data_8ILA # _model_server_result.job_id 4p28DliWT9GwtA7ly_757A _model_server_result.datetime_utc '2025-01-12 15:32:04' _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 8ila # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":501}' # _entry.id 8ILA # _exptl.entry_id 8ILA _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 4 _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 8ILA _cell.length_a 122.382 _cell.length_b 137.739 _cell.length_c 146.101 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8ILA _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P _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 E N N ? 2 G N N ? 2 I N N ? 2 K 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 8ILA _atom_sites.fract_transf_matrix[1][1] 0.008171 _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] 0.00726 _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] 0.006845 _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 2 GDP A 1 501 502 GDP GDP . F 3 Q3L A 1 502 503 Q3L L90 . G 2 GDP C 1 501 502 GDP GDP . H 3 Q3L C 1 502 503 Q3L L90 . I 2 GDP B 1 501 502 GDP GDP . J 3 Q3L B 1 502 503 Q3L L90 . K 2 GDP D 1 501 502 GDP GDP . L 3 Q3L D 1 502 503 Q3L L90 . M 4 HOH A 1 601 32 HOH HOH . M 4 HOH A 2 602 29 HOH HOH . M 4 HOH A 3 603 48 HOH HOH . M 4 HOH A 4 604 43 HOH HOH . M 4 HOH A 5 605 20 HOH HOH . M 4 HOH A 6 606 6 HOH HOH . M 4 HOH A 7 607 42 HOH HOH . M 4 HOH A 8 608 13 HOH HOH . M 4 HOH A 9 609 4 HOH HOH . M 4 HOH A 10 610 46 HOH HOH . M 4 HOH A 11 611 19 HOH HOH . M 4 HOH A 12 612 25 HOH HOH . M 4 HOH A 13 613 2 HOH HOH . M 4 HOH A 14 614 14 HOH HOH . M 4 HOH A 15 615 22 HOH HOH . M 4 HOH A 16 616 50 HOH HOH . M 4 HOH A 17 617 17 HOH HOH . M 4 HOH A 18 618 57 HOH HOH . M 4 HOH A 19 619 30 HOH HOH . N 4 HOH C 1 601 1 HOH HOH . N 4 HOH C 2 602 58 HOH HOH . N 4 HOH C 3 603 52 HOH HOH . N 4 HOH C 4 604 38 HOH HOH . N 4 HOH C 5 605 39 HOH HOH . N 4 HOH C 6 606 51 HOH HOH . N 4 HOH C 7 607 47 HOH HOH . N 4 HOH C 8 608 10 HOH HOH . N 4 HOH C 9 609 41 HOH HOH . N 4 HOH C 10 610 26 HOH HOH . N 4 HOH C 11 611 36 HOH HOH . N 4 HOH C 12 612 40 HOH HOH . N 4 HOH C 13 613 16 HOH HOH . N 4 HOH C 14 614 5 HOH HOH . N 4 HOH C 15 615 45 HOH HOH . N 4 HOH C 16 616 44 HOH HOH . N 4 HOH C 17 617 37 HOH HOH . N 4 HOH C 18 618 54 HOH HOH . O 4 HOH B 1 601 35 HOH HOH . O 4 HOH B 2 602 18 HOH HOH . O 4 HOH B 3 603 31 HOH HOH . O 4 HOH B 4 604 28 HOH HOH . O 4 HOH B 5 605 55 HOH HOH . O 4 HOH B 6 606 56 HOH HOH . O 4 HOH B 7 607 59 HOH HOH . P 4 HOH D 1 601 33 HOH HOH . P 4 HOH D 2 602 34 HOH HOH . P 4 HOH D 3 603 23 HOH HOH . P 4 HOH D 4 604 24 HOH HOH . P 4 HOH D 5 605 3 HOH HOH . P 4 HOH D 6 606 49 HOH HOH . P 4 HOH D 7 607 21 HOH HOH . P 4 HOH D 8 608 15 HOH HOH . P 4 HOH D 9 609 11 HOH HOH . P 4 HOH D 10 610 7 HOH HOH . P 4 HOH D 11 611 27 HOH HOH . P 4 HOH D 12 612 12 HOH HOH . P 4 HOH D 13 613 8 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 . . . I 2 30.187 -6.916 31.137 0.47 91.66 ? PB GDP 501 B 1 HETATM 2 O O1B GDP . . . I 2 30.987 -7.26 29.903 1 92.28 ? O1B GDP 501 B 1 HETATM 3 O O2B GDP . . . I 2 29.126 -5.898 30.787 0.35 90.65 ? O2B GDP 501 B 1 HETATM 4 O O3B GDP . . . I 2 31.1 -6.34 32.192 1 93.09 ? O3B GDP 501 B 1 HETATM 5 O O3A GDP . . . I 2 29.486 -8.242 31.719 0.93 90.25 ? O3A GDP 501 B 1 HETATM 6 P PA GDP . . . I 2 30.354 -9.549 32.085 0 89.61 ? PA GDP 501 B 1 HETATM 7 O O1A GDP . . . I 2 30.321 -10.552 30.957 1 85.91 ? O1A GDP 501 B 1 HETATM 8 O O2A GDP . . . I 2 31.777 -9.174 32.421 1 90.97 ? O2A GDP 501 B 1 HETATM 9 O O5' GDP . . . I 2 29.59 -10.12 33.38 1 90.03 ? O5' GDP 501 B 1 HETATM 10 C C5' GDP . . . I 2 28.359 -9.516 33.768 1 91.81 ? C5' GDP 501 B 1 HETATM 11 C C4' GDP . . . I 2 27.898 -10.042 35.119 0.95 93.97 ? C4' GDP 501 B 1 HETATM 12 O O4' GDP . . . I 2 26.667 -9.396 35.446 0.82 96.83 ? O4' GDP 501 B 1 HETATM 13 C C3' GDP . . . I 2 27.638 -11.54 35.087 0.92 95.98 ? C3' GDP 501 B 1 HETATM 14 O O3' GDP . . . I 2 28.59 -12.23 35.903 1 94.93 ? O3' GDP 501 B 1 HETATM 15 C C2' GDP . . . I 2 26.245 -11.732 35.649 0.63 99.91 ? C2' GDP 501 B 1 HETATM 16 O O2' GDP . . . I 2 26.319 -12.419 36.9 1 102.7 ? O2' GDP 501 B 1 HETATM 17 C C1' GDP . . . I 2 25.683 -10.339 35.871 0 101.25 ? C1' GDP 501 B 1 HETATM 18 N N9 GDP . . . I 2 24.455 -10.169 35.058 0.87 105.23 ? N9 GDP 501 B 1 HETATM 19 C C8 GDP . . . I 2 24.411 -9.72 33.79 1 105.32 ? C8 GDP 501 B 1 HETATM 20 N N7 GDP . . . I 2 23.135 -9.684 33.33 1 108.46 ? N7 GDP 501 B 1 HETATM 21 C C5 GDP . . . I 2 22.337 -10.12 34.322 0 110.77 ? C5 GDP 501 B 1 HETATM 22 C C6 GDP . . . I 2 20.884 -10.333 34.507 0.89 116.45 ? C6 GDP 501 B 1 HETATM 23 O O6 GDP . . . I 2 20.077 -10.084 33.585 1 118.35 ? O6 GDP 501 B 1 HETATM 24 N N1 GDP . . . I 2 20.463 -10.8 35.691 0.19 121.18 ? N1 GDP 501 B 1 HETATM 25 C C2 GDP . . . I 2 21.31 -11.077 36.701 1 119.87 ? C2 GDP 501 B 1 HETATM 26 N N2 GDP . . . I 2 20.801 -11.545 37.866 0.12 126.39 ? N2 GDP 501 B 1 HETATM 27 N N3 GDP . . . I 2 22.654 -10.905 36.601 1 113.05 ? N3 GDP 501 B 1 HETATM 28 C C4 GDP . . . I 2 23.213 -10.44 35.459 0.88 108.83 ? C4 GDP 501 B 1 # _model_server_stats.io_time_ms 31 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 37 _model_server_stats.query_time_ms 282 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 28 #