data_2GAO # _model_server_result.job_id iXDZsSoiTj572gKQSl0NAQ _model_server_result.datetime_utc '2024-11-26 02:19:02' _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":"E","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 . . . E 2 32.323 12.37 44.183 1 16.71 ? PB GDP 501 B 1 HETATM 2 O O1B GDP . . . E 2 31.388 13.535 44.336 1 15.01 ? O1B GDP 501 B 1 HETATM 3 O O2B GDP . . . E 2 33.562 12.811 43.479 1 15.11 ? O2B GDP 501 B 1 HETATM 4 O O3B GDP . . . E 2 32.74 11.819 45.484 1 14.54 ? O3B GDP 501 B 1 HETATM 5 O O3A GDP . . . E 2 31.66 11.135 43.409 1 17.54 ? O3A GDP 501 B 1 HETATM 6 P PA GDP . . . E 2 30.333 11.168 42.498 1 15.06 ? PA GDP 501 B 1 HETATM 7 O O1A GDP . . . E 2 29.055 11.315 43.295 1 19.36 ? O1A GDP 501 B 1 HETATM 8 O O2A GDP . . . E 2 30.533 12.179 41.36 1 17.34 ? O2A GDP 501 B 1 HETATM 9 O O5' GDP . . . E 2 30.376 9.674 41.904 1 15.21 ? O5' GDP 501 B 1 HETATM 10 C C5' GDP . . . E 2 31.437 9.245 41.071 1 15.81 ? C5' GDP 501 B 1 HETATM 11 C C4' GDP . . . E 2 30.986 8.079 40.209 1 16.76 ? C4' GDP 501 B 1 HETATM 12 O O4' GDP . . . E 2 30.672 6.983 41.077 1 18.75 ? O4' GDP 501 B 1 HETATM 13 C C3' GDP . . . E 2 29.716 8.379 39.391 1 19.01 ? C3' GDP 501 B 1 HETATM 14 O O3' GDP . . . E 2 29.79 7.706 38.133 1 20.98 ? O3' GDP 501 B 1 HETATM 15 C C2' GDP . . . E 2 28.615 7.778 40.213 1 18.21 ? C2' GDP 501 B 1 HETATM 16 O O2' GDP . . . E 2 27.482 7.342 39.479 1 14.69 ? O2' GDP 501 B 1 HETATM 17 C C1' GDP . . . E 2 29.335 6.588 40.836 1 17.72 ? C1' GDP 501 B 1 HETATM 18 N N9 GDP . . . E 2 28.634 6.161 42.045 1 16.63 ? N9 GDP 501 B 1 HETATM 19 C C8 GDP . . . E 2 28.284 6.858 43.141 1 16.54 ? C8 GDP 501 B 1 HETATM 20 N N7 GDP . . . E 2 27.625 6.056 43.997 1 16.29 ? N7 GDP 501 B 1 HETATM 21 C C5 GDP . . . E 2 27.564 4.844 43.44 1 15.35 ? C5 GDP 501 B 1 HETATM 22 C C6 GDP . . . E 2 27.008 3.531 43.793 1 17.34 ? C6 GDP 501 B 1 HETATM 23 O O6 GDP . . . E 2 26.404 3.299 44.878 1 15.67 ? O6 GDP 501 B 1 HETATM 24 N N1 GDP . . . E 2 27.186 2.553 42.884 1 18.2 ? N1 GDP 501 B 1 HETATM 25 C C2 GDP . . . E 2 27.815 2.712 41.69 1 17.37 ? C2 GDP 501 B 1 HETATM 26 N N2 GDP . . . E 2 27.943 1.676 40.875 1 16.39 ? N2 GDP 501 B 1 HETATM 27 N N3 GDP . . . E 2 28.356 3.877 41.291 1 17.77 ? N3 GDP 501 B 1 HETATM 28 C C4 GDP . . . E 2 28.229 4.942 42.145 1 17.96 ? C4 GDP 501 B 1 # _model_server_stats.io_time_ms 54 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #