data_6C8I # _model_server_result.job_id shfV2Kuw7tsFKTTyWAVjPg _model_server_result.datetime_utc '2024-11-22 06:45:34' _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 6c8i # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":102}' # _entry.id 6C8I # _exptl.entry_id 6C8I _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 428.297 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-O-[(R)-(2-amino-1H-imidazol-1-yl)(hydroxy)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 6C8I _cell.length_a 43.843 _cell.length_b 43.843 _cell.length_c 85.219 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6C8I _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,F,G,H,I,J _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 ? 3 D N N ? 3 E N N ? 3 G N N ? 3 H 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 ? ? ? ? ? ? ? ? ? ? ? ? 1.673 ? covale ? covale2 A O3' LCC 2 A LCC 2 1_555 A P LCC 3 A LCC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.696 ? covale ? covale3 A O3' LCC 3 A LCC 3 1_555 A P LCG 4 A LCG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.681 ? covale ? covale4 A O3' LCG 4 A LCG 4 1_555 A P A 5 A A 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.682 ? covale ? covale5 B O3' LCC 1 B LCC 1 1_555 B P LCC 2 B LCC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.649 ? covale ? covale6 B O3' LCC 2 B LCC 2 1_555 B P LCC 3 B LCC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.678 ? covale ? covale7 B O3' LCC 3 B LCC 3 1_555 B P LCG 4 B LCG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.701 ? covale ? covale8 B O3' LCG 4 B LCG 4 1_555 B P A 5 B A 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.66 ? metalc ? metalc1 C MG MG . A MG 101 1_555 G O6 EQ4 . B EQ4 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? metalc ? metalc2 C MG MG . A MG 101 1_555 G O5 EQ4 . B EQ4 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.573 ? metalc ? metalc3 C MG MG . A MG 101 1_555 G O6 EQ4 . B EQ4 102 3_665 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? metalc ? metalc4 C MG MG . A MG 101 1_555 G O5 EQ4 . B EQ4 102 3_665 ? ? ? ? ? ? ? ? ? ? ? ? 2.573 ? metalc ? metalc5 D O5 EQ4 . A EQ4 102 1_555 F MG MG . B MG 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? metalc ? metalc6 D O6 EQ4 . A EQ4 102 1_555 F MG MG . B MG 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.558 ? metalc ? metalc7 D O5 EQ4 . A EQ4 102 1_555 F MG MG . B MG 101 3_665 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? metalc ? metalc8 D O6 EQ4 . A EQ4 102 1_555 F MG MG . B MG 101 3_665 ? ? ? ? ? ? ? ? ? ? ? ? 2.524 ? hydrog WATSON-CRICK hydrog1 A N1 LCG 4 A LCG 4 1_555 B N3 C 13 B C 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N2 LCG 4 A LCG 4 1_555 B O2 C 13 B C 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O6 LCG 4 A LCG 4 1_555 B N4 C 13 B C 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N1 A 5 A A 5 1_555 B N3 U 12 B U 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N6 A 5 A A 5 1_555 B O4 U 12 B U 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A N3 C 6 A C 6 1_555 B N1 G 11 B G 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N4 C 6 A C 6 1_555 B O6 G 11 B G 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A O2 C 6 A C 6 1_555 B N2 G 11 B G 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A N3 U 7 A U 7 1_555 B N1 A 10 B A 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A O4 U 7 A U 7 1_555 B N6 A 10 B A 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A N3 U 8 A U 8 1_555 B N1 A 9 B A 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A O4 U 8 A U 8 1_555 B N6 A 9 B A 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N1 A 9 A A 9 1_555 B N3 U 8 B U 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A N6 A 9 A A 9 1_555 B O4 U 8 B U 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A N1 A 10 A A 10 1_555 B N3 U 7 B U 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A N6 A 10 A A 10 1_555 B O4 U 7 B U 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A N1 G 11 A G 11 1_555 B N3 C 6 B C 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A N2 G 11 A G 11 1_555 B O2 C 6 B C 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 A O6 G 11 A G 11 1_555 B N4 C 6 B C 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 A N3 U 12 A U 12 1_555 B N1 A 5 B A 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 A O4 U 12 A U 12 1_555 B N6 A 5 B A 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 A N3 C 13 A C 13 1_555 B N1 LCG 4 B LCG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 A N4 C 13 A C 13 1_555 B O6 LCG 4 B LCG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 A O2 C 13 A C 13 1_555 B N2 LCG 4 B LCG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C13 H17 N8 O7 P' _chem_comp.formula_weight 428.297 _chem_comp.id EQ4 _chem_comp.mon_nstd_flag n _chem_comp.name "5'-O-[(R)-(2-amino-1H-imidazol-1-yl)(hydroxy)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 C12 N7 EQ4 sing 76 n y C12 C11 EQ4 doub 77 n y N7 C13 EQ4 doub 78 n y C11 N6 EQ4 sing 79 n y C13 N8 EQ4 sing 80 n n C13 N6 EQ4 sing 81 n y N6 P1 EQ4 sing 82 n n O2 P1 EQ4 doub 83 n n O5 C3 EQ4 sing 84 n n P1 O3 EQ4 sing 85 n n P1 O1 EQ4 sing 86 n n O3 C1 EQ4 sing 87 n n C3 C2 EQ4 sing 88 n n C3 C4 EQ4 sing 89 n n O6 C4 EQ4 sing 90 n n C2 C1 EQ4 sing 91 n n C2 O4 EQ4 sing 92 n n C4 C5 EQ4 sing 93 n n O4 C5 EQ4 sing 94 n n C5 N5 EQ4 sing 95 n n C10 N5 EQ4 sing 96 n y C10 N4 EQ4 doub 97 n y N5 C7 EQ4 sing 98 n y N4 C8 EQ4 sing 99 n y C7 C8 EQ4 doub 100 n y C7 N3 EQ4 sing 101 n n C8 C9 EQ4 sing 102 n n N3 C6 EQ4 doub 103 n n C9 O7 EQ4 doub 104 n n C9 N1 EQ4 sing 105 n n C6 N1 EQ4 sing 106 n n C6 N2 EQ4 sing 107 n n O1 H1 EQ4 sing 108 n n C1 H2 EQ4 sing 109 n n C1 H3 EQ4 sing 110 n n C2 H4 EQ4 sing 111 n n C3 H5 EQ4 sing 112 n n O5 H6 EQ4 sing 113 n n C4 H7 EQ4 sing 114 n n O6 H8 EQ4 sing 115 n n C5 H9 EQ4 sing 116 n n N1 H10 EQ4 sing 117 n n N2 H11 EQ4 sing 118 n n N2 H12 EQ4 sing 119 n n C10 H13 EQ4 sing 120 n n C11 H14 EQ4 sing 121 n n C12 H15 EQ4 sing 122 n n N8 H16 EQ4 sing 123 n n N8 H17 EQ4 sing 124 n n # _atom_sites.entry_id 6C8I _atom_sites.fract_transf_matrix[1][1] 0.022809 _atom_sites.fract_transf_matrix[1][2] 0.013169 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.026337 _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] 0.011734 _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 MG A 1 101 2 MG MG . D 3 EQ4 A 1 102 1 EQ4 NG . E 3 EQ4 A 1 103 2 EQ4 NG . F 2 MG B 1 101 1 MG MG . G 3 EQ4 B 1 102 3 EQ4 NG . H 3 EQ4 B 1 103 4 EQ4 NG . I 4 HOH A 1 201 17 HOH HOH . I 4 HOH A 2 202 8 HOH HOH . I 4 HOH A 3 203 15 HOH HOH . I 4 HOH A 4 204 16 HOH HOH . I 4 HOH A 5 205 4 HOH HOH . I 4 HOH A 6 206 13 HOH HOH . I 4 HOH A 7 207 1 HOH HOH . I 4 HOH A 8 208 9 HOH HOH . I 4 HOH A 9 209 5 HOH HOH . J 4 HOH B 1 201 3 HOH HOH . J 4 HOH B 2 202 19 HOH HOH . J 4 HOH B 3 203 10 HOH HOH . J 4 HOH B 4 204 2 HOH HOH . J 4 HOH B 5 205 14 HOH HOH . J 4 HOH B 6 206 7 HOH HOH . J 4 HOH B 7 207 6 HOH HOH . J 4 HOH B 8 208 18 HOH HOH . J 4 HOH B 9 209 12 HOH HOH . J 4 HOH B 10 210 11 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 P P1 EQ4 . . . D 3 26.302 7.029 -0.14 1 53.12 ? P1 EQ4 102 A 1 HETATM 2 O O1 EQ4 . . . D 3 26.996 6.183 0.899 1 56.08 ? O1 EQ4 102 A 1 HETATM 3 O O2 EQ4 . . . D 3 25.056 6.464 -0.909 1 51.62 ? O2 EQ4 102 A 1 HETATM 4 C C1 EQ4 . . . D 3 24.308 8.491 0.851 1 35.41 ? C1 EQ4 102 A 1 HETATM 5 O O3 EQ4 . . . D 3 25.664 8.313 0.724 1 46.2 ? O3 EQ4 102 A 1 HETATM 6 C C2 EQ4 . . . D 3 24.135 9.757 1.706 1 32.56 ? C2 EQ4 102 A 1 HETATM 7 O O4 EQ4 . . . D 3 24.887 9.576 2.852 1 29.77 ? O4 EQ4 102 A 1 HETATM 8 C C3 EQ4 . . . D 3 24.793 11.067 1.138 1 31.31 ? C3 EQ4 102 A 1 HETATM 9 O O5 EQ4 . . . D 3 23.915 11.778 0.327 1 37.26 ? O5 EQ4 102 A 1 HETATM 10 C C4 EQ4 . . . D 3 24.988 11.878 2.403 1 29.11 ? C4 EQ4 102 A 1 HETATM 11 O O6 EQ4 . . . D 3 23.813 12.435 2.899 1 28.15 ? O6 EQ4 102 A 1 HETATM 12 C C5 EQ4 . . . D 3 25.498 10.801 3.375 1 28.61 ? C5 EQ4 102 A 1 HETATM 13 N N1 EQ4 . . . D 3 29.963 13.107 4.341 1 29.37 ? N1 EQ4 102 A 1 HETATM 14 C C6 EQ4 . . . D 3 28.67 13.624 4.43 1 29.24 ? C6 EQ4 102 A 1 HETATM 15 N N2 EQ4 . . . D 3 28.566 14.872 4.796 1 28.94 ? N2 EQ4 102 A 1 HETATM 16 N N3 EQ4 . . . D 3 27.586 12.853 4.145 1 26.54 ? N3 EQ4 102 A 1 HETATM 17 C C7 EQ4 . . . D 3 27.834 11.566 3.777 1 30.41 ? C7 EQ4 102 A 1 HETATM 18 C C8 EQ4 . . . D 3 29.107 11.03 3.653 1 26.8 ? C8 EQ4 102 A 1 HETATM 19 C C9 EQ4 . . . D 3 30.18 11.794 3.925 1 31.66 ? C9 EQ4 102 A 1 HETATM 20 O O7 EQ4 . . . D 3 31.367 11.408 3.867 1 25.15 ? O7 EQ4 102 A 1 HETATM 21 N N4 EQ4 . . . D 3 29.004 9.749 3.212 1 28.13 ? N4 EQ4 102 A 1 HETATM 22 C C10 EQ4 . . . D 3 27.682 9.503 3.089 1 27.79 ? C10 EQ4 102 A 1 HETATM 23 N N5 EQ4 . . . D 3 26.973 10.643 3.395 1 27.92 ? N5 EQ4 102 A 1 HETATM 24 N N6 EQ4 . . . D 3 27.18 7.979 -1.208 1 68.75 ? N6 EQ4 102 A 1 HETATM 25 C C11 EQ4 . . . D 3 28.477 8.269 -1.377 1 73.85 ? C11 EQ4 102 A 1 HETATM 26 C C12 EQ4 . . . D 3 28.557 9.131 -2.416 1 78.14 ? C12 EQ4 102 A 1 HETATM 27 N N7 EQ4 . . . D 3 27.341 9.379 -2.88 1 83.84 ? N7 EQ4 102 A 1 HETATM 28 C C13 EQ4 . . . D 3 26.496 8.675 -2.129 1 78.63 ? C13 EQ4 102 A 1 HETATM 29 N N8 EQ4 . . . D 3 25.159 8.667 -2.296 1 78.13 ? N8 EQ4 102 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 242 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 29 #