data_4LI0 # _model_server_result.job_id zYgWVSmlp8RDJmgG2DBY6Q _model_server_result.datetime_utc '2024-11-04 22:49:39' _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 4li0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":200}' # _entry.id 4LI0 # _exptl.entry_id 4LI0 _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 4LI0 _cell.length_a 110.93 _cell.length_b 160.38 _cell.length_c 166.51 _cell.Z_PDB 32 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4LI0 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # 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 trimeric 3 author_and_software_defined_assembly 1 PISA trimeric 3 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,E,F,G 1 1 B,C,D,H 2 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 ? 3 G N N ? 3 H 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 4LI0 _atom_sites.fract_transf_matrix[1][1] 0.009015 _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] 0.006235 _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] 0.006006 _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 G 3 GDP A 1 200 200 GDP GDP . H 3 GDP B 1 200 200 GDP GDP . # 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 . . . H 3 30.491 41.264 8.031 1 61.48 ? PB GDP 200 B 1 HETATM 2 O O1B GDP . . . H 3 29.005 41.272 7.798 1 69.92 ? O1B GDP 200 B 1 HETATM 3 O O2B GDP . . . H 3 30.943 40.114 8.873 1 60.47 ? O2B GDP 200 B 1 HETATM 4 O O3B GDP . . . H 3 31.313 41.542 6.814 1 59.83 ? O3B GDP 200 B 1 HETATM 5 O O3A GDP . . . H 3 30.717 42.533 8.965 1 71.92 ? O3A GDP 200 B 1 HETATM 6 P PA GDP . . . H 3 30.33 43.972 8.383 1 91.35 ? PA GDP 200 B 1 HETATM 7 O O1A GDP . . . H 3 31.531 44.543 7.674 1 88.88 ? O1A GDP 200 B 1 HETATM 8 O O2A GDP . . . H 3 28.981 43.89 7.697 1 91.53 ? O2A GDP 200 B 1 HETATM 9 O O5' GDP . . . H 3 30.094 44.824 9.718 1 101.01 ? O5' GDP 200 B 1 HETATM 10 C C5' GDP . . . H 3 29.574 46.147 9.583 1 109.59 ? C5' GDP 200 B 1 HETATM 11 C C4' GDP . . . H 3 28.787 46.582 10.817 1 110.96 ? C4' GDP 200 B 1 HETATM 12 O O4' GDP . . . H 3 29.393 46.125 12.031 1 105.48 ? O4' GDP 200 B 1 HETATM 13 C C3' GDP . . . H 3 28.699 48.102 10.881 1 111.72 ? C3' GDP 200 B 1 HETATM 14 O O3' GDP . . . H 3 27.326 48.511 10.852 1 117.69 ? O3' GDP 200 B 1 HETATM 15 C C2' GDP . . . H 3 29.393 48.501 12.168 1 112.03 ? C2' GDP 200 B 1 HETATM 16 O O2' GDP . . . H 3 28.465 49.101 13.081 1 119.71 ? O2' GDP 200 B 1 HETATM 17 C C1' GDP . . . H 3 29.932 47.218 12.779 1 106.81 ? C1' GDP 200 B 1 HETATM 18 N N9 GDP . . . H 3 31.423 47.136 12.777 1 102.47 ? N9 GDP 200 B 1 HETATM 19 C C8 GDP . . . H 3 32.21 46.567 11.835 1 101.46 ? C8 GDP 200 B 1 HETATM 20 N N7 GDP . . . H 3 33.526 46.654 12.159 1 95.97 ? N7 GDP 200 B 1 HETATM 21 C C5 GDP . . . H 3 33.614 47.283 13.344 1 99.05 ? C5 GDP 200 B 1 HETATM 22 C C6 GDP . . . H 3 34.721 47.701 14.265 1 94.84 ? C6 GDP 200 B 1 HETATM 23 O O6 GDP . . . H 3 35.925 47.484 13.996 1 79.86 ? O6 GDP 200 B 1 HETATM 24 N N1 GDP . . . H 3 34.365 48.35 15.408 1 93.73 ? N1 GDP 200 B 1 HETATM 25 C C2 GDP . . . H 3 33.049 48.606 15.713 1 98.75 ? C2 GDP 200 B 1 HETATM 26 N N2 GDP . . . H 3 32.763 49.26 16.863 1 102.82 ? N2 GDP 200 B 1 HETATM 27 N N3 GDP . . . H 3 32 48.244 14.917 1 95.15 ? N3 GDP 200 B 1 HETATM 28 C C4 GDP . . . H 3 32.218 47.595 13.745 1 99.6 ? C4 GDP 200 B 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 301 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #