data_5Z4U # _model_server_result.job_id l5-RK-hmo0LMRlmvhFe4-A _model_server_result.datetime_utc '2025-07-07 06:25:48' _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 5z4u # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":501}' # _entry.id 5Z4U # _exptl.entry_id 5Z4U _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 8 _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 5Z4U _cell.length_a 105.491 _cell.length_b 158.233 _cell.length_c 182.099 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5Z4U _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V _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 8 _struct_asym.id J _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 OD1 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.547 ? metalc ? metalc2 A O THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.996 ? metalc ? metalc3 A OG1 THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.464 ? metalc ? metalc4 A O GLY 44 A GLY 44 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.831 ? metalc ? metalc5 A OE2 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? metalc ? metalc6 G O1G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? metalc ? metalc7 G O1B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? metalc ? metalc8 B OE1 GLN 11 B GLN 11 1_555 K MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.534 ? metalc ? metalc9 B OE1 GLU 111 B GLU 111 1_555 M CA CA . B CA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.601 ? metalc ? metalc10 B OD2 ASP 177 B ASP 177 1_555 K MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.843 ? metalc ? metalc11 J O1A GDP . B GDP 501 1_555 K MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.502 ? metalc ? metalc12 C OD1 ASP 39 C ASP 39 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.549 ? metalc ? metalc13 C OD2 ASP 39 C ASP 39 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.824 ? metalc ? metalc14 C O THR 41 C THR 41 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.087 ? metalc ? metalc15 C OG1 THR 41 C THR 41 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.23 ? metalc ? metalc16 C O GLY 44 C GLY 44 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.751 ? metalc ? metalc17 C OE2 GLU 55 C GLU 55 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.166 ? metalc ? metalc18 P O1G GTP . C GTP 501 1_555 Q MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? metalc ? metalc19 P O1B GTP . C GTP 501 1_555 Q MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? metalc ? metalc20 S O1G GTP . D GTP 501 1_555 T MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.969 ? metalc ? metalc21 S O2G GTP . D GTP 501 1_555 T MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.422 ? # _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 187 n n PB O2B GDP sing 188 n n PB O3B GDP sing 189 n n PB O3A GDP sing 190 n n O2B HOB2 GDP sing 191 n n O3B HOB3 GDP sing 192 n n O3A PA GDP sing 193 n n PA O1A GDP doub 194 n n PA O2A GDP sing 195 n n PA O5' GDP sing 196 n n O2A HOA2 GDP sing 197 n n O5' C5' GDP sing 198 n n C5' C4' GDP sing 199 n n C5' H5' GDP sing 200 n n C5' "H5''" GDP sing 201 n n C4' O4' GDP sing 202 n n C4' C3' GDP sing 203 n n C4' H4' GDP sing 204 n n O4' C1' GDP sing 205 n n C3' O3' GDP sing 206 n n C3' C2' GDP sing 207 n n C3' H3' GDP sing 208 n n O3' HO3' GDP sing 209 n n C2' O2' GDP sing 210 n n C2' C1' GDP sing 211 n n C2' H2' GDP sing 212 n n O2' HO2' GDP sing 213 n n C1' N9 GDP sing 214 n n C1' H1' GDP sing 215 n n N9 C8 GDP sing 216 n y N9 C4 GDP sing 217 n y C8 N7 GDP doub 218 n y C8 H8 GDP sing 219 n n N7 C5 GDP sing 220 n y C5 C6 GDP sing 221 n n C5 C4 GDP doub 222 n y C6 O6 GDP doub 223 n n C6 N1 GDP sing 224 n n N1 C2 GDP sing 225 n n N1 HN1 GDP sing 226 n n C2 N2 GDP sing 227 n n C2 N3 GDP doub 228 n n N2 HN21 GDP sing 229 n n N2 HN22 GDP sing 230 n n N3 C4 GDP sing 231 n n # _atom_sites.entry_id 5Z4U _atom_sites.fract_transf_matrix[1][1] 0.009479 _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] 0.00632 _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] 0.005492 _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 G 5 GTP A 1 501 501 GTP GTP . H 6 MG A 1 502 502 MG MG . I 7 CA A 1 503 503 CA CA . J 8 GDP B 1 501 501 GDP GDP . K 6 MG B 1 502 502 MG MG . L 9 MES B 1 503 505 MES MES . M 7 CA B 1 504 2 CA CA . N 9 MES B 1 505 505 MES MES . O 10 96C B 1 506 1 96C 7A3 . P 5 GTP C 1 501 501 GTP GTP . Q 6 MG C 1 502 502 MG MG . R 7 CA C 1 503 1 CA CA . S 5 GTP D 1 501 501 GTP GTP . T 6 MG D 1 502 502 MG MG . U 10 96C D 1 503 2 96C 7A3 . V 11 ACP F 1 401 401 ACP ACP . # 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 . . . J 8 -18.371 -49.849 15.98 1 37.53 ? PB GDP 501 B 1 HETATM 2 O O1B GDP . . . J 8 -17.776 -50.846 15.026 1 37.69 ? O1B GDP 501 B 1 HETATM 3 O O2B GDP . . . J 8 -18.823 -50.428 17.302 1 40.46 ? O2B GDP 501 B 1 HETATM 4 O O3B GDP . . . J 8 -19.382 -48.935 15.345 1 38.5 ? O3B GDP 501 B 1 HETATM 5 O O3A GDP . . . J 8 -17.154 -48.864 16.377 1 38.95 ? O3A GDP 501 B 1 HETATM 6 P PA GDP . . . J 8 -15.723 -49.316 16.994 1 38.97 ? PA GDP 501 B 1 HETATM 7 O O1A GDP . . . J 8 -14.689 -48.939 15.956 1 40.4 ? O1A GDP 501 B 1 HETATM 8 O O2A GDP . . . J 8 -15.785 -50.739 17.496 1 39.57 ? O2A GDP 501 B 1 HETATM 9 O O5' GDP . . . J 8 -15.591 -48.372 18.293 1 36.94 ? O5' GDP 501 B 1 HETATM 10 C C5' GDP . . . J 8 -14.597 -47.362 18.443 1 37.45 ? C5' GDP 501 B 1 HETATM 11 C C4' GDP . . . J 8 -14.03 -47.423 19.854 1 37.85 ? C4' GDP 501 B 1 HETATM 12 O O4' GDP . . . J 8 -13.544 -48.74 20.106 1 38.62 ? O4' GDP 501 B 1 HETATM 13 C C3' GDP . . . J 8 -12.842 -46.499 20.043 1 37.56 ? C3' GDP 501 B 1 HETATM 14 O O3' GDP . . . J 8 -12.778 -46.061 21.406 1 37.08 ? O3' GDP 501 B 1 HETATM 15 C C2' GDP . . . J 8 -11.663 -47.379 19.687 1 37.86 ? C2' GDP 501 B 1 HETATM 16 O O2' GDP . . . J 8 -10.455 -46.987 20.346 1 39.82 ? O2' GDP 501 B 1 HETATM 17 C C1' GDP . . . J 8 -12.117 -48.746 20.161 1 37.56 ? C1' GDP 501 B 1 HETATM 18 N N9 GDP . . . J 8 -11.615 -49.881 19.348 1 36.68 ? N9 GDP 501 B 1 HETATM 19 C C8 GDP . . . J 8 -11.846 -50.118 18.047 1 36.35 ? C8 GDP 501 B 1 HETATM 20 N N7 GDP . . . J 8 -11.24 -51.268 17.657 1 36.43 ? N7 GDP 501 B 1 HETATM 21 C C5 GDP . . . J 8 -10.612 -51.792 18.724 1 36.74 ? C5 GDP 501 B 1 HETATM 22 C C6 GDP . . . J 8 -9.779 -52.99 19.035 1 36.7 ? C6 GDP 501 B 1 HETATM 23 O O6 GDP . . . J 8 -9.498 -53.845 18.166 1 37.26 ? O6 GDP 501 B 1 HETATM 24 N N1 GDP . . . J 8 -9.329 -53.137 20.292 1 35.86 ? N1 GDP 501 B 1 HETATM 25 C C2 GDP . . . J 8 -9.595 -52.261 21.274 1 35.25 ? C2 GDP 501 B 1 HETATM 26 N N2 GDP . . . J 8 -9.102 -52.491 22.511 1 34.94 ? N2 GDP 501 B 1 HETATM 27 N N3 GDP . . . J 8 -10.346 -51.153 21.063 1 36.95 ? N3 GDP 501 B 1 HETATM 28 C C4 GDP . . . J 8 -10.868 -50.869 19.837 1 36.94 ? C4 GDP 501 B 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 284 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #