data_2GAO # _model_server_result.job_id w5V9qMYhoUQjRybPcQ2Npg _model_server_result.datetime_utc '2024-11-01 11:33:10' _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 2gao # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 2GAO # _exptl.entry_id 2GAO _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 105.94 _cell.angle_gamma 90 _cell.entry_id 2GAO _cell.length_a 57.295 _cell.length_b 63.814 _cell.length_c 62.132 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2GAO _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H _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 # 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 # _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 2GAO _atom_sites.fract_transf_matrix[1][1] 0.01745 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00498 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01567 _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] 0.01674 _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 1 501 501 GDP GDP . D 3 UNX A 1 602 602 UNX UNX . E 2 GDP B 1 501 501 GDP GDP . F 3 UNX B 1 601 601 UNX UNX . G 4 HOH A 1 603 3 HOH HOH . G 4 HOH A 2 604 4 HOH HOH . G 4 HOH A 3 605 7 HOH HOH . G 4 HOH A 4 606 9 HOH HOH . G 4 HOH A 5 607 11 HOH HOH . G 4 HOH A 6 608 12 HOH HOH . G 4 HOH A 7 609 13 HOH HOH . G 4 HOH A 8 610 19 HOH HOH . G 4 HOH A 9 611 23 HOH HOH . G 4 HOH A 10 612 25 HOH HOH . G 4 HOH A 11 613 30 HOH HOH . G 4 HOH A 12 614 35 HOH HOH . G 4 HOH A 13 615 38 HOH HOH . G 4 HOH A 14 616 39 HOH HOH . G 4 HOH A 15 617 42 HOH HOH . G 4 HOH A 16 618 45 HOH HOH . G 4 HOH A 17 619 49 HOH HOH . G 4 HOH A 18 620 50 HOH HOH . G 4 HOH A 19 621 51 HOH HOH . G 4 HOH A 20 622 52 HOH HOH . G 4 HOH A 21 623 53 HOH HOH . G 4 HOH A 22 624 54 HOH HOH . G 4 HOH A 23 625 56 HOH HOH . G 4 HOH A 24 626 65 HOH HOH . G 4 HOH A 25 627 66 HOH HOH . G 4 HOH A 26 628 67 HOH HOH . G 4 HOH A 27 629 70 HOH HOH . G 4 HOH A 28 630 72 HOH HOH . G 4 HOH A 29 631 73 HOH HOH . G 4 HOH A 30 632 74 HOH HOH . H 4 HOH B 1 602 2 HOH HOH . H 4 HOH B 2 603 5 HOH HOH . H 4 HOH B 3 604 8 HOH HOH . H 4 HOH B 4 605 14 HOH HOH . H 4 HOH B 5 606 16 HOH HOH . H 4 HOH B 6 607 17 HOH HOH . H 4 HOH B 7 608 18 HOH HOH . H 4 HOH B 8 609 20 HOH HOH . H 4 HOH B 9 610 21 HOH HOH . H 4 HOH B 10 611 26 HOH HOH . H 4 HOH B 11 612 28 HOH HOH . H 4 HOH B 12 613 31 HOH HOH . H 4 HOH B 13 614 32 HOH HOH . H 4 HOH B 14 615 36 HOH HOH . H 4 HOH B 15 616 37 HOH HOH . H 4 HOH B 16 617 40 HOH HOH . H 4 HOH B 17 618 43 HOH HOH . H 4 HOH B 18 619 44 HOH HOH . H 4 HOH B 19 620 55 HOH HOH . H 4 HOH B 20 621 57 HOH HOH . H 4 HOH B 21 622 58 HOH HOH . H 4 HOH B 22 623 59 HOH HOH . H 4 HOH B 23 624 60 HOH HOH . H 4 HOH B 24 625 61 HOH HOH . H 4 HOH B 25 626 62 HOH HOH . H 4 HOH B 26 627 63 HOH HOH . H 4 HOH B 27 628 64 HOH HOH . H 4 HOH B 28 629 68 HOH HOH . H 4 HOH B 29 630 69 HOH HOH . H 4 HOH B 30 631 71 HOH HOH . H 4 HOH B 31 632 75 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 29.041 34.639 44.612 1 19.77 ? PB GDP 501 A 1 HETATM 2 O O1B GDP . . . C 2 28.433 33.472 45.39 1 15.65 ? O1B GDP 501 A 1 HETATM 3 O O2B GDP . . . C 2 30.399 34.284 44.103 1 20.72 ? O2B GDP 501 A 1 HETATM 4 O O3B GDP . . . C 2 28.211 35.049 43.458 1 20.25 ? O3B GDP 501 A 1 HETATM 5 O O3A GDP . . . C 2 29.199 35.884 45.579 1 19.96 ? O3A GDP 501 A 1 HETATM 6 P PA GDP . . . C 2 29.512 35.777 47.154 1 20.35 ? PA GDP 501 A 1 HETATM 7 O O1A GDP . . . C 2 28.278 35.591 47.973 1 19.83 ? O1A GDP 501 A 1 HETATM 8 O O2A GDP . . . C 2 30.555 34.718 47.396 1 22.38 ? O2A GDP 501 A 1 HETATM 9 O O5' GDP . . . C 2 30.057 37.272 47.384 1 23.55 ? O5' GDP 501 A 1 HETATM 10 C C5' GDP . . . C 2 31.377 37.642 46.956 1 27.06 ? C5' GDP 501 A 1 HETATM 11 C C4' GDP . . . C 2 31.905 38.66 47.95 1 27.65 ? C4' GDP 501 A 1 HETATM 12 O O4' GDP . . . C 2 31.108 39.857 47.883 1 26.25 ? O4' GDP 501 A 1 HETATM 13 C C3' GDP . . . C 2 31.795 38.114 49.364 1 27.53 ? C3' GDP 501 A 1 HETATM 14 O O3' GDP . . . C 2 32.951 38.451 50.124 1 30.65 ? O3' GDP 501 A 1 HETATM 15 C C2' GDP . . . C 2 30.598 38.814 49.949 1 27.17 ? C2' GDP 501 A 1 HETATM 16 O O2' GDP . . . C 2 30.723 39.009 51.339 1 25.6 ? O2' GDP 501 A 1 HETATM 17 C C1' GDP . . . C 2 30.554 40.133 49.185 1 24.8 ? C1' GDP 501 A 1 HETATM 18 N N9 GDP . . . C 2 29.177 40.676 49.126 1 24.7 ? N9 GDP 501 A 1 HETATM 19 C C8 GDP . . . C 2 28.019 40.028 48.823 1 23.89 ? C8 GDP 501 A 1 HETATM 20 N N7 GDP . . . C 2 26.974 40.856 48.892 1 22.99 ? N7 GDP 501 A 1 HETATM 21 C C5 GDP . . . C 2 27.437 42.05 49.236 1 22.88 ? C5 GDP 501 A 1 HETATM 22 C C6 GDP . . . C 2 26.867 43.388 49.466 1 22.59 ? C6 GDP 501 A 1 HETATM 23 O O6 GDP . . . C 2 25.654 43.622 49.382 1 22.88 ? O6 GDP 501 A 1 HETATM 24 N N1 GDP . . . C 2 27.708 44.347 49.803 1 23.15 ? N1 GDP 501 A 1 HETATM 25 C C2 GDP . . . C 2 29.049 44.159 49.933 1 23.76 ? C2 GDP 501 A 1 HETATM 26 N N2 GDP . . . C 2 29.84 45.184 50.278 1 24.62 ? N2 GDP 501 A 1 HETATM 27 N N3 GDP . . . C 2 29.643 42.979 49.736 1 23.99 ? N3 GDP 501 A 1 HETATM 28 C C4 GDP . . . C 2 28.887 41.919 49.39 1 24.64 ? C4 GDP 501 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 322 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #