data_4KJZ # _model_server_result.job_id f-_tyBVsaU970xKheq_gMA _model_server_result.datetime_utc '2024-11-05 00:37:06' _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 4kjz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":900}' # _entry.id 4KJZ # _exptl.entry_id 4KJZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 2 _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 89.87 _cell.angle_gamma 90 _cell.entry_id 4KJZ _cell.length_a 119.83 _cell.length_b 177.816 _cell.length_c 61.793 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4KJZ _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 ? monomeric 1 author_defined_assembly 3 ? monomeric 1 author_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,E,G 1 1 B,H 2 1 C,I 3 1 D,F,J 4 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 ? 2 E N N ? 2 F 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 4KJZ _atom_sites.fract_transf_matrix[1][1] 0.008345 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] -0.000019 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.005624 _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] 0.016183 _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 E 2 GDP A 1 900 900 GDP GDP . F 2 GDP C 1 900 900 GDP GDP . G 3 HOH A 1 1001 1001 HOH HOH . H 3 HOH D 1 501 502 HOH HOH . H 3 HOH D 2 502 503 HOH HOH . I 3 HOH B 1 901 901 HOH HOH . I 3 HOH B 2 902 902 HOH HOH . I 3 HOH B 3 903 903 HOH HOH . I 3 HOH B 4 904 904 HOH HOH . I 3 HOH B 5 905 905 HOH HOH . I 3 HOH B 6 906 906 HOH HOH . I 3 HOH B 7 907 907 HOH HOH . I 3 HOH B 8 908 908 HOH HOH . J 3 HOH C 1 1001 1001 HOH HOH . J 3 HOH C 2 1002 1002 HOH HOH . J 3 HOH C 3 1003 1003 HOH HOH . J 3 HOH C 4 1004 1004 HOH HOH . # 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 2 -8.696 -6.2 -13.333 1 58.11 ? PB GDP 900 A 1 HETATM 2 O O1B GDP . . . E 2 -7.469 -5.833 -14.134 1 59.12 ? O1B GDP 900 A 1 HETATM 3 O O2B GDP . . . E 2 -9.564 -5.002 -13.047 1 53.82 ? O2B GDP 900 A 1 HETATM 4 O O3B GDP . . . E 2 -8.409 -7.094 -12.134 1 57.51 ? O3B GDP 900 A 1 HETATM 5 O O3A GDP . . . E 2 -9.574 -7.117 -14.344 1 53.27 ? O3A GDP 900 A 1 HETATM 6 P PA GDP . . . E 2 -11.176 -7.217 -14.405 1 55.08 ? PA GDP 900 A 1 HETATM 7 O O1A GDP . . . E 2 -11.568 -7.379 -15.856 1 58.08 ? O1A GDP 900 A 1 HETATM 8 O O2A GDP . . . E 2 -11.842 -6.166 -13.562 1 50.66 ? O2A GDP 900 A 1 HETATM 9 O O5' GDP . . . E 2 -11.516 -8.617 -13.665 1 50.85 ? O5' GDP 900 A 1 HETATM 10 C C5' GDP . . . E 2 -10.704 -9.75 -13.982 1 50.07 ? C5' GDP 900 A 1 HETATM 11 C C4' GDP . . . E 2 -11.373 -11.079 -13.691 1 49.19 ? C4' GDP 900 A 1 HETATM 12 O O4' GDP . . . E 2 -11.525 -11.235 -12.278 1 50.42 ? O4' GDP 900 A 1 HETATM 13 C C3' GDP . . . E 2 -12.769 -11.189 -14.275 1 49.99 ? C3' GDP 900 A 1 HETATM 14 O O3' GDP . . . E 2 -12.723 -11.933 -15.5 1 50.96 ? O3' GDP 900 A 1 HETATM 15 C C2' GDP . . . E 2 -13.618 -11.876 -13.211 1 48.7 ? C2' GDP 900 A 1 HETATM 16 O O2' GDP . . . E 2 -14.054 -13.163 -13.636 1 50.07 ? O2' GDP 900 A 1 HETATM 17 C C1' GDP . . . E 2 -12.672 -12.065 -12.034 1 48.7 ? C1' GDP 900 A 1 HETATM 18 N N9 GDP . . . E 2 -13.239 -11.803 -10.676 1 45.58 ? N9 GDP 900 A 1 HETATM 19 C C8 GDP . . . E 2 -13.411 -10.594 -10.096 1 45.02 ? C8 GDP 900 A 1 HETATM 20 N N7 GDP . . . E 2 -13.93 -10.701 -8.866 1 46.67 ? N7 GDP 900 A 1 HETATM 21 C C5 GDP . . . E 2 -14.08 -12.025 -8.625 1 45.95 ? C5 GDP 900 A 1 HETATM 22 C C6 GDP . . . E 2 -14.568 -12.818 -7.498 1 44.96 ? C6 GDP 900 A 1 HETATM 23 O O6 GDP . . . E 2 -14.97 -12.275 -6.463 1 46.59 ? O6 GDP 900 A 1 HETATM 24 N N1 GDP . . . E 2 -14.58 -14.169 -7.639 1 44.47 ? N1 GDP 900 A 1 HETATM 25 C C2 GDP . . . E 2 -14.157 -14.773 -8.767 1 43.36 ? C2 GDP 900 A 1 HETATM 26 N N2 GDP . . . E 2 -14.216 -16.113 -8.826 1 42.7 ? N2 GDP 900 A 1 HETATM 27 N N3 GDP . . . E 2 -13.683 -14.094 -9.836 1 45.42 ? N3 GDP 900 A 1 HETATM 28 C C4 GDP . . . E 2 -13.633 -12.737 -9.797 1 43.97 ? C4 GDP 900 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 254 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #