data_5VQ8 # _model_server_result.job_id MykfdLeQB4XqUwDGisOS4Q _model_server_result.datetime_utc '2024-11-22 11:21:58' _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 5vq8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":201}' # _entry.id 5VQ8 # _exptl.entry_id 5VQ8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 2 _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 120 _cell.entry_id 5VQ8 _cell.length_a 93.9 _cell.length_b 93.9 _cell.length_c 120.562 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VQ8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3' # 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 monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,G 1 1 B,E,F,H 2 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 ? 2 C N N ? 2 E 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 OG SER 18 A SER 17 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? metalc ? metalc2 C O2B GDP . A GDP 201 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.695 ? metalc ? metalc3 D MG MG . A MG 202 1_555 G O HOH . A HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? metalc ? metalc4 D MG MG . A MG 202 1_555 G O HOH . A HOH 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? metalc ? metalc5 B OG SER 18 B SER 17 1_555 F MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.212 ? metalc ? metalc6 E O3B GDP . B GDP 201 1_555 F MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.549 ? metalc ? metalc7 F MG MG . B MG 202 1_555 H O HOH . B HOH 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.377 ? metalc ? metalc8 F MG MG . B MG 202 1_555 H O HOH . B HOH 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? # _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 5VQ8 _atom_sites.fract_transf_matrix[1][1] 0.01065 _atom_sites.fract_transf_matrix[1][2] 0.006149 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012297 _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] 0.008294 _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 2 GDP A 1 201 1 GDP GDP . D 3 MG A 1 202 1 MG MG . E 2 GDP B 1 201 2 GDP GDP . F 3 MG B 1 202 2 MG MG . G 4 HOH A 1 301 25 HOH HOH . G 4 HOH A 2 302 31 HOH HOH . G 4 HOH A 3 303 32 HOH HOH . G 4 HOH A 4 304 24 HOH HOH . G 4 HOH A 5 305 3 HOH HOH . G 4 HOH A 6 306 7 HOH HOH . G 4 HOH A 7 307 12 HOH HOH . G 4 HOH A 8 308 27 HOH HOH . G 4 HOH A 9 309 23 HOH HOH . G 4 HOH A 10 310 17 HOH HOH . G 4 HOH A 11 311 5 HOH HOH . G 4 HOH A 12 312 22 HOH HOH . G 4 HOH A 13 313 13 HOH HOH . G 4 HOH A 14 314 26 HOH HOH . G 4 HOH A 15 315 30 HOH HOH . G 4 HOH A 16 316 18 HOH HOH . G 4 HOH A 17 317 29 HOH HOH . G 4 HOH A 18 318 28 HOH HOH . H 4 HOH B 1 301 9 HOH HOH . H 4 HOH B 2 302 8 HOH HOH . H 4 HOH B 3 303 34 HOH HOH . H 4 HOH B 4 304 19 HOH HOH . H 4 HOH B 5 305 2 HOH HOH . H 4 HOH B 6 306 33 HOH HOH . H 4 HOH B 7 307 1 HOH HOH . H 4 HOH B 8 308 4 HOH HOH . H 4 HOH B 9 309 15 HOH HOH . H 4 HOH B 10 310 21 HOH HOH . H 4 HOH B 11 311 20 HOH HOH . H 4 HOH B 12 312 11 HOH HOH . H 4 HOH B 13 313 16 HOH HOH . H 4 HOH B 14 314 10 HOH HOH . H 4 HOH B 15 315 14 HOH HOH . H 4 HOH B 16 316 6 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 2 -8.573 -40.421 18.784 1 31.47 ? PB GDP 201 A 1 HETATM 2 O O1B GDP . . . C 2 -9.191 -41.424 17.842 1 36.57 ? O1B GDP 201 A 1 HETATM 3 O O2B GDP . . . C 2 -9.573 -39.44 19.307 1 35.43 ? O2B GDP 201 A 1 HETATM 4 O O3B GDP . . . C 2 -7.728 -41.04 19.857 1 36.51 ? O3B GDP 201 A 1 HETATM 5 O O3A GDP . . . C 2 -7.528 -39.565 17.879 1 33.15 ? O3A GDP 201 A 1 HETATM 6 P PA GDP . . . C 2 -6.988 -38.041 18.278 1 31.69 ? PA GDP 201 A 1 HETATM 7 O O1A GDP . . . C 2 -7.899 -37.017 17.706 1 31.36 ? O1A GDP 201 A 1 HETATM 8 O O2A GDP . . . C 2 -6.71 -38.034 19.754 1 35.63 ? O2A GDP 201 A 1 HETATM 9 O O5' GDP . . . C 2 -5.63 -37.917 17.476 1 28.02 ? O5' GDP 201 A 1 HETATM 10 C C5' GDP . . . C 2 -4.563 -38.81 17.734 1 31.44 ? C5' GDP 201 A 1 HETATM 11 C C4' GDP . . . C 2 -3.278 -38.239 17.15 1 32.51 ? C4' GDP 201 A 1 HETATM 12 O O4' GDP . . . C 2 -3.314 -38.307 15.713 1 32.36 ? O4' GDP 201 A 1 HETATM 13 C C3' GDP . . . C 2 -3.108 -36.759 17.512 1 33.41 ? C3' GDP 201 A 1 HETATM 14 O O3' GDP . . . C 2 -1.748 -36.484 17.767 1 33.85 ? O3' GDP 201 A 1 HETATM 15 C C2' GDP . . . C 2 -3.563 -36.002 16.287 1 33.74 ? C2' GDP 201 A 1 HETATM 16 O O2' GDP . . . C 2 -2.9 -34.727 16.104 1 32.29 ? O2' GDP 201 A 1 HETATM 17 C C1' GDP . . . C 2 -3.208 -36.958 15.18 1 30.91 ? C1' GDP 201 A 1 HETATM 18 N N9 GDP . . . C 2 -4.101 -36.799 14.06 1 27.76 ? N9 GDP 201 A 1 HETATM 19 C C8 GDP . . . C 2 -5.44 -36.979 14.074 1 28.04 ? C8 GDP 201 A 1 HETATM 20 N N7 GDP . . . C 2 -5.932 -36.774 12.821 1 27.26 ? N7 GDP 201 A 1 HETATM 21 C C5 GDP . . . C 2 -4.898 -36.502 12.03 1 25.34 ? C5 GDP 201 A 1 HETATM 22 C C6 GDP . . . C 2 -4.74 -36.182 10.634 1 27.37 ? C6 GDP 201 A 1 HETATM 23 O O6 GDP . . . C 2 -5.712 -36.151 9.853 1 29.01 ? O6 GDP 201 A 1 HETATM 24 N N1 GDP . . . C 2 -3.516 -35.945 10.185 1 28.39 ? N1 GDP 201 A 1 HETATM 25 C C2 GDP . . . C 2 -2.414 -35.962 11.001 1 25.62 ? C2 GDP 201 A 1 HETATM 26 N N2 GDP . . . C 2 -1.203 -35.691 10.468 1 25.62 ? N2 GDP 201 A 1 HETATM 27 N N3 GDP . . . C 2 -2.507 -36.236 12.306 1 24.73 ? N3 GDP 201 A 1 HETATM 28 C C4 GDP . . . C 2 -3.716 -36.503 12.85 1 25.41 ? C4 GDP 201 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 20 _model_server_stats.element_count 28 #