data_5GNR # _model_server_result.job_id on6JFNjDjAy3pDhoSNbvhg _model_server_result.datetime_utc '2024-11-13 00:06:11' _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 5gnr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1000}' # _entry.id 5GNR # _exptl.entry_id 5GNR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 2 _entity.src_method man _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation K88A _entity.pdbx_fragment 'UNP residues 1-364' _entity.pdbx_ec 3.6.5.- # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 5GNR _cell.length_a 71.34 _cell.length_b 74.975 _cell.length_c 94.451 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5GNR _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id O _struct_conn.ptnr1_label_comp_id VAL _struct_conn.ptnr1_label_seq_id 265 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id VAL _struct_conn.ptnr1_auth_seq_id 265 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id A _struct_conn.ptnr2_label_atom_id CG _struct_conn.ptnr2_label_comp_id LYS _struct_conn.ptnr2_label_seq_id 269 _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id LYS _struct_conn.ptnr2_auth_seq_id 269 _struct_conn.ptnr2_symmetry 1_555 _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 1.279 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C10 H15 N5 O11 P2' _chem_comp.formula_weight 443.201 _chem_comp.id GDP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-5'-DIPHOSPHATE" _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 PB O1B GDP doub 83 n n PB O2B GDP sing 84 n n PB O3B GDP sing 85 n n PB O3A GDP sing 86 n n O2B HOB2 GDP sing 87 n n O3B HOB3 GDP sing 88 n n O3A PA GDP sing 89 n n PA O1A GDP doub 90 n n PA O2A GDP sing 91 n n PA O5' GDP sing 92 n n O2A HOA2 GDP sing 93 n n O5' C5' GDP sing 94 n n C5' C4' GDP sing 95 n n C5' H5' GDP sing 96 n n C5' "H5''" GDP sing 97 n n C4' O4' GDP sing 98 n n C4' C3' GDP sing 99 n n C4' H4' GDP sing 100 n n O4' C1' GDP sing 101 n n C3' O3' GDP sing 102 n n C3' C2' GDP sing 103 n n C3' H3' GDP sing 104 n n O3' HO3' GDP sing 105 n n C2' O2' GDP sing 106 n n C2' C1' GDP sing 107 n n C2' H2' GDP sing 108 n n O2' HO2' GDP sing 109 n n C1' N9 GDP sing 110 n n C1' H1' GDP sing 111 n n N9 C8 GDP sing 112 n y N9 C4 GDP sing 113 n y C8 N7 GDP doub 114 n y C8 H8 GDP sing 115 n n N7 C5 GDP sing 116 n y C5 C6 GDP sing 117 n n C5 C4 GDP doub 118 n y C6 O6 GDP doub 119 n n C6 N1 GDP sing 120 n n N1 C2 GDP sing 121 n n N1 HN1 GDP sing 122 n n C2 N2 GDP sing 123 n n C2 N3 GDP doub 124 n n N2 HN21 GDP sing 125 n n N2 HN22 GDP sing 126 n n N3 C4 GDP sing 127 n n # _atom_sites.entry_id 5GNR _atom_sites.fract_transf_matrix[1][1] 0.014017 _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] 0.013338 _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] 0.010588 _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 GDP A 1 1000 1000 GDP GDP . C 3 HOH A 1 1101 7 HOH HOH . C 3 HOH A 2 1102 21 HOH HOH . C 3 HOH A 3 1103 5 HOH HOH . C 3 HOH A 4 1104 8 HOH HOH . C 3 HOH A 5 1105 10 HOH HOH . C 3 HOH A 6 1106 18 HOH HOH . C 3 HOH A 7 1107 12 HOH HOH . C 3 HOH A 8 1108 9 HOH HOH . C 3 HOH A 9 1109 20 HOH HOH . C 3 HOH A 10 1110 2 HOH HOH . C 3 HOH A 11 1111 1 HOH HOH . C 3 HOH A 12 1112 6 HOH HOH . C 3 HOH A 13 1113 4 HOH HOH . C 3 HOH A 14 1114 17 HOH HOH . C 3 HOH A 15 1115 3 HOH HOH . C 3 HOH A 16 1116 16 HOH HOH . C 3 HOH A 17 1117 19 HOH HOH . C 3 HOH A 18 1118 22 HOH HOH . C 3 HOH A 19 1119 15 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 PB GDP . . . B 2 78.628 -9.595 28.138 1 34.42 ? PB GDP 1000 A 1 HETATM 2 O O1B GDP . . . B 2 80.047 -9.433 27.594 1 20.7 1 O1B GDP 1000 A 1 HETATM 3 O O2B GDP . . . B 2 77.741 -8.496 27.613 1 37.62 ? O2B GDP 1000 A 1 HETATM 4 O O3B GDP . . . B 2 78.024 -10.906 27.668 1 33.5 ? O3B GDP 1000 A 1 HETATM 5 O O3A GDP . . . B 2 78.693 -9.528 29.751 1 31.23 ? O3A GDP 1000 A 1 HETATM 6 P PA GDP . . . B 2 77.741 -8.599 30.678 1 35.77 ? PA GDP 1000 A 1 HETATM 7 O O1A GDP . . . B 2 76.265 -8.854 30.475 1 39.93 ? O1A GDP 1000 A 1 HETATM 8 O O2A GDP . . . B 2 78.005 -7.117 30.533 1 30.36 1 O2A GDP 1000 A 1 HETATM 9 O O5' GDP . . . B 2 78.169 -9.128 32.128 1 36.71 ? O5' GDP 1000 A 1 HETATM 10 C C5' GDP . . . B 2 77.723 -10.444 32.508 1 41.42 ? C5' GDP 1000 A 1 HETATM 11 C C4' GDP . . . B 2 77.726 -10.632 34.023 1 38.48 ? C4' GDP 1000 A 1 HETATM 12 O O4' GDP . . . B 2 78.921 -10.054 34.555 1 43.69 ? O4' GDP 1000 A 1 HETATM 13 C C3' GDP . . . B 2 76.591 -9.893 34.707 1 40.3 ? C3' GDP 1000 A 1 HETATM 14 O O3' GDP . . . B 2 76.305 -10.602 35.924 1 37.23 ? O3' GDP 1000 A 1 HETATM 15 C C2' GDP . . . B 2 77.211 -8.53 34.978 1 34.9 ? C2' GDP 1000 A 1 HETATM 16 O O2' GDP . . . B 2 76.558 -7.722 35.969 1 39.29 ? O2' GDP 1000 A 1 HETATM 17 C C1' GDP . . . B 2 78.592 -8.959 35.416 1 35.04 ? C1' GDP 1000 A 1 HETATM 18 N N9 GDP . . . B 2 79.598 -7.883 35.297 1 38.72 ? N9 GDP 1000 A 1 HETATM 19 C C8 GDP . . . B 2 79.834 -7.066 34.247 1 34.09 ? C8 GDP 1000 A 1 HETATM 20 N N7 GDP . . . B 2 80.87 -6.221 34.531 1 31.98 ? N7 GDP 1000 A 1 HETATM 21 C C5 GDP . . . B 2 81.31 -6.505 35.776 1 32.46 ? C5 GDP 1000 A 1 HETATM 22 C C6 GDP . . . B 2 82.363 -6.018 36.698 1 35.35 ? C6 GDP 1000 A 1 HETATM 23 O O6 GDP . . . B 2 83.135 -5.087 36.373 1 34.08 ? O6 GDP 1000 A 1 HETATM 24 N N1 GDP . . . B 2 82.469 -6.609 37.905 1 41.75 ? N1 GDP 1000 A 1 HETATM 25 C C2 GDP . . . B 2 81.669 -7.623 38.299 1 36.75 ? C2 GDP 1000 A 1 HETATM 26 N N2 GDP . . . B 2 81.833 -8.157 39.528 1 33.01 ? N2 GDP 1000 A 1 HETATM 27 N N3 GDP . . . B 2 80.691 -8.117 37.507 1 42.38 ? N3 GDP 1000 A 1 HETATM 28 C C4 GDP . . . B 2 80.47 -7.607 36.268 1 39.72 ? C4 GDP 1000 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 269 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #