data_4HNA # _model_server_result.job_id EdE3xwDQqQ2oeb3KERMIBQ _model_server_result.datetime_utc '2024-11-15 10:32:36' _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 4hna # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":501}' # _entry.id 4HNA # _exptl.entry_id 4HNA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 7 _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 4HNA _cell.length_a 77.05 _cell.length_b 160.54 _cell.length_c 174.95 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4HNA _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 ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M _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 7 _struct_asym.id G _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 E O1G GTP . A GTP 600 1_555 F MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.188 ? metalc ? metalc2 E O1B GTP . A GTP 600 1_555 F MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? metalc ? metalc3 G O2B GDP . B GDP 501 1_555 H MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.942 ? metalc ? metalc4 G O3B GDP . B GDP 501 1_555 I AL ALF . B ALF 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? metalc ? metalc5 H MG MG . B MG 502 1_555 I F3 ALF . B ALF 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? metalc ? metalc6 D OG1 THR 92 K THR 92 1_555 K MG MG . K MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.944 ? metalc ? metalc7 D OG SER 202 K SER 202 1_555 K MG MG . K MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.563 ? metalc ? metalc8 J O2B ADP . K ADP 401 1_555 K MG MG . K MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? metalc ? metalc9 J O3B ADP . K ADP 401 1_555 L AL ALF . K ALF 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.898 ? metalc ? metalc10 K MG MG . K MG 402 1_555 L F4 ALF . K ALF 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? metalc ? metalc11 K MG MG . K MG 402 1_555 M O HOH . K HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? metalc ? metalc12 K MG MG . K MG 402 1_555 M O HOH . K HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? # _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 4HNA _atom_sites.fract_transf_matrix[1][1] 0.012979 _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] 0.006229 _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] 0.005716 _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 E 5 GTP A 1 600 600 GTP GTP . F 6 MG A 1 601 601 MG MG . G 7 GDP B 1 501 600 GDP GDP . H 6 MG B 1 502 601 MG MG . I 8 ALF B 1 503 650 ALF ALF . J 9 ADP K 1 401 600 ADP ADP . K 6 MG K 1 402 601 MG MG . L 8 ALF K 1 403 650 ALF ALF . M 10 HOH K 1 501 610 HOH HOH . M 10 HOH K 2 502 611 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 . . . G 7 -8.515 70.863 -10.791 1 79.64 ? PB GDP 501 B 1 HETATM 2 O O1B GDP . . . G 7 -8.149 70.449 -9.371 1 78.56 ? O1B GDP 501 B 1 HETATM 3 O O2B GDP . . . G 7 -9.984 70.571 -11.237 1 76.17 ? O2B GDP 501 B 1 HETATM 4 O O3B GDP . . . G 7 -8.156 72.351 -11.131 1 85.29 ? O3B GDP 501 B 1 HETATM 5 O O3A GDP . . . G 7 -7.514 69.955 -11.622 1 79.9 ? O3A GDP 501 B 1 HETATM 6 P PA GDP . . . G 7 -7.471 68.393 -11.902 1 73.38 ? PA GDP 501 B 1 HETATM 7 O O1A GDP . . . G 7 -8.118 68.184 -13.22 1 74.67 ? O1A GDP 501 B 1 HETATM 8 O O2A GDP . . . G 7 -8.146 67.607 -10.804 1 72.57 ? O2A GDP 501 B 1 HETATM 9 O O5' GDP . . . G 7 -5.932 68.092 -11.914 1 66.96 ? O5' GDP 501 B 1 HETATM 10 C C5' GDP . . . G 7 -5.314 67.377 -12.977 1 65.18 ? C5' GDP 501 B 1 HETATM 11 C C4' GDP . . . G 7 -4.573 66.255 -12.314 1 65.03 ? C4' GDP 501 B 1 HETATM 12 O O4' GDP . . . G 7 -5.535 65.338 -11.738 1 67.74 ? O4' GDP 501 B 1 HETATM 13 C C3' GDP . . . G 7 -3.767 65.432 -13.307 1 65.54 ? C3' GDP 501 B 1 HETATM 14 O O3' GDP . . . G 7 -2.613 64.845 -12.715 1 66.62 ? O3' GDP 501 B 1 HETATM 15 C C2' GDP . . . G 7 -4.797 64.406 -13.776 1 65.49 ? C2' GDP 501 B 1 HETATM 16 O O2' GDP . . . G 7 -4.085 63.263 -14.211 1 64.13 ? O2' GDP 501 B 1 HETATM 17 C C1' GDP . . . G 7 -5.554 64.127 -12.471 1 66.97 ? C1' GDP 501 B 1 HETATM 18 N N9 GDP . . . G 7 -6.958 63.681 -12.593 1 69.6 ? N9 GDP 501 B 1 HETATM 19 C C8 GDP . . . G 7 -8.03 64.383 -13.099 1 75.22 ? C8 GDP 501 B 1 HETATM 20 N N7 GDP . . . G 7 -9.172 63.743 -12.988 1 78.06 ? N7 GDP 501 B 1 HETATM 21 C C5 GDP . . . G 7 -8.838 62.549 -12.366 1 75.02 ? C5 GDP 501 B 1 HETATM 22 C C6 GDP . . . G 7 -9.644 61.395 -11.964 1 75.42 ? C6 GDP 501 B 1 HETATM 23 O O6 GDP . . . G 7 -10.856 61.273 -12.051 1 77.22 ? O6 GDP 501 B 1 HETATM 24 N N1 GDP . . . G 7 -8.891 60.381 -11.405 1 73.01 ? N1 GDP 501 B 1 HETATM 25 C C2 GDP . . . G 7 -7.539 60.42 -11.216 1 71.65 ? C2 GDP 501 B 1 HETATM 26 N N2 GDP . . . G 7 -6.976 59.323 -10.698 1 71.24 ? N2 GDP 501 B 1 HETATM 27 N N3 GDP . . . G 7 -6.777 61.475 -11.546 1 70.44 ? N3 GDP 501 B 1 HETATM 28 C C4 GDP . . . G 7 -7.479 62.494 -12.12 1 70.61 ? C4 GDP 501 B 1 # _model_server_stats.io_time_ms 29 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 345 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 28 #