data_1CRR # _model_server_result.job_id Vzrx2CMOkpwzUGA2uVQExg _model_server_result.datetime_utc '2024-11-22 23:51:42' _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 1crr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":200}' # _entry.id 1CRR # _exptl.entry_id 1CRR _exptl.method 'SOLUTION NMR' # _entity.details ? _entity.formula_weight 443.201 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _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 1CRR _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1CRR _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_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 metalc ? metalc1 A OG SER 17 A SER 17 1_555 B MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.469 ? metalc ? metalc2 C O2B GDP . A GDP 200 1_555 B MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.932 ? metalc ? metalc3 C O1B GDP . A GDP 200 1_555 B MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.458 ? metalc ? metalc4 B MG MG . A MG 201 1_555 D O HOH . A HOH 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.6 ? metalc ? metalc5 B MG MG . A MG 201 1_555 D O HOH . A HOH 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.743 ? metalc ? metalc6 B MG MG . A MG 201 1_555 D O HOH . A HOH 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.676 ? metalc ? metalc7 B MG MG . A MG 201 1_555 D O HOH . A HOH 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.719 ? # _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 1CRR _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 MG A 1 201 201 MG MG . C 3 GDP A 1 200 200 GDP GDP . D 4 HOH A 1 202 1 HOH HOH . D 4 HOH A 2 203 2 HOH HOH . D 4 HOH A 3 204 3 HOH HOH . D 4 HOH A 4 205 4 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 . . . C 3 62.73 76.845 49.151 1 0.76 ? PB GDP 200 A 21 HETATM 2 O O1B GDP . . . C 3 64.079 77.25 48.695 1 1.16 ? O1B GDP 200 A 21 HETATM 3 O O2B GDP . . . C 3 62.263 75.545 48.645 1 0.5 ? O2B GDP 200 A 21 HETATM 4 O O3B GDP . . . C 3 61.73 77.929 49.075 1 1.76 ? O3B GDP 200 A 21 HETATM 5 O O3A GDP . . . C 3 62.907 76.608 50.739 1 1.06 ? O3A GDP 200 A 21 HETATM 6 P PA GDP . . . C 3 64.242 75.915 51.318 1 0.86 ? PA GDP 200 A 21 HETATM 7 O O1A GDP . . . C 3 65.406 76.487 50.605 1 1.46 ? O1A GDP 200 A 21 HETATM 8 O O2A GDP . . . C 3 64.03 74.448 51.326 1 1.48 ? O2A GDP 200 A 21 HETATM 9 O O5' GDP . . . C 3 64.288 76.437 52.84 1 1.91 ? O5' GDP 200 A 21 HETATM 10 C C5' GDP . . . C 3 63.25 76.095 53.76 1 2.63 ? C5' GDP 200 A 21 HETATM 11 C C4' GDP . . . C 3 62.481 77.328 54.219 1 1.64 ? C4' GDP 200 A 21 HETATM 12 O O4' GDP . . . C 3 61.265 77.469 53.461 1 1.4 ? O4' GDP 200 A 21 HETATM 13 C C3' GDP . . . C 3 62.108 77.212 55.69 1 0.94 ? C3' GDP 200 A 21 HETATM 14 O O3' GDP . . . C 3 62.572 78.348 56.426 1 0.65 ? O3' GDP 200 A 21 HETATM 15 C C2' GDP . . . C 3 60.603 77.118 55.736 1 0.35 ? C2' GDP 200 A 21 HETATM 16 O O2' GDP . . . C 3 60.046 78.201 56.486 1 1.05 ? O2' GDP 200 A 21 HETATM 17 C C1' GDP . . . C 3 60.132 77.159 54.292 1 0.7 ? C1' GDP 200 A 21 HETATM 18 N N9 GDP . . . C 3 59.555 75.861 53.905 1 0.67 ? N9 GDP 200 A 21 HETATM 19 C C8 GDP . . . C 3 59.922 75.004 52.934 1 0.77 ? C8 GDP 200 A 21 HETATM 20 N N7 GDP . . . C 3 59.293 73.898 52.782 1 0.79 ? N7 GDP 200 A 21 HETATM 21 C C5 GDP . . . C 3 58.343 74.008 53.808 1 0.65 ? C5 GDP 200 A 21 HETATM 22 C C6 GDP . . . C 3 57.319 73.108 54.198 1 0.59 ? C6 GDP 200 A 21 HETATM 23 O O6 GDP . . . C 3 57.04 72.019 53.712 1 0.67 ? O6 GDP 200 A 21 HETATM 24 N N1 GDP . . . C 3 56.59 73.599 55.272 1 0.48 ? N1 GDP 200 A 21 HETATM 25 C C2 GDP . . . C 3 56.813 74.806 55.901 1 0.51 ? C2 GDP 200 A 21 HETATM 26 N N2 GDP . . . C 3 56.001 75.097 56.914 1 0.56 ? N2 GDP 200 A 21 HETATM 27 N N3 GDP . . . C 3 57.773 75.664 55.544 1 0.57 ? N3 GDP 200 A 21 HETATM 28 C C4 GDP . . . C 3 58.499 75.209 54.5 1 0.6 ? C4 GDP 200 A 21 HETATM 29 H H5' GDP . . . C 3 63.692 75.607 54.629 1 4.62 ? H5' GDP 200 A 21 HETATM 30 H "H5''" GDP . . . C 3 62.559 75.403 53.276 1 3.44 ? "H5''" GDP 200 A 21 HETATM 31 H H4' GDP . . . C 3 63.098 78.214 54.072 1 2.08 ? H4' GDP 200 A 21 HETATM 32 H H3' GDP . . . C 3 62.54 76.299 56.106 1 1.67 ? H3' GDP 200 A 21 HETATM 33 H HO3' GDP . . . C 3 63.505 78.211 56.605 1 1.05 ? HO3' GDP 200 A 21 HETATM 34 H H2' GDP . . . C 3 60.314 76.167 56.186 1 1.01 ? H2' GDP 200 A 21 HETATM 35 H HO2' GDP . . . C 3 60.32 78.087 57.399 1 1.42 ? HO2' GDP 200 A 21 HETATM 36 H H1' GDP . . . C 3 59.375 77.933 54.179 1 1.25 ? H1' GDP 200 A 21 HETATM 37 H H8 GDP . . . C 3 60.758 75.248 52.28 1 0.87 ? H8 GDP 200 A 21 HETATM 38 H HN1 GDP . . . C 3 55.867 73.024 55.596 1 0.44 ? HN1 GDP 200 A 21 HETATM 39 H HN21 GDP . . . C 3 56.034 74.549 57.761 1 0.96 ? HN21 GDP 200 A 21 HETATM 40 H HN22 GDP . . . C 3 55.35 75.864 56.834 1 1.37 ? HN22 GDP 200 A 21 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 408 _model_server_stats.query_time_ms 5252 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 40 #