data_5I4R # _model_server_result.job_id Gh4xRBnpM-ImTuTX0jBtmg _model_server_result.datetime_utc '2025-02-17 09:00:45' _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 5i4r # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":101}' # _entry.id 5I4R # _exptl.entry_id 5I4R _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 5 _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 109.58 _cell.angle_gamma 90 _cell.entry_id 5I4R _cell.length_a 74.395 _cell.length_b 128.354 _cell.length_c 100.358 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5I4R _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 octameric _pdbx_struct_assembly.oligomeric_count 8 _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,I,J _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 ? 5 I N N ? 5 J N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order covale ? covale1 A C GLY 21 A GLY 184 1_555 A N MSE 22 A MSE 185 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale2 A C MSE 22 A MSE 185 1_555 A N LYS 23 A LYS 186 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale3 A C GLU 73 A GLU 236 1_555 A N MSE 74 A MSE 237 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.317 ? covale ? covale4 A C MSE 74 A MSE 237 1_555 A N ILE 75 A ILE 238 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale5 D C GLU 12 B GLU 12 1_555 D N MSE 13 B MSE 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale6 D C MSE 13 B MSE 13 1_555 D N TYR 14 B TYR 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale7 D C ARG 56 B ARG 56 1_555 D N MSE 57 B MSE 57 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale8 D C MSE 57 B MSE 57 1_555 D N GLN 58 B GLN 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale9 D C THR 63 B THR 63 1_555 D N MSE 64 B MSE 64 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.32 ? covale ? covale10 D C MSE 64 B MSE 64 1_555 D N LEU 65 B LEU 65 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale11 E C GLY 21 E GLY 184 1_555 E N MSE 22 E MSE 185 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale12 E C MSE 22 E MSE 185 1_555 E N LYS 23 E LYS 186 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale13 E C GLU 73 E GLU 236 1_555 E N MSE 74 E MSE 237 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.316 ? covale ? covale14 E C MSE 74 E MSE 237 1_555 E N ILE 75 E ILE 238 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale15 H C GLU 12 F GLU 12 1_555 H N MSE 13 F MSE 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale16 H C MSE 13 F MSE 13 1_555 H N TYR 14 F TYR 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale17 H C ARG 56 F ARG 56 1_555 H N MSE 57 F MSE 57 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale18 H C MSE 57 F MSE 57 1_555 H N GLN 58 F GLN 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale19 H C THR 63 F THR 63 1_555 H N MSE 64 F MSE 64 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.319 ? covale ? covale20 H C MSE 64 F MSE 64 1_555 H N LEU 65 F LEU 65 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? # _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 5I4R _atom_sites.fract_transf_matrix[1][1] 0.013442 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004782 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007791 _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] 0.010576 _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 I 5 GDP C 1 101 1 GDP GDP . J 5 GDP G 1 101 2 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 . . . J 5 112.837 -39.475 77.448 1 125.86 ? PB GDP 101 G 1 HETATM 2 O O1B GDP . . . J 5 113.911 -39.307 76.398 1 129.8 ? O1B GDP 101 G 1 HETATM 3 O O2B GDP . . . J 5 112.605 -38.173 78.143 1 127.91 ? O2B GDP 101 G 1 HETATM 4 O O3B GDP . . . J 5 111.612 -40.149 76.962 1 122.16 ? O3B GDP 101 G 1 HETATM 5 O O3A GDP . . . J 5 113.34 -40.452 78.58 1 129.37 ? O3A GDP 101 G 1 HETATM 6 P PA GDP . . . J 5 113.148 -42.017 78.618 1 130.01 ? PA GDP 101 G 1 HETATM 7 O O1A GDP . . . J 5 113.145 -42.443 77.201 1 130.28 ? O1A GDP 101 G 1 HETATM 8 O O2A GDP . . . J 5 111.868 -42.388 79.325 1 127.04 ? O2A GDP 101 G 1 HETATM 9 O O5' GDP . . . J 5 114.421 -42.56 79.376 1 136.59 ? O5' GDP 101 G 1 HETATM 10 C C5' GDP . . . J 5 115.516 -43.2 78.685 1 141.82 ? C5' GDP 101 G 1 HETATM 11 C C4' GDP . . . J 5 116.46 -43.795 79.699 1 144.82 ? C4' GDP 101 G 1 HETATM 12 O O4' GDP . . . J 5 116.476 -42.967 80.871 1 144.27 ? O4' GDP 101 G 1 HETATM 13 C C3' GDP . . . J 5 116.077 -45.198 80.164 1 147.22 ? C3' GDP 101 G 1 HETATM 14 O O3' GDP . . . J 5 116.823 -46.174 79.45 1 147.93 ? O3' GDP 101 G 1 HETATM 15 C C2' GDP . . . J 5 116.437 -45.221 81.657 1 149.28 ? C2' GDP 101 G 1 HETATM 16 O O2' GDP . . . J 5 117.597 -46.003 81.911 1 156.01 ? O2' GDP 101 G 1 HETATM 17 C C1' GDP . . . J 5 116.715 -43.757 82.016 1 148.84 ? C1' GDP 101 G 1 HETATM 18 N N9 GDP . . . J 5 115.83 -43.292 83.093 1 150.09 ? N9 GDP 101 G 1 HETATM 19 C C8 GDP . . . J 5 114.542 -42.843 82.949 1 150.85 ? C8 GDP 101 G 1 HETATM 20 N N7 GDP . . . J 5 113.947 -42.572 84.088 1 150.6 ? N7 GDP 101 G 1 HETATM 21 C C5 GDP . . . J 5 114.903 -42.857 85.051 1 153.8 ? C5 GDP 101 G 1 HETATM 22 C C6 GDP . . . J 5 114.868 -42.784 86.516 1 154.59 ? C6 GDP 101 G 1 HETATM 23 O O6 GDP . . . J 5 113.921 -42.44 87.223 1 149.41 ? O6 GDP 101 G 1 HETATM 24 N N1 GDP . . . J 5 116.063 -43.183 87.09 1 155.03 ? N1 GDP 101 G 1 HETATM 25 C C2 GDP . . . J 5 117.173 -43.605 86.398 1 153.53 ? C2 GDP 101 G 1 HETATM 26 N N2 GDP . . . J 5 118.232 -43.969 87.123 1 153.48 ? N2 GDP 101 G 1 HETATM 27 N N3 GDP . . . J 5 117.232 -43.677 85.064 1 153.72 ? N3 GDP 101 G 1 HETATM 28 C C4 GDP . . . J 5 116.075 -43.297 84.454 1 153.25 ? C4 GDP 101 G 1 # _model_server_stats.io_time_ms 60 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 35 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 28 #