data_4QJ5 # _model_server_result.job_id jc8JNTQp0VgT6Oa7-G01AQ _model_server_result.datetime_utc '2024-11-01 07:36:02' _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 4qj5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":400}' # _entry.id 4QJ5 # _exptl.entry_id 4QJ5 _exptl.method 'X-RAY DIFFRACTION' # _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 101.8 _cell.angle_gamma 90 _cell.entry_id 4QJ5 _cell.length_a 205.918 _cell.length_b 89.869 _cell.length_c 93.261 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4QJ5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _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 _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 73 A SER 53 1_555 E MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.188 ? metalc ? metalc2 A OG1 THR 206 A THR 186 1_555 E MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc3 C O2B GDP . A GDP 400 1_555 E MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? metalc ? metalc4 C O2A GDP . A GDP 400 1_555 E MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.883 ? metalc ? metalc5 E MG MG . A MG 402 1_555 H O HOH . A HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.417 ? metalc ? metalc6 B OD1 ASN 334 B ASN 333 1_555 F CA CA . B CA 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.322 ? metalc ? metalc7 B OE2 GLU 363 B GLU 362 1_555 F CA CA . B CA 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? metalc ? metalc8 B OD2 ASP 365 B ASP 364 1_555 F CA CA . B CA 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? metalc ? metalc9 B OD1 ASP 365 B ASP 364 1_555 F CA CA . B CA 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? metalc ? metalc10 B OE1 GLU 414 B GLU 413 1_555 F CA CA . B CA 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.323 ? metalc ? metalc11 F CA CA . B CA 901 1_555 G O11 I3P . B I3P 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.459 ? metalc ? metalc12 F CA CA . B CA 901 1_555 G O2 I3P . B I3P 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.067 ? # _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 87 n n PB O2B GDP sing 88 n n PB O3B GDP sing 89 n n PB O3A GDP sing 90 n n O2B HOB2 GDP sing 91 n n O3B HOB3 GDP sing 92 n n O3A PA GDP sing 93 n n PA O1A GDP doub 94 n n PA O2A GDP sing 95 n n PA O5' GDP sing 96 n n O2A HOA2 GDP sing 97 n n O5' C5' GDP sing 98 n n C5' C4' GDP sing 99 n n C5' H5' GDP sing 100 n n C5' "H5''" GDP sing 101 n n C4' O4' GDP sing 102 n n C4' C3' GDP sing 103 n n C4' H4' GDP sing 104 n n O4' C1' GDP sing 105 n n C3' O3' GDP sing 106 n n C3' C2' GDP sing 107 n n C3' H3' GDP sing 108 n n O3' HO3' GDP sing 109 n n C2' O2' GDP sing 110 n n C2' C1' GDP sing 111 n n C2' H2' GDP sing 112 n n O2' HO2' GDP sing 113 n n C1' N9 GDP sing 114 n n C1' H1' GDP sing 115 n n N9 C8 GDP sing 116 n y N9 C4 GDP sing 117 n y C8 N7 GDP doub 118 n y C8 H8 GDP sing 119 n n N7 C5 GDP sing 120 n y C5 C6 GDP sing 121 n n C5 C4 GDP doub 122 n y C6 O6 GDP doub 123 n n C6 N1 GDP sing 124 n n N1 C2 GDP sing 125 n n N1 HN1 GDP sing 126 n n C2 N2 GDP sing 127 n n C2 N3 GDP doub 128 n n N2 HN21 GDP sing 129 n n N2 HN22 GDP sing 130 n n N3 C4 GDP sing 131 n n # _atom_sites.entry_id 4QJ5 _atom_sites.fract_transf_matrix[1][1] 0.004856 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001015 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011127 _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] 0.010954 _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 GDP A 1 400 400 GDP GDP . D 4 ALF A 1 401 401 ALF ALF . E 5 MG A 1 402 402 MG MG . F 6 CA B 1 901 900 CA CA . G 7 I3P B 1 902 1 I3P I3P . H 8 HOH A 1 501 1 HOH HOH . H 8 HOH A 2 502 24 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 14.265 -1.952 45.347 1 57.81 ? PB GDP 400 A 1 HETATM 2 O O1B GDP . . . C 3 15.058 -2.682 46.406 1 57.97 ? O1B GDP 400 A 1 HETATM 3 O O2B GDP . . . C 3 14.451 -0.46 45.365 1 58.17 ? O2B GDP 400 A 1 HETATM 4 O O3B GDP . . . C 3 14.361 -2.541 43.964 1 58.07 ? O3B GDP 400 A 1 HETATM 5 O O3A GDP . . . C 3 12.723 -2.195 45.767 1 57.28 ? O3A GDP 400 A 1 HETATM 6 P PA GDP . . . C 3 11.596 -1.122 45.364 1 57 ? PA GDP 400 A 1 HETATM 7 O O1A GDP . . . C 3 11.741 0.056 46.287 1 57.19 ? O1A GDP 400 A 1 HETATM 8 O O2A GDP . . . C 3 11.688 -0.882 43.879 1 57.11 ? O2A GDP 400 A 1 HETATM 9 O O5' GDP . . . C 3 10.197 -1.832 45.72 1 56.6 ? O5' GDP 400 A 1 HETATM 10 C C5' GDP . . . C 3 9.976 -3.217 45.486 1 56.36 ? C5' GDP 400 A 1 HETATM 11 C C4' GDP . . . C 3 8.496 -3.521 45.245 1 56.16 ? C4' GDP 400 A 1 HETATM 12 O O4' GDP . . . C 3 7.946 -4.23 46.364 1 56.11 ? O4' GDP 400 A 1 HETATM 13 C C3' GDP . . . C 3 7.625 -2.291 45.03 1 56.16 ? C3' GDP 400 A 1 HETATM 14 O O3' GDP . . . C 3 6.792 -2.48 43.883 1 56.13 ? O3' GDP 400 A 1 HETATM 15 C C2' GDP . . . C 3 6.794 -2.154 46.29 1 56.18 ? C2' GDP 400 A 1 HETATM 16 O O2' GDP . . . C 3 5.422 -1.867 46.034 1 56.24 ? O2' GDP 400 A 1 HETATM 17 C C1' GDP . . . C 3 6.875 -3.501 46.979 1 56.13 ? C1' GDP 400 A 1 HETATM 18 N N9 GDP . . . C 3 7.092 -3.279 48.435 1 56.27 ? N9 GDP 400 A 1 HETATM 19 C C8 GDP . . . C 3 8.159 -2.672 48.998 1 56.37 ? C8 GDP 400 A 1 HETATM 20 N N7 GDP . . . C 3 8.043 -2.634 50.347 1 56.56 ? N7 GDP 400 A 1 HETATM 21 C C5 GDP . . . C 3 6.883 -3.215 50.659 1 56.61 ? C5 GDP 400 A 1 HETATM 22 C C6 GDP . . . C 3 6.157 -3.496 51.904 1 56.91 ? C6 GDP 400 A 1 HETATM 23 O O6 GDP . . . C 3 6.643 -3.161 52.999 1 57.21 ? O6 GDP 400 A 1 HETATM 24 N N1 GDP . . . C 3 4.977 -4.116 51.82 1 56.97 ? N1 GDP 400 A 1 HETATM 25 C C2 GDP . . . C 3 4.45 -4.487 50.636 1 56.76 ? C2 GDP 400 A 1 HETATM 26 N N2 GDP . . . C 3 3.252 -5.114 50.617 1 56.92 ? N2 GDP 400 A 1 HETATM 27 N N3 GDP . . . C 3 5.063 -4.259 49.448 1 56.48 ? N3 GDP 400 A 1 HETATM 28 C C4 GDP . . . C 3 6.257 -3.638 49.405 1 56.41 ? C4 GDP 400 A 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 323 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #