data_4ZCM # _model_server_result.job_id 9vr3iCRCgXzS8KmOi3I03A _model_server_result.datetime_utc '2024-12-07 16:52:20' _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 4zcm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1003}' # _entry.id 4ZCM # _exptl.entry_id 4ZCM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 603.16 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5',3'-TETRAPHOSPHATE" _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 98.04 _cell.angle_gamma 90 _cell.entry_id 4ZCM _cell.length_a 56.821 _cell.length_b 160.125 _cell.length_c 89.718 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4ZCM _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F 1 1 B,G,H,I,J 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 E N N ? 3 I N N # _chem_comp.formula 'C10 H17 N5 O17 P4' _chem_comp.formula_weight 603.16 _chem_comp.id G4P _chem_comp.mon_nstd_flag . _chem_comp.name "GUANOSINE-5',3'-TETRAPHOSPHATE" _chem_comp.type 'rna linking' _chem_comp.pdbx_synonyms 'guanosine tetraphosphate;ppGpp' # 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 G4P doub 83 n n PB O2B G4P sing 84 n n PB O3B G4P sing 85 n n PB O3A G4P sing 86 n n O2B HOB2 G4P sing 87 n n O3B HOB3 G4P sing 88 n n O3A PA G4P sing 89 n n PA O1A G4P doub 90 n n PA O2A G4P sing 91 n n PA O5' G4P sing 92 n n O2A HOA2 G4P sing 93 n n O5' C5' G4P sing 94 n n C5' C4' G4P sing 95 n n C5' H5' G4P sing 96 n n C5' "H5''" G4P sing 97 n n C4' O4' G4P sing 98 n n C4' C3' G4P sing 99 n n C4' H4' G4P sing 100 n n O4' C1' G4P sing 101 n n C3' O3' G4P sing 102 n n C3' C2' G4P sing 103 n n C3' H3' G4P sing 104 n n O3' PC G4P sing 105 n n C2' O2' G4P sing 106 n n C2' C1' G4P sing 107 n n C2' H2' G4P sing 108 n n O2' HO2' G4P sing 109 n n C1' N9 G4P sing 110 n n C1' H1' G4P sing 111 n n N9 C8 G4P sing 112 n y N9 C4 G4P sing 113 n y C8 N7 G4P doub 114 n y C8 H8 G4P sing 115 n n N7 C5 G4P sing 116 n y C5 C6 G4P sing 117 n n C5 C4 G4P doub 118 n y C6 O6 G4P doub 119 n n C6 N1 G4P sing 120 n n N1 C2 G4P sing 121 n n N1 HN1 G4P sing 122 n n C2 N2 G4P sing 123 n n C2 N3 G4P doub 124 n n N2 HN21 G4P sing 125 n n N2 HN22 G4P sing 126 n n N3 C4 G4P sing 127 n n PC O1C G4P doub 128 n n PC O2C G4P sing 129 n n PC O3C G4P sing 130 n n O2C H2C G4P sing 131 n n O3C PD G4P sing 132 n n PD O1D G4P doub 133 n n PD O2D G4P sing 134 n n PD O3D G4P sing 135 n n O2D H2D G4P sing 136 n n O3D H3D G4P sing 137 n n # _atom_sites.entry_id 4ZCM _atom_sites.fract_transf_matrix[1][1] 0.017599 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002487 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006245 _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] 0.011257 _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 NCO A 1 1001 1001 NCO NCO . D 2 NCO A 1 1002 1002 NCO NCO . E 3 G4P A 1 1003 1101 G4P G4P . F 4 MG A 1 1004 1102 MG MG . G 2 NCO B 1 1001 1001 NCO NCO . H 2 NCO B 1 1002 1002 NCO NCO . I 3 G4P B 1 1003 1101 G4P G4P . J 4 MG B 1 1004 1102 MG MG . # 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 G4P . . . E 3 -4.245 -8.964 17.826 1 79.12 ? PB G4P 1003 A 1 HETATM 2 O O1B G4P . . . E 3 -3.291 -8.858 16.662 1 101.58 ? O1B G4P 1003 A 1 HETATM 3 O O2B G4P . . . E 3 -4.693 -7.578 18.222 1 70.05 ? O2B G4P 1003 A 1 HETATM 4 O O3B G4P . . . E 3 -3.546 -9.618 18.994 1 94.62 ? O3B G4P 1003 A 1 HETATM 5 O O3A G4P . . . E 3 -5.551 -9.866 17.373 1 93.03 ? O3A G4P 1003 A 1 HETATM 6 P PA G4P . . . E 3 -6.552 -9.442 16.135 1 85.64 ? PA G4P 1003 A 1 HETATM 7 O O1A G4P . . . E 3 -6.837 -7.966 16.234 1 101.45 ? O1A G4P 1003 A 1 HETATM 8 O O2A G4P . . . E 3 -5.898 -9.754 14.809 1 60.7 ? O2A G4P 1003 A 1 HETATM 9 O O5' G4P . . . E 3 -7.98 -10.255 16.249 1 96.7 ? O5' G4P 1003 A 1 HETATM 10 C C5' G4P . . . E 3 -8.686 -10.496 15.066 1 96.42 ? C5' G4P 1003 A 1 HETATM 11 C C4' G4P . . . E 3 -10.129 -10.171 15.252 1 93.75 ? C4' G4P 1003 A 1 HETATM 12 O O4' G4P . . . E 3 -10.324 -8.89 15.087 1 91.61 ? O4' G4P 1003 A 1 HETATM 13 C C3' G4P . . . E 3 -11.028 -11.009 14.123 1 99.35 ? C3' G4P 1003 A 1 HETATM 14 O O3' G4P . . . E 3 -11.867 -12.023 14.802 1 95.07 ? O3' G4P 1003 A 1 HETATM 15 C C2' G4P . . . E 3 -11.769 -10.203 13.54 1 115.07 ? C2' G4P 1003 A 1 HETATM 16 O O2' G4P . . . E 3 -13.177 -10.406 14.024 1 143.35 ? O2' G4P 1003 A 1 HETATM 17 C C1' G4P . . . E 3 -11.293 -8.719 13.946 1 102 ? C1' G4P 1003 A 1 HETATM 18 N N9 G4P . . . E 3 -10.702 -8.079 12.952 1 100.5 ? N9 G4P 1003 A 1 HETATM 19 C C8 G4P . . . E 3 -9.422 -8.048 12.533 1 113.64 ? C8 G4P 1003 A 1 HETATM 20 N N7 G4P . . . E 3 -9.354 -7.212 11.478 1 102.29 ? N7 G4P 1003 A 1 HETATM 21 C C5 G4P . . . E 3 -10.572 -6.729 11.252 1 80.89 ? C5 G4P 1003 A 1 HETATM 22 C C6 G4P . . . E 3 -11.104 -5.746 10.201 1 75.54 ? C6 G4P 1003 A 1 HETATM 23 O O6 G4P . . . E 3 -10.368 -5.281 9.399 1 88.91 ? O6 G4P 1003 A 1 HETATM 24 N N1 G4P . . . E 3 -12.49 -5.394 10.188 1 66.51 ? N1 G4P 1003 A 1 HETATM 25 C C2 G4P . . . E 3 -13.38 -5.966 11.166 1 65.11 ? C2 G4P 1003 A 1 HETATM 26 N N2 G4P . . . E 3 -14.788 -5.612 11.158 1 63.7 ? N2 G4P 1003 A 1 HETATM 27 N N3 G4P . . . E 3 -12.865 -6.901 12.166 1 78.54 ? N3 G4P 1003 A 1 HETATM 28 C C4 G4P . . . E 3 -11.418 -7.267 12.177 1 83.52 ? C4 G4P 1003 A 1 HETATM 29 P PC G4P . . . E 3 -11.18 -13.264 15.644 1 89.55 ? PC G4P 1003 A 1 HETATM 30 O O1C G4P . . . E 3 -10.034 -13.857 14.859 1 114.98 ? O1C G4P 1003 A 1 HETATM 31 O O2C G4P . . . E 3 -12.223 -14.329 15.888 1 92.18 ? O2C G4P 1003 A 1 HETATM 32 O O3C G4P . . . E 3 -10.628 -12.721 17.099 1 83.4 ? O3C G4P 1003 A 1 HETATM 33 P PD G4P . . . E 3 -9.955 -13.706 18.235 1 109.16 ? PD G4P 1003 A 1 HETATM 34 O O1D G4P . . . E 3 -9.702 -12.921 19.501 1 119.54 ? O1D G4P 1003 A 1 HETATM 35 O O2D G4P . . . E 3 -10.902 -14.845 18.526 1 104.4 ? O2D G4P 1003 A 1 HETATM 36 O O3D G4P . . . E 3 -8.649 -14.255 17.715 1 120.85 ? O3D G4P 1003 A 1 # _model_server_stats.io_time_ms 81 _model_server_stats.parse_time_ms 26 _model_server_stats.create_model_time_ms 28 _model_server_stats.query_time_ms 271 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 36 #