 27 N N7 8OS . . . D 2 -6.798 -16.837 -3.299 1 140.7 ? N7 8OS 102 A 1 HETATM 28 C C13 8OS . . . D 2 -6.522 -16.201 -2.159 1 139.87 ? C13 8OS 102 A 1 HETATM 29 C C14 8OS . . . D 2 -6.404 -14.668 -1.997 1 128.23 ? C14 8OS 102 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 251 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 29 #