data_4ZCL # _model_server_result.job_id RVwCwS_fddUULf7-LO_evg _model_server_result.datetime_utc '2025-01-05 00:05:15' _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 4zcl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1003}' # _entry.id 4ZCL # _exptl.entry_id 4ZCL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 3 _entity.src_method man _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 97.7 _cell.angle_gamma 90 _cell.entry_id 4ZCL _cell.length_a 56.43 _cell.length_b 160.01 _cell.length_c 90.02 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4ZCL _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 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 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 4ZCL _atom_sites.fract_transf_matrix[1][1] 0.017721 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002396 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00625 _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] 0.01121 _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 GDP A 1 1003 1101 GDP GDP . 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 GDP B 1 1003 1101 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 . . . E 3 -4.397 -8.955 17.581 1 56.89 ? PB GDP 1003 A 1 HETATM 2 O O1B GDP . . . E 3 -3.236 -9.805 17.127 1 65.68 ? O1B GDP 1003 A 1 HETATM 3 O O2B GDP . . . E 3 -3.882 -7.624 18.077 1 56 ? O2B GDP 1003 A 1 HETATM 4 O O3B GDP . . . E 3 -5.13 -9.659 18.699 1 78.71 ? O3B GDP 1003 A 1 HETATM 5 O O3A GDP . . . E 3 -5.412 -8.71 16.359 1 45.68 ? O3A GDP 1003 A 1 HETATM 6 P PA GDP . . . E 3 -6.199 -9.933 15.667 1 53.53 ? PA GDP 1003 A 1 HETATM 7 O O1A GDP . . . E 3 -5.698 -10.167 14.262 1 49.62 ? O1A GDP 1003 A 1 HETATM 8 O O2A GDP . . . E 3 -6.1 -11.195 16.49 1 66.35 ? O2A GDP 1003 A 1 HETATM 9 O O5' GDP . . . E 3 -7.711 -9.386 15.618 1 66.93 ? O5' GDP 1003 A 1 HETATM 10 C C5' GDP . . . E 3 -8.703 -9.962 16.462 1 65.44 ? C5' GDP 1003 A 1 HETATM 11 C C4' GDP . . . E 3 -10.046 -9.949 15.748 1 53.54 ? C4' GDP 1003 A 1 HETATM 12 O O4' GDP . . . E 3 -10.211 -8.736 15.008 1 47.23 ? O4' GDP 1003 A 1 HETATM 13 C C3' GDP . . . E 3 -10.133 -11.094 14.753 1 51.75 ? C3' GDP 1003 A 1 HETATM 14 O O3' GDP . . . E 3 -11.197 -11.978 15.118 1 51.13 ? O3' GDP 1003 A 1 HETATM 15 C C2' GDP . . . E 3 -10.441 -10.445 13.421 1 49.81 ? C2' GDP 1003 A 1 HETATM 16 O O2' GDP . . . E 3 -11.476 -11.158 12.742 1 52.32 ? O2' GDP 1003 A 1 HETATM 17 C C1' GDP . . . E 3 -10.88 -9.036 13.782 1 53.43 ? C1' GDP 1003 A 1 HETATM 18 N N9 GDP . . . E 3 -10.519 -8.093 12.695 1 56.55 ? N9 GDP 1003 A 1 HETATM 19 C C8 GDP . . . E 3 -9.284 -7.839 12.224 1 51.46 ? C8 GDP 1003 A 1 HETATM 20 N N7 GDP . . . E 3 -9.325 -6.921 11.224 1 53.71 ? N7 GDP 1003 A 1 HETATM 21 C C5 GDP . . . E 3 -10.612 -6.57 11.048 1 57.64 ? C5 GDP 1003 A 1 HETATM 22 C C6 GDP . . . E 3 -11.362 -5.649 10.164 1 66.01 ? C6 GDP 1003 A 1 HETATM 23 O O6 GDP . . . E 3 -10.77 -4.955 9.312 1 67.61 ? O6 GDP 1003 A 1 HETATM 24 N N1 GDP . . . E 3 -12.692 -5.579 10.306 1 70.64 ? N1 GDP 1003 A 1 HETATM 25 C C2 GDP . . . E 3 -13.358 -6.316 11.215 1 69.96 ? C2 GDP 1003 A 1 HETATM 26 N N2 GDP . . . E 3 -14.704 -6.189 11.295 1 71.38 ? N2 GDP 1003 A 1 HETATM 27 N N3 GDP . . . E 3 -12.736 -7.179 12.058 1 69.78 ? N3 GDP 1003 A 1 HETATM 28 C C4 GDP . . . E 3 -11.393 -7.345 12.021 1 62.46 ? C4 GDP 1003 A 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 211 _model_server_stats.create_model_time_ms 131 _model_server_stats.query_time_ms 285 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 28 #