data_5V0J # _model_server_result.job_id 5_tAHndybkiD1VWwYNwbYA _model_server_result.datetime_utc '2024-11-13 18:35:23' _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":"C","auth_seq_id":101}' # _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 . . . C 2 -8.86 -21.324 3.618 1 33.61 ? O1 8OS 101 A 1 HETATM 2 C C1 8OS . . . C 2 -7.836 -21.93 3.651 1 28.34 ? C1 8OS 101 A 1 HETATM 3 N N1 8OS . . . C 2 -8.016 -23.272 3.953 1 26.83 ? N1 8OS 101 A 1 HETATM 4 C C2 8OS . . . C 2 -6.887 -24.055 3.994 1 29.43 ? C2 8OS 101 A 1 HETATM 5 N N2 8OS . . . C 2 -7.012 -25.335 4.342 1 29.54 ? N2 8OS 101 A 1 HETATM 6 N N3 8OS . . . C 2 -5.672 -23.642 3.713 1 31.34 ? N3 8OS 101 A 1 HETATM 7 C C3 8OS . . . C 2 -5.579 -22.34 3.416 1 28.26 ? C3 8OS 101 A 1 HETATM 8 C C4 8OS . . . C 2 -6.629 -21.507 3.361 1 26.85 ? C4 8OS 101 A 1 HETATM 9 N N4 8OS . . . C 2 -6.207 -20.287 2.987 1 30.37 ? N4 8OS 101 A 1 HETATM 10 C C5 8OS . . . C 2 -4.92 -20.428 2.851 1 30.34 ? C5 8OS 101 A 1 HETATM 11 N N5 8OS . . . C 2 -4.499 -21.677 3.075 1 32.74 ? N5 8OS 101 A 1 HETATM 12 C C6 8OS . . . C 2 -3.077 -22.223 2.976 1 37.95 ? C6 8OS 101 A 1 HETATM 13 O O2 8OS . . . C 2 -2.393 -20.987 2.61 1 45.79 ? O2 8OS 101 A 1 HETATM 14 C C7 8OS . . . C 2 -2.844 -23.25 1.858 1 45.44 ? C7 8OS 101 A 1 HETATM 15 O O3 8OS . . . C 2 -1.824 -24.3 2.18 1 47.04 ? O3 8OS 101 A 1 HETATM 16 C C8 8OS . . . C 2 -2.309 -22.354 0.735 1 44.35 ? C8 8OS 101 A 1 HETATM 17 O O4 8OS . . . C 2 -1.406 -23.08 -0.079 1 52.77 ? O4 8OS 101 A 1 HETATM 18 C C9 8OS . . . C 2 -1.493 -21.357 1.551 1 53.77 ? C9 8OS 101 A 1 HETATM 19 C C10 8OS . . . C 2 -1.069 -20.168 0.687 1 57.24 ? C10 8OS 101 A 1 HETATM 20 O O5 8OS . . . C 2 -2.124 -19.202 0.59 1 71.15 ? O5 8OS 101 A 1 HETATM 21 P P1 8OS . . . C 2 -2.175 -18.192 -0.666 1 85.16 ? P1 8OS 101 A 1 HETATM 22 O O6 8OS . . . C 2 -3.655 -18.513 -1.057 1 61.75 ? O6 8OS 101 A 1 HETATM 23 O O7 8OS . . . C 2 -1.25 -18.698 -1.715 1 86.08 ? O7 8OS 101 A 1 HETATM 24 C C11 8OS . . . C 2 -2.05 -16.298 -0.22 1 94.37 ? C11 8OS 101 A 1 HETATM 25 N N6 8OS . . . C 2 -3.018 -15.386 -0.358 1 105.31 ? N6 8OS 101 A 1 HETATM 26 C C12 8OS . . . C 2 -2.53 -14.199 0.032 1 104.46 ? C12 8OS 101 A 1 HETATM 27 N N7 8OS . . . C 2 -1.258 -14.366 0.398 1 102.01 ? N7 8OS 101 A 1 HETATM 28 C C13 8OS . . . C 2 -0.97 -15.661 0.231 1 99.58 ? C13 8OS 101 A 1 HETATM 29 C C14 8OS . . . C 2 0.384 -16.319 0.525 1 89.64 ? C14 8OS 101 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 285 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 29 #