data_4ZCL # _model_server_result.job_id xZTYLvmUMnhJINy5lkVn4g _model_server_result.datetime_utc '2025-01-05 00:14:48' _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":"I","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 . . . I 3 -5.535 -36.745 26.859 1 98.22 ? PB GDP 1003 B 1 HETATM 2 O O1B GDP . . . I 3 -5.767 -36.4 25.408 1 107.77 ? O1B GDP 1003 B 1 HETATM 3 O O2B GDP . . . I 3 -4.834 -38.08 26.943 1 93.58 ? O2B GDP 1003 B 1 HETATM 4 O O3B GDP . . . I 3 -4.668 -35.681 27.488 1 111.54 ? O3B GDP 1003 B 1 HETATM 5 O O3A GDP . . . I 3 -6.947 -36.823 27.633 1 81.28 ? O3A GDP 1003 B 1 HETATM 6 P PA GDP . . . I 3 -7.934 -35.551 27.663 1 86.78 ? PA GDP 1003 B 1 HETATM 7 O O1A GDP . . . I 3 -7.968 -34.88 26.311 1 108.09 ? O1A GDP 1003 B 1 HETATM 8 O O2A GDP . . . I 3 -7.504 -34.571 28.726 1 81.39 ? O2A GDP 1003 B 1 HETATM 9 O O5' GDP . . . I 3 -9.391 -36.146 28.013 1 98.65 ? O5' GDP 1003 B 1 HETATM 10 C C5' GDP . . . I 3 -10.438 -35.901 27.076 1 98.14 ? C5' GDP 1003 B 1 HETATM 11 C C4' GDP . . . I 3 -11.803 -35.669 27.718 1 97.94 ? C4' GDP 1003 B 1 HETATM 12 O O4' GDP . . . I 3 -12.404 -36.881 28.175 1 93.39 ? O4' GDP 1003 B 1 HETATM 13 C C3' GDP . . . I 3 -11.749 -34.755 28.929 1 104.92 ? C3' GDP 1003 B 1 HETATM 14 O O3' GDP . . . I 3 -11.98 -33.402 28.532 1 111.05 ? O3' GDP 1003 B 1 HETATM 15 C C2' GDP . . . I 3 -12.871 -35.247 29.823 1 105.31 ? C2' GDP 1003 B 1 HETATM 16 O O2' GDP . . . I 3 -13.962 -34.323 29.777 1 103.71 ? O2' GDP 1003 B 1 HETATM 17 C C1' GDP . . . I 3 -13.308 -36.585 29.243 1 103.32 ? C1' GDP 1003 B 1 HETATM 18 N N9 GDP . . . I 3 -13.229 -37.638 30.286 1 108.72 ? N9 GDP 1003 B 1 HETATM 19 C C8 GDP . . . I 3 -12.088 -38.133 30.798 1 108.67 ? C8 GDP 1003 B 1 HETATM 20 N N7 GDP . . . I 3 -12.342 -39.086 31.729 1 105.73 ? N7 GDP 1003 B 1 HETATM 21 C C5 GDP . . . I 3 -13.677 -39.213 31.823 1 108.06 ? C5 GDP 1003 B 1 HETATM 22 C C6 GDP . . . I 3 -14.612 -40.045 32.614 1 114.42 ? C6 GDP 1003 B 1 HETATM 23 O O6 GDP . . . I 3 -14.186 -40.877 33.443 1 121.74 ? O6 GDP 1003 B 1 HETATM 24 N N1 GDP . . . I 3 -15.924 -39.878 32.415 1 110.44 ? N1 GDP 1003 B 1 HETATM 25 C C2 GDP . . . I 3 -16.409 -38.989 31.528 1 99.87 ? C2 GDP 1003 B 1 HETATM 26 N N2 GDP . . . I 3 -17.753 -38.884 31.389 1 93.11 ? N2 GDP 1003 B 1 HETATM 27 N N3 GDP . . . I 3 -15.61 -38.194 30.767 1 99.83 ? N3 GDP 1003 B 1 HETATM 28 C C4 GDP . . . I 3 -14.26 -38.26 30.867 1 104.56 ? C4 GDP 1003 B 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 343 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #