data_4OJK # _model_server_result.job_id VM5ZoYfZ05WduqPNNTbTNw _model_server_result.datetime_utc '2024-11-05 21:07:49' _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 4ojk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":301}' # _entry.id 4OJK # _exptl.entry_id 4OJK _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 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 90 _cell.entry_id 4OJK _cell.length_a 136.007 _cell.length_b 136.007 _cell.length_c 76.997 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4OJK _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # 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 tetrameric 4 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 PISA dimeric 2 author_and_software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E,G,I 1 1 B,D,F,H 1 2 A,C,E,G,I 2 1 B,D,F,H 3 1 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 5_444 -x-1/2,y-1/2,-z-1/4 -1 0 0 0 1 0 0 0 -1 -68.0035 -68.0035 -19.24925 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 E N N ? 3 F N 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 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 4OJK _atom_sites.fract_transf_matrix[1][1] 0.007353 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007353 _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] 0.012987 _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 E 3 GDP A 1 301 1 GDP GDP . F 3 GDP B 1 301 2 GDP GDP . G 4 HOH A 1 401 2 HOH HOH . G 4 HOH A 2 402 4 HOH HOH . G 4 HOH A 3 403 6 HOH HOH . G 4 HOH A 4 404 8 HOH HOH . G 4 HOH A 5 405 11 HOH HOH . G 4 HOH A 6 406 13 HOH HOH . G 4 HOH A 7 407 14 HOH HOH . G 4 HOH A 8 408 15 HOH HOH . G 4 HOH A 9 409 16 HOH HOH . G 4 HOH A 10 410 17 HOH HOH . G 4 HOH A 11 411 19 HOH HOH . G 4 HOH A 12 412 20 HOH HOH . G 4 HOH A 13 413 21 HOH HOH . G 4 HOH A 14 414 22 HOH HOH . G 4 HOH A 15 415 23 HOH HOH . G 4 HOH A 16 416 27 HOH HOH . G 4 HOH A 17 417 28 HOH HOH . H 4 HOH B 1 401 24 HOH HOH . H 4 HOH B 2 402 25 HOH HOH . H 4 HOH B 3 403 29 HOH HOH . I 4 HOH C 1 101 26 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 . . . F 3 -23.372 34.029 0.375 1 74.49 ? PB GDP 301 B 1 HETATM 2 O O1B GDP . . . F 3 -21.984 34.223 0.934 1 86.14 ? O1B GDP 301 B 1 HETATM 3 O O2B GDP . . . F 3 -23.823 35.262 -0.371 1 78.77 ? O2B GDP 301 B 1 HETATM 4 O O3B GDP . . . F 3 -24.334 33.765 1.508 1 68.65 ? O3B GDP 301 B 1 HETATM 5 O O3A GDP . . . F 3 -23.395 32.774 -0.624 1 48.22 ? O3A GDP 301 B 1 HETATM 6 P PA GDP . . . F 3 -22.313 32.624 -1.799 1 71.76 ? PA GDP 301 B 1 HETATM 7 O O1A GDP . . . F 3 -22.874 33.197 -3.077 1 69.48 ? O1A GDP 301 B 1 HETATM 8 O O2A GDP . . . F 3 -21.011 33.298 -1.444 1 85.44 ? O2A GDP 301 B 1 HETATM 9 O O5' GDP . . . F 3 -22.148 31.026 -1.939 1 63.97 ? O5' GDP 301 B 1 HETATM 10 C C5' GDP . . . F 3 -20.932 30.389 -1.548 1 68.66 ? C5' GDP 301 B 1 HETATM 11 C C4' GDP . . . F 3 -20.801 29.038 -2.238 1 63.61 ? C4' GDP 301 B 1 HETATM 12 O O4' GDP . . . F 3 -22.054 28.35 -2.225 1 68.58 ? O4' GDP 301 B 1 HETATM 13 C C3' GDP . . . F 3 -20.395 29.213 -3.692 1 60 ? C3' GDP 301 B 1 HETATM 14 O O3' GDP . . . F 3 -19.157 28.543 -3.943 1 62.92 ? O3' GDP 301 B 1 HETATM 15 C C2' GDP . . . F 3 -21.484 28.551 -4.505 1 57.94 ? C2' GDP 301 B 1 HETATM 16 O O2' GDP . . . F 3 -20.902 27.713 -5.504 1 80.14 ? O2' GDP 301 B 1 HETATM 17 C C1' GDP . . . F 3 -22.274 27.733 -3.496 1 63.64 ? C1' GDP 301 B 1 HETATM 18 N N9 GDP . . . F 3 -23.713 27.72 -3.862 1 69.01 ? N9 GDP 301 B 1 HETATM 19 C C8 GDP . . . F 3 -24.538 28.781 -3.929 1 69.25 ? C8 GDP 301 B 1 HETATM 20 N N7 GDP . . . F 3 -25.79 28.404 -4.297 1 71.65 ? N7 GDP 301 B 1 HETATM 21 C C5 GDP . . . F 3 -25.775 27.069 -4.468 1 84.79 ? C5 GDP 301 B 1 HETATM 22 C C6 GDP . . . F 3 -26.753 26.024 -4.854 1 89.89 ? C6 GDP 301 B 1 HETATM 23 O O6 GDP . . . F 3 -27.94 26.316 -5.114 1 76.08 ? O6 GDP 301 B 1 HETATM 24 N N1 GDP . . . F 3 -26.326 24.755 -4.909 1 97.53 ? N1 GDP 301 B 1 HETATM 25 C C2 GDP . . . F 3 -25.052 24.41 -4.632 1 81.4 ? C2 GDP 301 B 1 HETATM 26 N N2 GDP . . . F 3 -24.693 23.107 -4.713 1 78.56 ? N2 GDP 301 B 1 HETATM 27 N N3 GDP . . . F 3 -24.107 25.313 -4.275 1 72.21 ? N3 GDP 301 B 1 HETATM 28 C C4 GDP . . . F 3 -24.405 26.627 -4.179 1 76.3 ? C4 GDP 301 B 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 220 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 28 #