data_5C4G # _model_server_result.job_id Kh9txAkdI45EE1Dng3eNLQ _model_server_result.datetime_utc '2025-01-14 03:59:19' _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 5c4g # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":302}' # _entry.id 5C4G # _exptl.entry_id 5C4G _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 4 _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 5C4G _cell.length_a 48.82 _cell.length_b 105.4 _cell.length_c 188.85 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5C4G _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 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 _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 4 _struct_asym.id D _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 28 B SER 25 1_555 C MG MG . B MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.513 ? metalc ? metalc2 C MG MG . B MG 301 1_555 D O3B GDP . B GDP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.275 ? # _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 131 n n PB O2B GDP sing 132 n n PB O3B GDP sing 133 n n PB O3A GDP sing 134 n n O2B HOB2 GDP sing 135 n n O3B HOB3 GDP sing 136 n n O3A PA GDP sing 137 n n PA O1A GDP doub 138 n n PA O2A GDP sing 139 n n PA O5' GDP sing 140 n n O2A HOA2 GDP sing 141 n n O5' C5' GDP sing 142 n n C5' C4' GDP sing 143 n n C5' H5' GDP sing 144 n n C5' "H5''" GDP sing 145 n n C4' O4' GDP sing 146 n n C4' C3' GDP sing 147 n n C4' H4' GDP sing 148 n n O4' C1' GDP sing 149 n n C3' O3' GDP sing 150 n n C3' C2' GDP sing 151 n n C3' H3' GDP sing 152 n n O3' HO3' GDP sing 153 n n C2' O2' GDP sing 154 n n C2' C1' GDP sing 155 n n C2' H2' GDP sing 156 n n O2' HO2' GDP sing 157 n n C1' N9 GDP sing 158 n n C1' H1' GDP sing 159 n n N9 C8 GDP sing 160 n y N9 C4 GDP sing 161 n y C8 N7 GDP doub 162 n y C8 H8 GDP sing 163 n n N7 C5 GDP sing 164 n y C5 C6 GDP sing 165 n n C5 C4 GDP doub 166 n y C6 O6 GDP doub 167 n n C6 N1 GDP sing 168 n n N1 C2 GDP sing 169 n n N1 HN1 GDP sing 170 n n C2 N2 GDP sing 171 n n C2 N3 GDP doub 172 n n N2 HN21 GDP sing 173 n n N2 HN22 GDP sing 174 n n N3 C4 GDP sing 175 n n # _atom_sites.entry_id 5C4G _atom_sites.fract_transf_matrix[1][1] 0.020483 _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] 0.009488 _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] 0.005295 _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 3 MG B 1 301 301 MG MG . D 4 GDP B 1 302 302 GDP GDP . E 5 SO4 E 1 801 801 SO4 SO4 . F 5 SO4 E 1 802 802 SO4 SO4 . G 6 BQR E 1 803 803 BQR BQR . # 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 . . . D 4 -9.296 4.085 14.762 1 127.89 ? PB GDP 302 B 1 HETATM 2 O O1B GDP . . . D 4 -8.5 3.781 13.515 1 124.55 ? O1B GDP 302 B 1 HETATM 3 O O2B GDP . . . D 4 -9.723 2.788 15.402 1 132.67 -1 O2B GDP 302 B 1 HETATM 4 O O3B GDP . . . D 4 -8.443 4.87 15.73 1 128.33 ? O3B GDP 302 B 1 HETATM 5 O O3A GDP . . . D 4 -10.599 4.942 14.359 1 62.12 ? O3A GDP 302 B 1 HETATM 6 P PA GDP . . . D 4 -10.447 6.372 13.637 1 126.23 ? PA GDP 302 B 1 HETATM 7 O O1A GDP . . . D 4 -9.033 6.577 13.148 1 133.19 ? O1A GDP 302 B 1 HETATM 8 O O2A GDP . . . D 4 -10.85 7.483 14.575 1 120.81 -1 O2A GDP 302 B 1 HETATM 9 O O5' GDP . . . D 4 -11.485 6.279 12.407 1 103.76 ? O5' GDP 302 B 1 HETATM 10 C C5' GDP . . . D 4 -10.999 6.327 11.066 1 98.27 ? C5' GDP 302 B 1 HETATM 11 C C4' GDP . . . D 4 -12.052 6.882 10.111 1 90.37 ? C4' GDP 302 B 1 HETATM 12 O O4' GDP . . . D 4 -13.27 6.136 10.17 1 82.72 ? O4' GDP 302 B 1 HETATM 13 C C3' GDP . . . D 4 -12.406 8.325 10.444 1 90.77 ? C3' GDP 302 B 1 HETATM 14 O O3' GDP . . . D 4 -11.861 9.202 9.455 1 94.95 ? O3' GDP 302 B 1 HETATM 15 C C2' GDP . . . D 4 -13.919 8.392 10.413 1 86.33 ? C2' GDP 302 B 1 HETATM 16 O O2' GDP . . . D 4 -14.36 9.423 9.525 1 88.67 ? O2' GDP 302 B 1 HETATM 17 C C1' GDP . . . D 4 -14.36 7.026 9.915 1 86.23 ? C1' GDP 302 B 1 HETATM 18 N N9 GDP . . . D 4 -15.587 6.614 10.635 1 96.14 ? N9 GDP 302 B 1 HETATM 19 C C8 GDP . . . D 4 -15.691 6.325 11.946 1 102.76 ? C8 GDP 302 B 1 HETATM 20 N N7 GDP . . . D 4 -16.965 5.985 12.27 1 103.74 ? N7 GDP 302 B 1 HETATM 21 C C5 GDP . . . D 4 -17.7 6.055 11.144 1 104.43 ? C5 GDP 302 B 1 HETATM 22 C C6 GDP . . . D 4 -19.114 5.824 10.769 1 107.78 ? C6 GDP 302 B 1 HETATM 23 O O6 GDP . . . D 4 -19.956 5.469 11.622 1 109.91 ? O6 GDP 302 B 1 HETATM 24 N N1 GDP . . . D 4 -19.461 6.008 9.488 1 105.69 ? N1 GDP 302 B 1 HETATM 25 C C2 GDP . . . D 4 -18.58 6.39 8.546 1 100.6 ? C2 GDP 302 B 1 HETATM 26 N N2 GDP . . . D 4 -19.016 6.553 7.273 1 98.19 ? N2 GDP 302 B 1 HETATM 27 N N3 GDP . . . D 4 -17.27 6.618 8.817 1 100.01 ? N3 GDP 302 B 1 HETATM 28 C C4 GDP . . . D 4 -16.785 6.469 10.071 1 100.99 ? C4 GDP 302 B 1 # _model_server_stats.io_time_ms 24 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 220 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 28 #