data_1AS3 # _model_server_result.job_id H_MX4u9vLqrHqehNybGDqA _model_server_result.datetime_utc '2024-10-18 17:23:37' _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 1as3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":355}' # _entry.id 1AS3 # _exptl.entry_id 1AS3 _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 1 _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 1AS3 _cell.length_a 121.44 _cell.length_b 121.44 _cell.length_c 68.29 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1AS3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 79 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 4' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _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 3 _struct_asym.id C _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 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 1AS3 _atom_sites.fract_transf_matrix[1][1] 0.008235 _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] 0.008235 _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] 0.014643 _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 SO4 A 1 356 356 SO4 SO4 . C 3 GDP A 1 355 355 GDP GDP . D 4 HOH A 1 403 403 HOH HOH . D 4 HOH A 2 404 404 HOH HOH . D 4 HOH A 3 407 407 HOH HOH . D 4 HOH A 4 415 415 HOH HOH . D 4 HOH A 5 416 416 HOH HOH . D 4 HOH A 6 417 417 HOH HOH . D 4 HOH A 7 418 418 HOH HOH . D 4 HOH A 8 421 421 HOH HOH . D 4 HOH A 9 422 422 HOH HOH . D 4 HOH A 10 434 434 HOH HOH . D 4 HOH A 11 439 439 HOH HOH . D 4 HOH A 12 459 459 HOH HOH . D 4 HOH A 13 477 477 HOH HOH . D 4 HOH A 14 481 481 HOH HOH . D 4 HOH A 15 484 484 HOH HOH . D 4 HOH A 16 491 491 HOH HOH . D 4 HOH A 17 600 600 HOH HOH . D 4 HOH A 18 601 601 HOH HOH . D 4 HOH A 19 602 602 HOH HOH . D 4 HOH A 20 604 604 HOH HOH . D 4 HOH A 21 605 605 HOH HOH . D 4 HOH A 22 606 606 HOH HOH . D 4 HOH A 23 607 607 HOH HOH . D 4 HOH A 24 611 611 HOH HOH . D 4 HOH A 25 612 612 HOH HOH . D 4 HOH A 26 613 613 HOH HOH . D 4 HOH A 27 614 614 HOH HOH . D 4 HOH A 28 615 615 HOH HOH . D 4 HOH A 29 616 616 HOH HOH . D 4 HOH A 30 617 617 HOH HOH . D 4 HOH A 31 623 623 HOH HOH . D 4 HOH A 32 624 624 HOH HOH . D 4 HOH A 33 625 625 HOH HOH . D 4 HOH A 34 626 626 HOH HOH . D 4 HOH A 35 627 627 HOH HOH . D 4 HOH A 36 628 628 HOH HOH . D 4 HOH A 37 634 634 HOH HOH . D 4 HOH A 38 635 635 HOH HOH . D 4 HOH A 39 636 636 HOH HOH . D 4 HOH A 40 637 637 HOH HOH . D 4 HOH A 41 638 638 HOH HOH . D 4 HOH A 42 640 640 HOH HOH . D 4 HOH A 43 701 701 HOH HOH . D 4 HOH A 44 702 702 HOH HOH . D 4 HOH A 45 703 703 HOH HOH . D 4 HOH A 46 704 704 HOH HOH . D 4 HOH A 47 705 705 HOH HOH . D 4 HOH A 48 706 706 HOH HOH . D 4 HOH A 49 707 707 HOH HOH . D 4 HOH A 50 708 708 HOH HOH . D 4 HOH A 51 709 709 HOH HOH . D 4 HOH A 52 710 710 HOH HOH . D 4 HOH A 53 711 711 HOH HOH . D 4 HOH A 54 712 712 HOH HOH . D 4 HOH A 55 713 713 HOH HOH . D 4 HOH A 56 714 714 HOH HOH . D 4 HOH A 57 715 715 HOH HOH . D 4 HOH A 58 716 716 HOH HOH . D 4 HOH A 59 717 717 HOH HOH . D 4 HOH A 60 718 718 HOH HOH . D 4 HOH A 61 719 719 HOH HOH . D 4 HOH A 62 720 720 HOH HOH . D 4 HOH A 63 721 721 HOH HOH . D 4 HOH A 64 722 722 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 3 38.199 21.782 35.995 1 30.5 ? PB GDP 355 A 1 HETATM 2 O O1B GDP . . . C 3 38.553 21.347 37.367 1 31.14 ? O1B GDP 355 A 1 HETATM 3 O O2B GDP . . . C 3 37.285 20.839 35.262 1 37.89 ? O2B GDP 355 A 1 HETATM 4 O O3B GDP . . . C 3 37.755 23.15 35.835 1 33.39 ? O3B GDP 355 A 1 HETATM 5 O O3A GDP . . . C 3 39.615 21.676 35.156 1 29.46 ? O3A GDP 355 A 1 HETATM 6 P PA GDP . . . C 3 40.619 22.839 34.619 1 28.29 ? PA GDP 355 A 1 HETATM 7 O O1A GDP . . . C 3 41.141 23.686 35.675 1 28.2 ? O1A GDP 355 A 1 HETATM 8 O O2A GDP . . . C 3 40.006 23.487 33.431 1 31.39 ? O2A GDP 355 A 1 HETATM 9 O O5' GDP . . . C 3 41.713 21.794 34.158 1 26.45 ? O5' GDP 355 A 1 HETATM 10 C C5' GDP . . . C 3 42.712 21.41 35.098 1 26.21 ? C5' GDP 355 A 1 HETATM 11 C C4' GDP . . . C 3 44.09 21.43 34.452 1 26.81 ? C4' GDP 355 A 1 HETATM 12 O O4' GDP . . . C 3 44.028 20.629 33.257 1 29.86 ? O4' GDP 355 A 1 HETATM 13 C C3' GDP . . . C 3 44.621 22.846 34 1 29.2 ? C3' GDP 355 A 1 HETATM 14 O O3' GDP . . . C 3 46.036 22.806 34.239 1 37.4 ? O3' GDP 355 A 1 HETATM 15 C C2' GDP . . . C 3 44.308 22.882 32.513 1 29.59 ? C2' GDP 355 A 1 HETATM 16 O O2' GDP . . . C 3 45.129 23.792 31.831 1 24.44 ? O2' GDP 355 A 1 HETATM 17 C C1' GDP . . . C 3 44.551 21.409 32.152 1 28.43 ? C1' GDP 355 A 1 HETATM 18 N N9 GDP . . . C 3 43.833 21.109 30.928 1 28.9 ? N9 GDP 355 A 1 HETATM 19 C C8 GDP . . . C 3 42.481 21.208 30.678 1 28.12 ? C8 GDP 355 A 1 HETATM 20 N N7 GDP . . . C 3 42.13 20.625 29.559 1 31.56 ? N7 GDP 355 A 1 HETATM 21 C C5 GDP . . . C 3 43.338 20.082 29.025 1 27.71 ? C5 GDP 355 A 1 HETATM 22 C C6 GDP . . . C 3 43.605 19.341 27.812 1 29.07 ? C6 GDP 355 A 1 HETATM 23 O O6 GDP . . . C 3 42.856 18.933 26.919 1 29.03 ? O6 GDP 355 A 1 HETATM 24 N N1 GDP . . . C 3 44.955 19.088 27.664 1 30.7 ? N1 GDP 355 A 1 HETATM 25 C C2 GDP . . . C 3 45.951 19.479 28.524 1 26.62 ? C2 GDP 355 A 1 HETATM 26 N N2 GDP . . . C 3 47.193 19.127 28.229 1 27.46 ? N2 GDP 355 A 1 HETATM 27 N N3 GDP . . . C 3 45.713 20.122 29.641 1 26.71 ? N3 GDP 355 A 1 HETATM 28 C C4 GDP . . . C 3 44.39 20.414 29.829 1 29.64 ? C4 GDP 355 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 28 #