data_4ZKD # _model_server_result.job_id ZOAVwkbNRCFQP4DprRA2hg _model_server_result.datetime_utc '2025-09-18 18:53:46' _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 4zkd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":802}' # _entry.id 4ZKD # _exptl.entry_id 4ZKD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 4ZKD _cell.length_a 93.136 _cell.length_b 120.617 _cell.length_c 105.269 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4ZKD _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 metalc ? metalc1 A OG SER 33 A SER 281 1_555 D MG MG . A MG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.197 ? metalc ? metalc2 A OG SER 85 A SER 333 1_555 D MG MG . A MG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? metalc ? metalc3 B O1 PO4 . A PO4 801 1_555 D MG MG . A MG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.982 ? metalc ? metalc4 C O1B GDP . A GDP 802 1_555 D MG MG . A MG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? metalc ? metalc5 D MG MG . A MG 803 1_555 E O HOH . A HOH 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? metalc ? metalc6 D MG MG . A MG 803 1_555 E O HOH . A HOH 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.224 ? # _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 4ZKD _atom_sites.fract_transf_matrix[1][1] 0.010737 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008291 _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] 0.009499 _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 B 2 PO4 A 1 801 1 PO4 PO4 . C 3 GDP A 1 802 1 GDP GDP . D 4 MG A 1 803 1 MG MG . E 5 HOH A 1 901 8 HOH HOH . E 5 HOH A 2 902 2 HOH HOH . E 5 HOH A 3 903 1 HOH HOH . E 5 HOH A 4 904 3 HOH HOH . E 5 HOH A 5 905 10 HOH HOH . E 5 HOH A 6 906 4 HOH HOH . E 5 HOH A 7 907 5 HOH HOH . E 5 HOH A 8 908 6 HOH HOH . E 5 HOH A 9 909 9 HOH HOH . E 5 HOH A 10 910 7 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 . . . C 3 76.759 -13.295 54.955 1 60.35 ? PB GDP 802 A 1 HETATM 2 O O1B GDP . . . C 3 77.079 -14.135 53.742 1 57.02 ? O1B GDP 802 A 1 HETATM 3 O O2B GDP . . . C 3 77.206 -14.02 56.203 1 62.28 ? O2B GDP 802 A 1 HETATM 4 O O3B GDP . . . C 3 75.28 -13.018 55.025 1 56.03 ? O3B GDP 802 A 1 HETATM 5 O O3A GDP . . . C 3 77.564 -11.91 54.871 1 62.72 ? O3A GDP 802 A 1 HETATM 6 P PA GDP . . . C 3 77.458 -10.945 53.59 1 60.38 ? PA GDP 802 A 1 HETATM 7 O O1A GDP . . . C 3 76.272 -11.279 52.715 1 51.59 ? O1A GDP 802 A 1 HETATM 8 O O2A GDP . . . C 3 78.743 -10.987 52.802 1 59.77 ? O2A GDP 802 A 1 HETATM 9 O O5' GDP . . . C 3 77.322 -9.513 54.303 1 62.54 ? O5' GDP 802 A 1 HETATM 10 C C5' GDP . . . C 3 76.047 -8.982 54.641 1 68.51 ? C5' GDP 802 A 1 HETATM 11 C C4' GDP . . . C 3 76.242 -7.504 54.93 1 67.9 ? C4' GDP 802 A 1 HETATM 12 O O4' GDP . . . C 3 77.332 -7.323 55.836 1 56.31 ? O4' GDP 802 A 1 HETATM 13 C C3' GDP . . . C 3 76.573 -6.748 53.656 1 68.06 ? C3' GDP 802 A 1 HETATM 14 O O3' GDP . . . C 3 75.571 -5.758 53.413 1 90.18 ? O3' GDP 802 A 1 HETATM 15 C C2' GDP . . . C 3 77.937 -6.121 53.868 1 67.98 ? C2' GDP 802 A 1 HETATM 16 O O2' GDP . . . C 3 77.944 -4.732 53.522 1 80.78 ? O2' GDP 802 A 1 HETATM 17 C C1' GDP . . . C 3 78.215 -6.307 55.352 1 65.04 ? C1' GDP 802 A 1 HETATM 18 N N9 GDP . . . C 3 79.622 -6.703 55.573 1 57.81 ? N9 GDP 802 A 1 HETATM 19 C C8 GDP . . . C 3 80.19 -7.874 55.229 1 60.73 ? C8 GDP 802 A 1 HETATM 20 N N7 GDP . . . C 3 81.498 -7.892 55.595 1 62.73 ? N7 GDP 802 A 1 HETATM 21 C C5 GDP . . . C 3 81.773 -6.717 56.19 1 58.71 ? C5 GDP 802 A 1 HETATM 22 C C6 GDP . . . C 3 82.952 -6.078 56.81 1 61.37 ? C6 GDP 802 A 1 HETATM 23 O O6 GDP . . . C 3 84.05 -6.671 56.866 1 63.11 ? O6 GDP 802 A 1 HETATM 24 N N1 GDP . . . C 3 82.81 -4.844 57.309 1 65.87 ? N1 GDP 802 A 1 HETATM 25 C C2 GDP . . . C 3 81.64 -4.179 57.263 1 55.66 ? C2 GDP 802 A 1 HETATM 26 N N2 GDP . . . C 3 81.564 -2.933 57.787 1 60.89 ? N2 GDP 802 A 1 HETATM 27 N N3 GDP . . . C 3 80.521 -4.702 56.711 1 61.96 ? N3 GDP 802 A 1 HETATM 28 C C4 GDP . . . C 3 80.53 -5.94 56.171 1 65.36 ? C4 GDP 802 A 1 HETATM 29 H H4' GDP . . . C 3 75.317 -7.095 55.361 1 81.48 ? H4' GDP 802 A 1 HETATM 30 H H3' GDP . . . C 3 76.625 -7.456 52.817 1 81.67 ? H3' GDP 802 A 1 HETATM 31 H HO3' GDP . . . C 3 75.756 -5.309 52.577 1 108.22 ? HO3' GDP 802 A 1 HETATM 32 H H2' GDP . . . C 3 78.688 -6.67 53.284 1 81.57 ? H2' GDP 802 A 1 HETATM 33 H HO2' GDP . . . C 3 77.706 -4.631 52.59 1 96.93 ? HO2' GDP 802 A 1 HETATM 34 H H1' GDP . . . C 3 78.009 -5.359 55.869 1 78.05 ? H1' GDP 802 A 1 HETATM 35 H H8 GDP . . . C 3 79.678 -8.685 54.725 1 72.87 ? H8 GDP 802 A 1 HETATM 36 H HN1 GDP . . . C 3 83.632 -4.382 57.747 1 79.05 ? HN1 GDP 802 A 1 HETATM 37 H HN21 GDP . . . C 3 80.691 -2.425 57.759 1 73.07 ? HN21 GDP 802 A 1 HETATM 38 H HN22 GDP . . . C 3 82.38 -2.511 58.207 1 73.07 ? HN22 GDP 802 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 346 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 38 #