data_1K5G # _model_server_result.job_id llBpS1hdrSXSWAgKMln7dw _model_server_result.datetime_utc '2025-02-27 01:31:43' _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 1k5g # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"T","auth_seq_id":3250}' # _entry.id 1K5G # _exptl.entry_id 1K5G _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 71.67 _cell.angle_beta 79.09 _cell.angle_gamma 67.81 _cell.entry_id 1K5G _cell.length_a 99.93 _cell.length_b 102.568 _cell.length_c 118.85 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1K5G _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA trimeric 3 author_and_software_defined_assembly 1 PISA trimeric 3 author_and_software_defined_assembly 2 PISA trimeric 3 author_and_software_defined_assembly 3 PISA trimeric 3 author_and_software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,M,N,O 1 1 D,E,F,P,Q,R 2 1 G,H,I,S,T,U 3 1 J,K,L,V,W,X 4 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 N N N ? 5 Q N N ? 5 T N N ? 5 W N 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 OG1 THR 24 A THR 24 1_555 M MG MG . A MG 1251 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.902 ? metalc ? metalc2 A OG1 THR 42 A THR 42 1_555 M MG MG . A MG 1251 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? metalc ? metalc3 N O2B GDP . A GDP 1250 1_555 M MG MG . A MG 1251 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.781 ? metalc ? metalc4 N O2B GDP . A GDP 1250 1_555 O AL AF3 . A AF3 1252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.562 ? metalc ? metalc5 N O3B GDP . A GDP 1250 1_555 O AL AF3 . A AF3 1252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.29 ? metalc ? metalc6 M MG MG . A MG 1251 1_555 O F1 AF3 . A AF3 1252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.582 ? metalc ? metalc7 M MG MG . A MG 1251 1_555 O F3 AF3 . A AF3 1252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.885 ? metalc ? metalc8 M MG MG . A MG 1251 1_555 O AL AF3 . A AF3 1252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.218 ? metalc ? metalc9 D OG1 THR 24 D THR 24 1_555 P MG MG . D MG 2251 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.862 ? metalc ? metalc10 D OG1 THR 42 D THR 42 1_555 P MG MG . D MG 2251 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.282 ? metalc ? metalc11 Q O2B GDP . D GDP 2250 1_555 P MG MG . D MG 2251 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.741 ? metalc ? metalc12 Q O3B GDP . D GDP 2250 1_555 R AL AF3 . D AF3 2252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.212 ? metalc ? metalc13 Q O2B GDP . D GDP 2250 1_555 R AL AF3 . D AF3 2252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.432 ? metalc ? metalc14 P MG MG . D MG 2251 1_555 R AL AF3 . D AF3 2252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.093 ? metalc ? metalc15 P MG MG . D MG 2251 1_555 R F1 AF3 . D AF3 2252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.957 ? metalc ? metalc16 G OG1 THR 24 G THR 24 1_555 S MG MG . G MG 3251 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.876 ? metalc ? metalc17 G OG1 THR 42 G THR 42 1_555 S MG MG . G MG 3251 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.258 ? metalc ? metalc18 T O2B GDP . G GDP 3250 1_555 S MG MG . G MG 3251 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.76 ? metalc ? metalc19 T O3B GDP . G GDP 3250 1_555 U AL AF3 . G AF3 3252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.365 ? metalc ? metalc20 T O2B GDP . G GDP 3250 1_555 U AL AF3 . G AF3 3252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.528 ? metalc ? metalc21 S MG MG . G MG 3251 1_555 U F3 AF3 . G AF3 3252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.766 ? metalc ? metalc22 S MG MG . G MG 3251 1_555 U AL AF3 . G AF3 3252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.047 ? metalc ? metalc23 S MG MG . G MG 3251 1_555 U F1 AF3 . G AF3 3252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.871 ? metalc ? metalc24 J OG1 THR 24 J THR 24 1_555 V MG MG . J MG 4251 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.874 ? metalc ? metalc25 J OG1 THR 42 J THR 42 1_555 V MG MG . J MG 4251 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.386 ? metalc ? metalc26 W O2B GDP . J GDP 4250 1_555 V MG MG . J MG 4251 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.709 ? metalc ? metalc27 W O2B GDP . J GDP 4250 1_555 X AL AF3 . J AF3 4252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.43 ? metalc ? metalc28 W O3B GDP . J GDP 4250 1_555 X AL AF3 . J AF3 4252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.197 ? metalc ? metalc29 V MG MG . J MG 4251 1_555 X F3 AF3 . J AF3 4252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.032 ? metalc ? metalc30 V MG MG . J MG 4251 1_555 X F1 AF3 . J AF3 4252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.275 ? metalc ? metalc31 V MG MG . J MG 4251 1_555 X AL AF3 . J AF3 4252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.982 ? # _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 86 n n PB O2B GDP sing 87 n n PB O3B GDP sing 88 n n PB O3A GDP sing 89 n n O2B HOB2 GDP sing 90 n n O3B HOB3 GDP sing 91 n n O3A PA GDP sing 92 n n PA O1A GDP doub 93 n n PA O2A GDP sing 94 n n PA O5' GDP sing 95 n n O2A HOA2 GDP sing 96 n n O5' C5' GDP sing 97 n n C5' C4' GDP sing 98 n n C5' H5' GDP sing 99 n n C5' "H5''" GDP sing 100 n n C4' O4' GDP sing 101 n n C4' C3' GDP sing 102 n n C4' H4' GDP sing 103 n n O4' C1' GDP sing 104 n n C3' O3' GDP sing 105 n n C3' C2' GDP sing 106 n n C3' H3' GDP sing 107 n n O3' HO3' GDP sing 108 n n C2' O2' GDP sing 109 n n C2' C1' GDP sing 110 n n C2' H2' GDP sing 111 n n O2' HO2' GDP sing 112 n n C1' N9 GDP sing 113 n n C1' H1' GDP sing 114 n n N9 C8 GDP sing 115 n y N9 C4 GDP sing 116 n y C8 N7 GDP doub 117 n y C8 H8 GDP sing 118 n n N7 C5 GDP sing 119 n y C5 C6 GDP sing 120 n n C5 C4 GDP doub 121 n y C6 O6 GDP doub 122 n n C6 N1 GDP sing 123 n n N1 C2 GDP sing 124 n n N1 HN1 GDP sing 125 n n C2 N2 GDP sing 126 n n C2 N3 GDP doub 127 n n N2 HN21 GDP sing 128 n n N2 HN22 GDP sing 129 n n N3 C4 GDP sing 130 n n # _atom_sites.entry_id 1K5G _atom_sites.fract_transf_matrix[1][1] 0.010007 _atom_sites.fract_transf_matrix[1][2] -0.004082 _atom_sites.fract_transf_matrix[1][3] -0.000869 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01053 _atom_sites.fract_transf_matrix[2][3] -0.002922 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.008892 _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 M 4 MG A 1 1251 1251 MG MG . N 5 GDP A 1 1250 1250 GDP GDP . O 6 AF3 A 1 1252 1252 AF3 AF3 . P 4 MG D 1 2251 2251 MG MG . Q 5 GDP D 1 2250 2250 GDP GDP . R 6 AF3 D 1 2252 2252 AF3 AF3 . S 4 MG G 1 3251 3251 MG MG . T 5 GDP G 1 3250 3250 GDP GDP . U 6 AF3 G 1 3252 3252 AF3 AF3 . V 4 MG J 1 4251 4251 MG MG . W 5 GDP J 1 4250 4250 GDP GDP . X 6 AF3 J 1 4252 4252 AF3 AF3 . # 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 . . . T 5 92.124 5.979 60.532 1 35.41 ? PB GDP 3250 G 1 HETATM 2 O O1B GDP . . . T 5 93.147 5.351 61.347 1 35.41 ? O1B GDP 3250 G 1 HETATM 3 O O2B GDP . . . T 5 92.108 7.459 60.595 1 35.41 ? O2B GDP 3250 G 1 HETATM 4 O O3B GDP . . . T 5 92.253 5.518 59.07 1 35.41 ? O3B GDP 3250 G 1 HETATM 5 O O3A GDP . . . T 5 90.677 5.354 60.762 1 35.41 ? O3A GDP 3250 G 1 HETATM 6 P PA GDP . . . T 5 89.417 6.276 61.058 1 35.41 ? PA GDP 3250 G 1 HETATM 7 O O1A GDP . . . T 5 89.529 6.62 62.477 1 35.41 ? O1A GDP 3250 G 1 HETATM 8 O O2A GDP . . . T 5 89.297 7.381 60.121 1 35.41 ? O2A GDP 3250 G 1 HETATM 9 O O5' GDP . . . T 5 88.216 5.253 60.962 1 35.41 ? O5' GDP 3250 G 1 HETATM 10 C C5' GDP . . . T 5 87.88 4.757 59.712 1 35.41 ? C5' GDP 3250 G 1 HETATM 11 C C4' GDP . . . T 5 86.549 4.029 59.617 1 35.41 ? C4' GDP 3250 G 1 HETATM 12 O O4' GDP . . . T 5 86.439 2.83 60.385 1 35.41 ? O4' GDP 3250 G 1 HETATM 13 C C3' GDP . . . T 5 85.357 4.876 60.008 1 35.41 ? C3' GDP 3250 G 1 HETATM 14 O O3' GDP . . . T 5 84.364 4.572 59.023 1 35.41 ? O3' GDP 3250 G 1 HETATM 15 C C2' GDP . . . T 5 85.033 4.298 61.37 1 35.41 ? C2' GDP 3250 G 1 HETATM 16 O O2' GDP . . . T 5 83.668 4.492 61.805 1 35.41 ? O2' GDP 3250 G 1 HETATM 17 C C1' GDP . . . T 5 85.321 2.843 61.206 1 35.41 ? C1' GDP 3250 G 1 HETATM 18 N N9 GDP . . . T 5 85.669 2.119 62.419 1 35.41 ? N9 GDP 3250 G 1 HETATM 19 C C8 GDP . . . T 5 86.553 2.419 63.383 1 35.41 ? C8 GDP 3250 G 1 HETATM 20 N N7 GDP . . . T 5 86.638 1.572 64.35 1 35.41 ? N7 GDP 3250 G 1 HETATM 21 C C5 GDP . . . T 5 85.736 0.61 64.017 1 35.41 ? C5 GDP 3250 G 1 HETATM 22 C C6 GDP . . . T 5 85.344 -0.633 64.686 1 35.41 ? C6 GDP 3250 G 1 HETATM 23 O O6 GDP . . . T 5 85.747 -1.139 65.752 1 35.41 ? O6 GDP 3250 G 1 HETATM 24 N N1 GDP . . . T 5 84.344 -1.324 63.965 1 35.41 ? N1 GDP 3250 G 1 HETATM 25 C C2 GDP . . . T 5 83.787 -0.906 62.774 1 35.41 ? C2 GDP 3250 G 1 HETATM 26 N N2 GDP . . . T 5 82.854 -1.661 62.235 1 35.41 ? N2 GDP 3250 G 1 HETATM 27 N N3 GDP . . . T 5 84.166 0.246 62.159 1 35.41 ? N3 GDP 3250 G 1 HETATM 28 C C4 GDP . . . T 5 85.13 0.944 62.825 1 35.41 ? C4 GDP 3250 G 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 170 _model_server_stats.query_time_ms 334 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 28 #