data_8QW7 # _model_server_result.job_id WzReOz8-fGm62hA-Nl4qiw _model_server_result.datetime_utc '2025-01-10 13:25:32' _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 8qw7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":201}' # _entry.id 8QW7 # _exptl.entry_id 8QW7 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 6 _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 111.61 _cell.angle_gamma 90 _cell.entry_id 8QW7 _cell.length_a 72.52 _cell.length_b 125.929 _cell.length_c 81.056 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8QW7 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall 'P 2yb' _symmetry.space_group_name_H-M 'P 1 21 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 ? tetrameric 4 author_defined_assembly 1 ? tetrameric 4 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,G,I,K,L,O,P,T 1 1 D,E,F,H,J,M,N,Q,R,S,U 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 ? 6 K N N ? 6 M 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 G OG SER 18 A SER 17 1_555 L MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.214 ? metalc ? metalc2 K O1B GDP . A GDP 201 1_555 L MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.218 ? metalc ? metalc3 H OG SER 18 E SER 17 1_555 N MG MG . E MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.412 ? metalc ? metalc4 H O PRO 35 E PRO 34 1_555 N MG MG . E MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.657 ? metalc ? metalc5 M O2B GDP . E GDP 201 1_555 N MG MG . E MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? # _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 8QW7 _atom_sites.fract_transf_matrix[1][1] 0.013789 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.005462 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007941 _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] 0.01327 _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 I 5 X53 B 1 401 401 X53 LIG . J 5 X53 F 1 401 401 X53 LIG . K 6 GDP A 1 201 201 GDP GDP . L 7 MG A 1 202 301 MG MG . M 6 GDP E 1 201 201 GDP GDP . N 7 MG E 1 202 301 MG MG . O 8 HOH C 1 201 22 HOH HOH . O 8 HOH C 2 202 8 HOH HOH . P 8 HOH B 1 501 6 HOH HOH . P 8 HOH B 2 502 19 HOH HOH . P 8 HOH B 3 503 3 HOH HOH . P 8 HOH B 4 504 12 HOH HOH . P 8 HOH B 5 505 16 HOH HOH . P 8 HOH B 6 506 18 HOH HOH . P 8 HOH B 7 507 17 HOH HOH . P 8 HOH B 8 508 24 HOH HOH . Q 8 HOH H 1 201 7 HOH HOH . Q 8 HOH H 2 202 2 HOH HOH . R 8 HOH G 1 201 1 HOH HOH . R 8 HOH G 2 202 5 HOH HOH . S 8 HOH F 1 501 13 HOH HOH . S 8 HOH F 2 502 10 HOH HOH . S 8 HOH F 3 503 20 HOH HOH . S 8 HOH F 4 504 21 HOH HOH . S 8 HOH F 5 505 23 HOH HOH . T 8 HOH A 1 301 11 HOH HOH . T 8 HOH A 2 302 14 HOH HOH . U 8 HOH E 1 301 4 HOH HOH . U 8 HOH E 2 302 9 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 . . . K 6 37.77 44.376 43.401 1 80.56 ? PB GDP 201 A 1 HETATM 2 O O1B GDP . . . K 6 39.082 44.226 42.782 1 71.86 ? O1B GDP 201 A 1 HETATM 3 O O2B GDP . . . K 6 36.98 43.24 43.735 1 72.06 -1 O2B GDP 201 A 1 HETATM 4 O O3B GDP . . . K 6 36.955 45.403 42.829 1 77.19 ? O3B GDP 201 A 1 HETATM 5 O O3A GDP . . . K 6 37.806 44.869 44.856 1 86.18 ? O3A GDP 201 A 1 HETATM 6 P PA GDP . . . K 6 39.143 45.218 45.521 1 86.72 ? PA GDP 201 A 1 HETATM 7 O O1A GDP . . . K 6 39.939 45.883 44.514 1 86.94 ? O1A GDP 201 A 1 HETATM 8 O O2A GDP . . . K 6 39.684 44.108 46.298 1 79.61 -1 O2A GDP 201 A 1 HETATM 9 O O5' GDP . . . K 6 38.649 46.311 46.479 1 83.16 ? O5' GDP 201 A 1 HETATM 10 C C5' GDP . . . K 6 37.796 46.02 47.562 1 86.44 ? C5' GDP 201 A 1 HETATM 11 C C4' GDP . . . K 6 37.277 47.355 48.079 1 93.34 ? C4' GDP 201 A 1 HETATM 12 O O4' GDP . . . K 6 36.611 47.24 49.315 1 88.17 ? O4' GDP 201 A 1 HETATM 13 C C3' GDP . . . K 6 38.424 48.228 48.432 1 89.01 ? C3' GDP 201 A 1 HETATM 14 O O3' GDP . . . K 6 37.86 49.522 48.525 1 85.81 ? O3' GDP 201 A 1 HETATM 15 C C2' GDP . . . K 6 38.818 47.667 49.763 1 80.94 ? C2' GDP 201 A 1 HETATM 16 O O2' GDP . . . K 6 39.318 48.696 50.558 1 84.08 ? O2' GDP 201 A 1 HETATM 17 C C1' GDP . . . K 6 37.536 47.23 50.377 1 84.44 ? C1' GDP 201 A 1 HETATM 18 N N9 GDP . . . K 6 37.512 45.846 50.83 1 82.66 ? N9 GDP 201 A 1 HETATM 19 C C8 GDP . . . K 6 37.895 44.794 50.136 1 81.21 ? C8 GDP 201 A 1 HETATM 20 N N7 GDP . . . K 6 37.692 43.681 50.837 1 77.99 ? N7 GDP 201 A 1 HETATM 21 C C5 GDP . . . K 6 37.151 44.029 51.991 1 82.75 ? C5 GDP 201 A 1 HETATM 22 C C6 GDP . . . K 6 36.67 43.366 53.191 1 86.59 ? C6 GDP 201 A 1 HETATM 23 O O6 GDP . . . K 6 36.711 42.16 53.321 1 85.1 ? O6 GDP 201 A 1 HETATM 24 N N1 GDP . . . K 6 36.172 44.051 54.179 1 85.27 ? N1 GDP 201 A 1 HETATM 25 C C2 GDP . . . K 6 36.075 45.338 54.112 1 85.74 ? C2 GDP 201 A 1 HETATM 26 N N2 GDP . . . K 6 35.537 45.934 55.184 1 83.53 ? N2 GDP 201 A 1 HETATM 27 N N3 GDP . . . K 6 36.486 46.029 53.037 1 84.02 ? N3 GDP 201 A 1 HETATM 28 C C4 GDP . . . K 6 37.023 45.448 51.973 1 81.85 ? C4 GDP 201 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 28 #