data_4ZV4 # _model_server_result.job_id NDDmwoMr1LhJSDqKK4YCbg _model_server_result.datetime_utc '2025-09-17 15:39:32' _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 4zv4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":501}' # _entry.id 4ZV4 # _exptl.entry_id 4ZV4 _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 2 _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 4ZV4 _cell.length_a 176.109 _cell.length_b 176.109 _cell.length_c 86.31 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4ZV4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 41 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? dimeric 2 author_defined_assembly 1 ? dimeric 2 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,B,E,F 1 1 C,D,G,H 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 G N 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 OG1 THR 26 A THR 26 1_555 F MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.154 ? metalc ? metalc2 E O1B GDP . A GDP 501 1_555 F MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.27 ? metalc ? metalc3 E O2B GDP . A GDP 501 1_555 F MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.907 ? metalc ? metalc4 D OG1 THR 26 B THR 26 1_555 H MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? metalc ? metalc5 G O3B GDP . B GDP 501 1_555 H MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? # _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 4ZV4 _atom_sites.fract_transf_matrix[1][1] 0.005678 _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] 0.005678 _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] 0.011586 _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 3 GDP A 1 501 1 GDP GDP . F 4 MG A 1 502 1 MG MG . G 3 GDP B 1 501 2 GDP GDP . H 4 MG B 1 502 2 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 GDP . . . E 3 -23.4 13.251 3.954 1 129.41 ? PB GDP 501 A 1 HETATM 2 O O1B GDP . . . E 3 -23.747 14.148 2.79 1 120.68 ? O1B GDP 501 A 1 HETATM 3 O O2B GDP . . . E 3 -24.028 13.802 5.211 1 145.08 -1 O2B GDP 501 A 1 HETATM 4 O O3B GDP . . . E 3 -23.937 11.863 3.695 1 115.82 ? O3B GDP 501 A 1 HETATM 5 O O3A GDP . . . E 3 -21.8 13.193 4.143 1 162.41 ? O3A GDP 501 A 1 HETATM 6 P PA GDP . . . E 3 -20.857 12.512 3.03 1 109.14 ? PA GDP 501 A 1 HETATM 7 O O1A GDP . . . E 3 -20.572 13.483 1.91 1 129.3 -1 O1A GDP 501 A 1 HETATM 8 O O2A GDP . . . E 3 -21.485 11.249 2.492 1 95.79 ? O2A GDP 501 A 1 HETATM 9 O O5' GDP . . . E 3 -19.505 12.171 3.837 1 69.36 ? O5' GDP 501 A 1 HETATM 10 C C5' GDP . . . E 3 -19.436 10.933 4.54 1 79.44 ? C5' GDP 501 A 1 HETATM 11 C C4' GDP . . . E 3 -18.01 10.425 4.723 1 97.93 ? C4' GDP 501 A 1 HETATM 12 O O4' GDP . . . E 3 -17.544 9.77 3.541 1 84.2 ? O4' GDP 501 A 1 HETATM 13 C C3' GDP . . . E 3 -17.007 11.53 5.015 1 125.65 ? C3' GDP 501 A 1 HETATM 14 O O3' GDP . . . E 3 -16.736 11.588 6.418 1 144.03 ? O3' GDP 501 A 1 HETATM 15 C C2' GDP . . . E 3 -15.755 11.133 4.256 1 103.26 ? C2' GDP 501 A 1 HETATM 16 O O2' GDP . . . E 3 -14.683 10.879 5.169 1 90.8 ? O2' GDP 501 A 1 HETATM 17 C C1' GDP . . . E 3 -16.119 9.854 3.516 1 86.55 ? C1' GDP 501 A 1 HETATM 18 N N9 GDP . . . E 3 -15.596 9.881 2.127 1 97.89 ? N9 GDP 501 A 1 HETATM 19 C C8 GDP . . . E 3 -16.115 10.563 1.088 1 95.68 ? C8 GDP 501 A 1 HETATM 20 N N7 GDP . . . E 3 -15.387 10.362 -0.041 1 84.41 ? N7 GDP 501 A 1 HETATM 21 C C5 GDP . . . E 3 -14.377 9.529 0.273 1 87.18 ? C5 GDP 501 A 1 HETATM 22 C C6 GDP . . . E 3 -13.239 8.905 -0.443 1 84.86 ? C6 GDP 501 A 1 HETATM 23 O O6 GDP . . . E 3 -13.049 9.122 -1.658 1 84.06 ? O6 GDP 501 A 1 HETATM 24 N N1 GDP . . . E 3 -12.42 8.102 0.25 1 85.43 ? N1 GDP 501 A 1 HETATM 25 C C2 GDP . . . E 3 -12.6 7.849 1.56 1 111.91 ? C2 GDP 501 A 1 HETATM 26 N N2 GDP . . . E 3 -11.728 7.025 2.189 1 115.55 ? N2 GDP 501 A 1 HETATM 27 N N3 GDP . . . E 3 -13.62 8.385 2.279 1 129.07 ? N3 GDP 501 A 1 HETATM 28 C C4 GDP . . . E 3 -14.52 9.215 1.701 1 110.84 ? C4 GDP 501 A 1 # _model_server_stats.io_time_ms 39 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 310 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #