data_6LL6 # _model_server_result.job_id 0Bfowp6-1w4ejJZy5jp7LA _model_server_result.datetime_utc '2025-04-28 00:00:47' _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 6ll6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 6LL6 # _exptl.entry_id 6LL6 _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 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 88.789 _cell.angle_beta 72.057 _cell.angle_gamma 72.445 _cell.entry_id 6LL6 _cell.length_a 38.28 _cell.length_b 41.67 _cell.length_c 45.03 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6LL6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall 'P 1' _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _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 70 n n PB O2B GDP sing 71 n n PB O3B GDP sing 72 n n PB O3A GDP sing 73 n n O2B HOB2 GDP sing 74 n n O3B HOB3 GDP sing 75 n n O3A PA GDP sing 76 n n PA O1A GDP doub 77 n n PA O2A GDP sing 78 n n PA O5' GDP sing 79 n n O2A HOA2 GDP sing 80 n n O5' C5' GDP sing 81 n n C5' C4' GDP sing 82 n n C5' H5' GDP sing 83 n n C5' "H5''" GDP sing 84 n n C4' O4' GDP sing 85 n n C4' C3' GDP sing 86 n n C4' H4' GDP sing 87 n n O4' C1' GDP sing 88 n n C3' O3' GDP sing 89 n n C3' C2' GDP sing 90 n n C3' H3' GDP sing 91 n n O3' HO3' GDP sing 92 n n C2' O2' GDP sing 93 n n C2' C1' GDP sing 94 n n C2' H2' GDP sing 95 n n O2' HO2' GDP sing 96 n n C1' N9 GDP sing 97 n n C1' H1' GDP sing 98 n n N9 C8 GDP sing 99 n y N9 C4 GDP sing 100 n y C8 N7 GDP doub 101 n y C8 H8 GDP sing 102 n n N7 C5 GDP sing 103 n y C5 C6 GDP sing 104 n n C5 C4 GDP doub 105 n y C6 O6 GDP doub 106 n n C6 N1 GDP sing 107 n n N1 C2 GDP sing 108 n n N1 HN1 GDP sing 109 n n C2 N2 GDP sing 110 n n C2 N3 GDP doub 111 n n N2 HN21 GDP sing 112 n n N2 HN22 GDP sing 113 n n N3 C4 GDP sing 114 n n # _atom_sites.entry_id 6LL6 _atom_sites.fract_transf_matrix[1][1] 0.026123 _atom_sites.fract_transf_matrix[1][2] -0.008264 _atom_sites.fract_transf_matrix[1][3] -0.009142 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.02517 _atom_sites.fract_transf_matrix[2][3] 0.001998 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.023416 _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 B 2 GDP A 1 401 401 GDP GDP . C 3 HOH A 1 501 9 HOH HOH . C 3 HOH A 2 502 7 HOH HOH . C 3 HOH A 3 503 3 HOH HOH . C 3 HOH A 4 504 2 HOH HOH . C 3 HOH A 5 505 1 HOH HOH . C 3 HOH A 6 506 4 HOH HOH . C 3 HOH A 7 507 10 HOH HOH . C 3 HOH A 8 508 8 HOH HOH . C 3 HOH A 9 509 5 HOH HOH . C 3 HOH A 10 510 11 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 . . . B 2 8.502 -15.605 -6.125 1 36.61 ? PB GDP 401 A 1 HETATM 2 O O1B GDP . . . B 2 9.707 -16.099 -6.888 1 39.57 ? O1B GDP 401 A 1 HETATM 3 O O2B GDP . . . B 2 7.184 -16.077 -6.718 1 29.5 ? O2B GDP 401 A 1 HETATM 4 O O3B GDP . . . B 2 8.576 -14.087 -6.097 1 37.1 ? O3B GDP 401 A 1 HETATM 5 O O3A GDP . . . B 2 8.681 -16.202 -4.648 1 34.22 ? O3A GDP 401 A 1 HETATM 6 P PA GDP . . . B 2 7.529 -16.117 -3.557 1 34.28 ? PA GDP 401 A 1 HETATM 7 O O1A GDP . . . B 2 6.601 -14.954 -3.839 1 35.01 ? O1A GDP 401 A 1 HETATM 8 O O2A GDP . . . B 2 6.83 -17.459 -3.421 1 37.81 ? O2A GDP 401 A 1 HETATM 9 O O5' GDP . . . B 2 8.39 -15.819 -2.236 1 37.35 ? O5' GDP 401 A 1 HETATM 10 C C5' GDP . . . B 2 8.968 -14.539 -2.067 1 35 ? C5' GDP 401 A 1 HETATM 11 C C4' GDP . . . B 2 8.829 -14.099 -0.625 1 34.01 ? C4' GDP 401 A 1 HETATM 12 O O4' GDP . . . B 2 7.467 -13.815 -0.377 1 35.27 ? O4' GDP 401 A 1 HETATM 13 C C3' GDP . . . B 2 9.211 -15.141 0.397 1 37.06 ? C3' GDP 401 A 1 HETATM 14 O O3' GDP . . . B 2 10.566 -14.912 0.775 1 42.36 ? O3' GDP 401 A 1 HETATM 15 C C2' GDP . . . B 2 8.274 -14.864 1.556 1 35.24 ? C2' GDP 401 A 1 HETATM 16 O O2' GDP . . . B 2 8.924 -14.02 2.513 1 38.46 ? O2' GDP 401 A 1 HETATM 17 C C1' GDP . . . B 2 7.124 -14.066 0.982 1 35.67 ? C1' GDP 401 A 1 HETATM 18 N N9 GDP . . . B 2 5.892 -14.881 0.956 1 36.4 ? N9 GDP 401 A 1 HETATM 19 C C8 GDP . . . B 2 5.877 -16.205 0.711 1 32.57 ? C8 GDP 401 A 1 HETATM 20 N N7 GDP . . . B 2 4.612 -16.678 0.735 1 34.29 ? N7 GDP 401 A 1 HETATM 21 C C5 GDP . . . B 2 3.796 -15.638 0.969 1 35.16 ? C5 GDP 401 A 1 HETATM 22 C C6 GDP . . . B 2 2.334 -15.469 1.101 1 35.7 ? C6 GDP 401 A 1 HETATM 23 O O6 GDP . . . B 2 1.585 -16.458 0.971 1 37.09 ? O6 GDP 401 A 1 HETATM 24 N N1 GDP . . . B 2 1.852 -14.244 1.355 1 34.44 ? N1 GDP 401 A 1 HETATM 25 C C2 GDP . . . B 2 2.667 -13.181 1.483 1 34.3 ? C2 GDP 401 A 1 HETATM 26 N N2 GDP . . . B 2 2.078 -11.999 1.731 1 31.8 ? N2 GDP 401 A 1 HETATM 27 N N3 GDP . . . B 2 4.028 -13.25 1.356 1 36.01 ? N3 GDP 401 A 1 HETATM 28 C C4 GDP . . . B 2 4.636 -14.438 1.102 1 33.25 ? C4 GDP 401 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 280 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 28 #