data_5UX3 # _model_server_result.job_id WDp21tWYlR5xBAs_J7OLhA _model_server_result.datetime_utc '2024-11-20 15:24:13' _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 5ux3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":101}' # _entry.id 5UX3 # _exptl.entry_id 5UX3 _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 5UX3 _cell.length_a 46.527 _cell.length_b 46.527 _cell.length_c 156.938 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5UX3 _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 _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 5 A G 5 1_555 A P 5BU 6 A 5BU 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.674 ? covale ? covale2 A O3' 5BU 6 A 5BU 6 1_555 A P G 7 A G 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.705 ? covale ? covale3 A O3' G 7 A G 7 1_555 A P LCC 8 A LCC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.626 ? covale ? covale4 A O3' LCC 8 A LCC 8 1_555 A P LCC 9 A LCC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.656 ? covale ? covale5 A O3' LCC 9 A LCC 9 1_555 A P G 10 A G 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.704 ? covale ? covale6 B O4 8OS 1 B 8OS 1 1_555 B P C 2 B C 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.681 ? 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 5BU 6 A 5BU 6 1_555 B N1 A 3 B A 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A O4 5BU 6 A 5BU 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 'G-A MISPAIR' hydrog34 A N2 G 16 A G 16 1_555 A N7 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 36 n n O7 P1 8OS doub 37 n n C13 N7 8OS sing 38 n y C13 C11 8OS doub 39 n y C10 C9 8OS sing 40 n n C10 O5 8OS sing 41 n n N7 C12 8OS doub 42 n y O4 C8 8OS sing 43 n n P1 C11 8OS sing 44 n n P1 O5 8OS sing 45 n n P1 O6 8OS sing 46 n n C11 N6 8OS sing 47 n y C9 C8 8OS sing 48 n n C9 O2 8OS sing 49 n n C8 C7 8OS sing 50 n n C12 N6 8OS sing 51 n y O2 C6 8OS sing 52 n n O3 C7 8OS sing 53 n n C7 C6 8OS sing 54 n n C6 N5 8OS sing 55 n n C5 N5 8OS sing 56 n y C5 N4 8OS doub 57 n y N5 C3 8OS sing 58 n y N4 C4 8OS sing 59 n y C3 N3 8OS sing 60 n n C3 C4 8OS doub 61 n y N3 C2 8OS doub 62 n n C4 C1 8OS sing 63 n n C2 N2 8OS sing 64 n n C2 N1 8OS sing 65 n n C1 N1 8OS sing 66 n n C1 O1 8OS doub 67 n n N1 H1 8OS sing 68 n n N2 H2 8OS sing 69 n n N2 H3 8OS sing 70 n n C5 H4 8OS sing 71 n n C6 H5 8OS sing 72 n n C7 H6 8OS sing 73 n n O3 H7 8OS sing 74 n n C8 H8 8OS sing 75 n n O4 H9 8OS sing 76 n n C9 H10 8OS sing 77 n n C10 H11 8OS sing 78 n n C10 H12 8OS sing 79 n n O6 H13 8OS sing 80 n n N6 H14 8OS sing 81 n n C12 H15 8OS sing 82 n n C14 H17 8OS sing 83 n n C14 H18 8OS sing 84 n n C14 H19 8OS sing 85 n n # _atom_sites.entry_id 5UX3 _atom_sites.fract_transf_matrix[1][1] 0.021493 _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] 0.021493 _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] 0.006372 _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 B 1 101 1 8OS rG . D 4 HOH A 1 101 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 62.589 41.803 182.04 1 79.09 ? O1 8OS 101 B 1 HETATM 2 C C1 8OS . . . C 3 63.551 41.844 181.295 1 78.93 ? C1 8OS 101 B 1 HETATM 3 N N1 8OS . . . C 3 64.681 41.151 181.678 1 77.35 ? N1 8OS 101 B 1 HETATM 4 C C2 8OS . . . C 3 65.783 41.175 180.862 1 78.52 ? C2 8OS 101 B 1 HETATM 5 N N2 8OS . . . C 3 66.894 40.519 181.186 1 76.12 ? N2 8OS 101 B 1 HETATM 6 N N3 8OS . . . C 3 65.696 41.873 179.732 1 86.83 ? N3 8OS 101 B 1 HETATM 7 C C3 8OS . . . C 3 64.576 42.522 179.375 1 82.63 ? C3 8OS 101 B 1 HETATM 8 C C4 8OS . . . C 3 63.502 42.505 180.143 1 83.51 ? C4 8OS 101 B 1 HETATM 9 N N4 8OS . . . C 3 62.549 43.225 179.552 1 85.94 ? N4 8OS 101 B 1 HETATM 10 C C5 8OS . . . C 3 63.052 43.659 178.407 1 87.07 ? C5 8OS 101 B 1 HETATM 11 N N5 8OS . . . C 3 64.302 43.229 178.292 1 84.12 ? N5 8OS 101 B 1 HETATM 12 C C6 8OS . . . C 3 65.305 43.379 177.166 1 75.15 ? C6 8OS 101 B 1 HETATM 13 O O2 8OS . . . C 3 64.979 44.415 176.229 1 73.98 ? O2 8OS 101 B 1 HETATM 14 C C7 8OS . . . C 3 65.248 42.034 176.327 1 72.26 ? C7 8OS 101 B 1 HETATM 15 O O3 8OS . . . C 3 66.466 41.727 175.634 1 74.27 ? O3 8OS 101 B 1 HETATM 16 C C8 8OS . . . C 3 64.149 42.356 175.369 1 71.26 ? C8 8OS 101 B 1 HETATM 17 O O4 8OS . . . C 3 64.147 41.517 174.206 1 71.67 ? O4 8OS 101 B 1 HETATM 18 C C9 8OS . . . C 3 64.561 43.738 174.989 1 71.35 ? C9 8OS 101 B 1 HETATM 19 C C10 8OS . . . C 3 63.419 44.386 174.175 1 79.82 ? C10 8OS 101 B 1 HETATM 20 O O5 8OS . . . C 3 62.509 45.266 174.85 1 78.95 ? O5 8OS 101 B 1 HETATM 21 P P1 8OS . . . C 3 61.074 44.701 175.211 1 93.74 ? P1 8OS 101 B 1 HETATM 22 O O6 8OS . . . C 3 60.451 45.554 176.104 1 94.74 ? O6 8OS 101 B 1 HETATM 23 O O7 8OS . . . C 3 61.046 43.119 175.298 1 95.95 ? O7 8OS 101 B 1 HETATM 24 C C11 8OS . . . C 3 60.412 44.774 173.431 1 108.41 ? C11 8OS 101 B 1 HETATM 25 N N6 8OS . . . C 3 59.949 43.735 172.684 1 94.68 ? N6 8OS 101 B 1 HETATM 26 C C12 8OS . . . C 3 59.541 44.256 171.536 1 97.31 ? C12 8OS 101 B 1 HETATM 27 N N7 8OS . . . C 3 59.737 45.598 171.578 1 106.24 ? N7 8OS 101 B 1 HETATM 28 C C13 8OS . . . C 3 60.265 45.927 172.753 1 102.94 ? C13 8OS 101 B 1 HETATM 29 C C14 8OS . . . C 3 60.649 47.374 173.199 1 94.61 ? C14 8OS 101 B 1 # _model_server_stats.io_time_ms 58 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 287 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 29 #