data_5V0K # _model_server_result.job_id dzJHItXUmLLficZcZX48EQ _model_server_result.datetime_utc '2024-11-14 12:36:49' _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 5v0k # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":102}' # _entry.id 5V0K # _exptl.entry_id 5V0K _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 2 _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 5V0K _cell.length_a 42.229 _cell.length_b 42.229 _cell.length_c 40.098 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5V0K _symmetry.cell_setting ? _symmetry.Int_Tables_number 150 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 3 2 1' # _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 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 5_676 x-y+1,-y+2,-z+1 1 0 0 0 -1 0 0 0 -1 0 73.142774 40.098 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 B N N ? 2 C 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 ? ? ? ? ? ? ? ? ? ? ? ? 1.697 ? covale ? covale2 A O3' LCC 2 A LCC 2 1_555 A P LCC 3 A LCC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.693 ? covale ? covale3 A O3' LCC 3 A LCC 3 1_555 A P LCG 4 A LCG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.644 ? covale ? covale4 A O3' LCG 4 A LCG 4 1_555 A P A 5 A A 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.563 ? metalc ? metalc1 A O1P LCC 2 A LCC 2 1_555 D MG MG . A MG 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? metalc ? metalc2 A O1P LCC 2 A LCC 2 1_555 D MG MG . A MG 103 2_775 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? metalc ? metalc3 D MG MG . A MG 103 1_555 E O HOH . A HOH 219 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.217 ? metalc ? metalc4 D MG MG . A MG 103 1_555 E O HOH . A HOH 219 3_575 ? ? ? ? ? ? ? ? ? ? ? ? 2.217 ? hydrog WATSON-CRICK hydrog1 A N1 LCG 4 A LCG 4 1_555 A N3 C 13 A C 13 5_676 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N2 LCG 4 A LCG 4 1_555 A O2 C 13 A C 13 5_676 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O6 LCG 4 A LCG 4 1_555 A N4 C 13 A C 13 5_676 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N1 A 5 A A 5 1_555 A N3 U 12 A U 12 5_676 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N6 A 5 A A 5 1_555 A O4 U 12 A U 12 5_676 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A N3 C 6 A C 6 1_555 A N1 G 11 A G 11 5_676 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N4 C 6 A C 6 1_555 A O6 G 11 A G 11 5_676 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A O2 C 6 A C 6 1_555 A N2 G 11 A G 11 5_676 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A N3 U 7 A U 7 1_555 A N1 A 10 A A 10 5_676 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A O4 U 7 A U 7 1_555 A N6 A 10 A A 10 5_676 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A N3 U 8 A U 8 1_555 A N1 A 9 A A 9 5_676 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A O4 U 8 A U 8 1_555 A N6 A 9 A A 9 5_676 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N1 A 9 A A 9 1_555 A N3 U 8 A U 8 5_676 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A N6 A 9 A A 9 1_555 A O4 U 8 A U 8 5_676 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A N1 A 10 A A 10 1_555 A N3 U 7 A U 7 5_676 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A N6 A 10 A A 10 1_555 A O4 U 7 A U 7 5_676 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A N1 G 11 A G 11 1_555 A N3 C 6 A C 6 5_676 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A N2 G 11 A G 11 1_555 A O2 C 6 A C 6 5_676 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 A O6 G 11 A G 11 1_555 A N4 C 6 A C 6 5_676 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 A N3 U 12 A U 12 1_555 A N1 A 5 A A 5 5_676 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 A O4 U 12 A U 12 1_555 A N6 A 5 A A 5 5_676 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 A N3 C 13 A C 13 1_555 A N1 LCG 4 A LCG 4 5_676 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 A N4 C 13 A C 13 1_555 A O6 LCG 4 A LCG 4 5_676 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 A O2 C 13 A C 13 1_555 A N2 LCG 4 A LCG 4 5_676 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _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 5V0K _atom_sites.fract_transf_matrix[1][1] 0.02368 _atom_sites.fract_transf_matrix[1][2] 0.013672 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.027344 _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] 0.024939 _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 B 2 8OS A 1 101 1 8OS rG . C 2 8OS A 1 102 2 8OS rG . D 3 MG A 1 103 1 MG MG . E 4 HOH A 1 201 24 HOH HOH . E 4 HOH A 2 202 8 HOH HOH . E 4 HOH A 3 203 22 HOH HOH . E 4 HOH A 4 204 25 HOH HOH . E 4 HOH A 5 205 7 HOH HOH . E 4 HOH A 6 206 15 HOH HOH . E 4 HOH A 7 207 13 HOH HOH . E 4 HOH A 8 208 11 HOH HOH . E 4 HOH A 9 209 30 HOH HOH . E 4 HOH A 10 210 9 HOH HOH . E 4 HOH A 11 211 1 HOH HOH . E 4 HOH A 12 212 4 HOH HOH . E 4 HOH A 13 213 14 HOH HOH . E 4 HOH A 14 214 16 HOH HOH . E 4 HOH A 15 215 28 HOH HOH . E 4 HOH A 16 216 18 HOH HOH . E 4 HOH A 17 217 29 HOH HOH . E 4 HOH A 18 218 23 HOH HOH . E 4 HOH A 19 219 12 HOH HOH . E 4 HOH A 20 220 3 HOH HOH . E 4 HOH A 21 221 10 HOH HOH . E 4 HOH A 22 222 26 HOH HOH . E 4 HOH A 23 223 31 HOH HOH . E 4 HOH A 24 224 5 HOH HOH . E 4 HOH A 25 225 27 HOH HOH . E 4 HOH A 26 226 21 HOH HOH . E 4 HOH A 27 227 2 HOH HOH . E 4 HOH A 28 228 6 HOH HOH . E 4 HOH A 29 229 17 HOH HOH . E 4 HOH A 30 230 20 HOH HOH . E 4 HOH A 31 231 19 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 2 -1.843 37.231 -1.624 1 18.94 ? O1 8OS 102 A 1 HETATM 2 C C1 8OS . . . C 2 -3.018 37.718 -1.602 1 18.44 ? C1 8OS 102 A 1 HETATM 3 N N1 8OS . . . C 2 -3.094 39.112 -1.648 1 18.68 ? N1 8OS 102 A 1 HETATM 4 C C2 8OS . . . C 2 -4.323 39.759 -1.658 1 21.55 ? C2 8OS 102 A 1 HETATM 5 N N2 8OS . . . C 2 -4.266 41.088 -1.608 1 22.89 ? N2 8OS 102 A 1 HETATM 6 N N3 8OS . . . C 2 -5.47 39.082 -1.689 1 19.6 ? N3 8OS 102 A 1 HETATM 7 C C3 8OS . . . C 2 -5.4 37.714 -1.73 1 19.56 ? C3 8OS 102 A 1 HETATM 8 C C4 8OS . . . C 2 -4.188 37.046 -1.686 1 19.63 ? C4 8OS 102 A 1 HETATM 9 N N4 8OS . . . C 2 -4.462 35.73 -1.725 1 21.76 ? N4 8OS 102 A 1 HETATM 10 C C5 8OS . . . C 2 -5.763 35.559 -1.74 1 19.32 ? C5 8OS 102 A 1 HETATM 11 N N5 8OS . . . C 2 -6.361 36.802 -1.722 1 21.64 ? N5 8OS 102 A 1 HETATM 12 C C6 8OS . . . C 2 -7.79 37.181 -1.704 1 21.36 ? C6 8OS 102 A 1 HETATM 13 O O2 8OS . . . C 2 -8.559 35.894 -1.552 1 23.5 ? O2 8OS 102 A 1 HETATM 14 C C7 8OS . . . C 2 -8.202 37.73 -3.023 1 23.28 ? C7 8OS 102 A 1 HETATM 15 O O3 8OS . . . C 2 -9.351 38.652 -2.761 1 25.63 ? O3 8OS 102 A 1 HETATM 16 C C8 8OS . . . C 2 -8.615 36.469 -3.748 1 25.25 ? C8 8OS 102 A 1 HETATM 17 O O4 8OS . . . C 2 -9.521 36.72 -4.81 1 26.87 ? O4 8OS 102 A 1 HETATM 18 C C9 8OS . . . C 2 -9.279 35.664 -2.706 1 25.56 ? C9 8OS 102 A 1 HETATM 19 C C10 8OS . . . C 2 -9.24 34.137 -3.053 1 27.47 ? C10 8OS 102 A 1 HETATM 20 O O5 8OS . . . C 2 -9.967 33.627 -1.978 1 32.98 ? O5 8OS 102 A 1 HETATM 21 P P1 8OS . . . C 2 -10.845 32.202 -2.165 1 39.31 ? P1 8OS 102 A 1 HETATM 22 O O6 8OS . . . C 2 -11.608 32.074 -0.896 1 37.6 ? O6 8OS 102 A 1 HETATM 23 O O7 8OS . . . C 2 -11.669 32.374 -3.507 1 43.45 ? O7 8OS 102 A 1 HETATM 24 C C11 8OS . . . C 2 -9.574 30.97 -2.378 1 43.95 ? C11 8OS 102 A 1 HETATM 25 N N6 8OS . . . C 2 -8.618 30.807 -1.423 1 51.3 ? N6 8OS 102 A 1 HETATM 26 C C12 8OS . . . C 2 -7.855 29.799 -1.841 1 51.87 ? C12 8OS 102 A 1 HETATM 27 N N7 8OS . . . C 2 -8.351 29.351 -3.03 1 53.16 ? N7 8OS 102 A 1 HETATM 28 C C13 8OS . . . C 2 -9.444 30.067 -3.348 1 49.82 ? C13 8OS 102 A 1 HETATM 29 C C14 8OS . . . C 2 -10.312 29.891 -4.632 1 49.18 ? C14 8OS 102 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 197 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 29 #