data_5VCF # _model_server_result.job_id U_si1ZBzwxcMUJy2_mGgfw _model_server_result.datetime_utc '2024-12-02 15:18:49' _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 5vcf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":101}' # _entry.id 5VCF # _exptl.entry_id 5VCF _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 120 _cell.entry_id 5VCF _cell.length_a 71.073 _cell.length_b 71.073 _cell.length_c 71.274 _cell.Z_PDB 9 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VCF _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3' # _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 _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 hydrog WATSON-CRICK hydrog1 A N3 C 1 A C 1 1_555 B N1 G 12 B G 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N4 C 1 A C 1 1_555 B O6 G 12 B G 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O2 C 1 A C 1 1_555 B N2 G 12 B G 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_16_PAIR hydrog4 A N3 U 2 A U 2 1_555 B O2 U 11 B U 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_16_PAIR hydrog5 A O4 U 2 A U 2 1_555 B N3 U 11 B U 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A N1 G 3 A G 3 1_555 B N3 C 10 B C 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N2 G 3 A G 3 1_555 B O2 C 10 B C 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A O6 G 3 A G 3 1_555 B N4 C 10 B C 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A N3 C 4 A C 4 1_555 B N1 G 9 B G 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N4 C 4 A C 4 1_555 B O6 G 9 B G 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A O2 C 4 A C 4 1_555 B N2 G 9 B G 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_16_PAIR hydrog12 A N3 U 5 A U 5 1_555 B O2 U 8 B U 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_16_PAIR hydrog13 A O4 U 5 A U 5 1_555 B N3 U 8 B U 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A N1 G 6 A G 6 1_555 B N3 C 7 B C 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A N2 G 6 A G 6 1_555 B O2 C 7 B C 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A O6 G 6 A G 6 1_555 B N4 C 7 B C 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A N1 G 7 A G 7 1_555 B N3 C 6 B C 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A N2 G 7 A G 7 1_555 B O2 C 6 B C 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 A O6 G 7 A G 7 1_555 B N4 C 6 B C 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 A N3 C 8 A C 8 1_555 B N1 G 5 B G 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 A N4 C 8 A C 8 1_555 B O6 G 5 B G 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 A O2 C 8 A C 8 1_555 B N2 G 5 B G 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'REVERSED HOOGSTEEN' hydrog23 A N3 U 9 A U 9 1_555 B N7 A 3 B A 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'REVERSED HOOGSTEEN' hydrog24 A O2 U 9 A U 9 1_555 B N6 A 3 B A 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 A N1 A 11 A A 11 1_555 B N3 U 4 B U 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 A N6 A 11 A A 11 1_555 B O4 U 4 B U 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_28_PAIR hydrog27 A N1 G 12 A G 12 1_555 B O2 U 2 B U 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_28_PAIR hydrog28 A O6 G 12 A G 12 1_555 B N3 U 2 B U 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'G-U MISPAIR' hydrog29 A N2 G 12 A G 12 1_555 B O4 U 4 B U 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 A N1 G 13 A G 13 1_555 B N3 C 1 B C 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 A N2 G 13 A G 13 1_555 B O2 C 1 B C 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 A O6 G 13 A G 13 1_555 B N4 C 1 B C 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 A N3 C 15 A C 15 1_555 A N1 G 22 A G 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog34 A N4 C 15 A C 15 1_555 A O6 G 22 A G 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog35 A O2 C 15 A C 15 1_555 A N2 G 22 A G 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog36 A N3 C 16 A C 16 1_555 A N1 G 21 A G 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog37 A N4 C 16 A C 16 1_555 A O6 G 21 A G 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog38 A O2 C 16 A C 16 1_555 A N2 G 21 A G 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'G-A MISPAIR' hydrog39 A N2 G 17 A G 17 1_555 A N7 A 20 A A 20 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 5VCF _atom_sites.fract_transf_matrix[1][1] 0.01407 _atom_sites.fract_transf_matrix[1][2] 0.008123 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016247 _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] 0.01403 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # _pdbx_nonpoly_scheme.asym_id C _pdbx_nonpoly_scheme.entity_id 3 _pdbx_nonpoly_scheme.mon_id 8OS _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 101 _pdbx_nonpoly_scheme.auth_seq_num 1 _pdbx_nonpoly_scheme.pdb_mon_id 8OS _pdbx_nonpoly_scheme.auth_mon_id rG _pdbx_nonpoly_scheme.pdb_ins_code . # 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 57.494 37.897 10.739 1 57.85 ? O1 8OS 101 A 1 HETATM 2 C C1 8OS . . . C 3 58.708 38.183 10.739 1 63.71 ? C1 8OS 101 A 1 HETATM 3 N N1 8OS . . . C 3 59.691 37.206 11.06 1 59.85 ? N1 8OS 101 A 1 HETATM 4 C C2 8OS . . . C 3 61.047 37.538 11.057 1 59.2 ? C2 8OS 101 A 1 HETATM 5 N N2 8OS . . . C 3 61.963 36.639 11.36 1 57.5 ? N2 8OS 101 A 1 HETATM 6 N N3 8OS . . . C 3 61.415 38.787 10.751 1 62.32 ? N3 8OS 101 A 1 HETATM 7 C C3 8OS . . . C 3 60.45 39.71 10.433 1 68.41 ? C3 8OS 101 A 1 HETATM 8 C C4 8OS . . . C 3 59.122 39.415 10.429 1 63.57 ? C4 8OS 101 A 1 HETATM 9 N N4 8OS . . . C 3 58.436 40.522 10.104 1 63.75 ? N4 8OS 101 A 1 HETATM 10 C C5 8OS . . . C 3 59.345 41.502 9.893 1 64.78 ? C5 8OS 101 A 1 HETATM 11 N N5 8OS . . . C 3 60.57 40.998 10.076 1 65.85 ? N5 8OS 101 A 1 HETATM 12 C C6 8OS . . . C 3 61.901 41.635 10.12 1 72.92 ? C6 8OS 101 A 1 HETATM 13 O O2 8OS . . . C 3 61.735 43.03 9.884 1 81.62 ? O2 8OS 101 A 1 HETATM 14 C C7 8OS . . . C 3 62.965 41.166 9.217 1 80.89 ? C7 8OS 101 A 1 HETATM 15 O O3 8OS . . . C 3 64.225 41.447 9.839 1 74.39 ? O3 8OS 101 A 1 HETATM 16 C C8 8OS . . . C 3 62.724 42.061 8.033 1 88.58 ? C8 8OS 101 A 1 HETATM 17 O O4 8OS . . . C 3 63.914 42.183 7.197 1 97.53 ? O4 8OS 101 A 1 HETATM 18 C C9 8OS . . . C 3 62.381 43.383 8.651 1 89.82 ? C9 8OS 101 A 1 HETATM 19 C C10 8OS . . . C 3 61.394 44.143 7.722 1 94.49 ? C10 8OS 101 A 1 HETATM 20 O O5 8OS . . . C 3 60.142 43.416 7.591 1 101.67 ? O5 8OS 101 A 1 HETATM 21 P P1 8OS . . . C 3 58.982 43.853 6.508 1 110.1 ? P1 8OS 101 A 1 HETATM 22 O O6 8OS . . . C 3 58.598 42.464 5.739 1 122.93 ? O6 8OS 101 A 1 HETATM 23 O O7 8OS . . . C 3 59.542 44.881 5.572 1 117.81 ? O7 8OS 101 A 1 HETATM 24 C C11 8OS . . . C 3 57.514 44.105 7.264 1 130.42 ? C11 8OS 101 A 1 HETATM 25 N N6 8OS . . . C 3 56.768 43.119 7.8 1 120.9 ? N6 8OS 101 A 1 HETATM 26 C C12 8OS . . . C 3 55.677 43.722 8.292 1 144.72 ? C12 8OS 101 A 1 HETATM 27 N N7 8OS . . . C 3 55.767 45.049 8.04 1 162.31 ? N7 8OS 101 A 1 HETATM 28 C C13 8OS . . . C 3 56.912 45.29 7.389 1 145.73 ? C13 8OS 101 A 1 HETATM 29 C C14 8OS . . . C 3 57.427 46.686 6.9 1 120.91 ? C14 8OS 101 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 287 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 29 #