data_1XZ8 # _model_server_result.job_id 9717PBVldgbsfjK5m4pHlA _model_server_result.datetime_utc '2025-08-31 22:47:43' _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 1xz8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":200}' # _entry.id 1XZ8 # _exptl.entry_id 1XZ8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 363.221 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-MONOPHOSPHATE" _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 120 _cell.entry_id 1XZ8 _cell.length_a 128.54 _cell.length_b 128.54 _cell.length_c 128.76 _cell.Z_PDB 36 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1XZ8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,F,G,H,I _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 D _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 OD2 ASP 104 A ASP 104 1_555 C MG MG . A MG 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? metalc ? metalc2 A OD1 ASP 105 A ASP 105 1_555 C MG MG . A MG 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.991 ? metalc ? metalc3 C MG MG . A MG 180 1_555 E O1P 3GP . A 3GP 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? metalc ? metalc4 C MG MG . A MG 180 1_555 H O HOH . A HOH 322 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.682 ? metalc ? metalc5 C MG MG . A MG 180 1_555 H O HOH . A HOH 323 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.968 ? metalc ? metalc6 C MG MG . A MG 180 1_555 H O HOH . A HOH 324 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.978 ? metalc ? metalc7 B OD2 ASP 104 B ASP 104 1_555 F MG MG . B MG 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? metalc ? metalc8 B OD1 ASP 104 B ASP 104 1_555 F MG MG . B MG 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.916 ? metalc ? metalc9 B OD1 ASP 105 B ASP 105 1_555 F MG MG . B MG 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? metalc ? metalc10 F MG MG . B MG 180 1_555 G O3' U5P . B U5P 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.926 ? metalc ? metalc11 F MG MG . B MG 180 1_555 I O HOH . B HOH 424 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.748 ? metalc ? metalc12 F MG MG . B MG 180 1_555 I O HOH . B HOH 425 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.522 ? # _chem_comp.formula 'C10 H14 N5 O8 P' _chem_comp.formula_weight 363.221 _chem_comp.id 5GP _chem_comp.mon_nstd_flag . _chem_comp.name "GUANOSINE-5'-MONOPHOSPHATE" _chem_comp.type non-polymer _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 P O1P 5GP doub 41 n n P O2P 5GP sing 42 n n P O3P 5GP sing 43 n n P O5' 5GP sing 44 n n O2P HOP2 5GP sing 45 n n O3P HOP3 5GP sing 46 n n O5' C5' 5GP sing 47 n n C5' C4' 5GP sing 48 n n C5' "H5'1" 5GP sing 49 n n C5' "H5'2" 5GP sing 50 n n C4' O4' 5GP sing 51 n n C4' C3' 5GP sing 52 n n C4' H4' 5GP sing 53 n n O4' C1' 5GP sing 54 n n C3' O3' 5GP sing 55 n n C3' C2' 5GP sing 56 n n C3' H3' 5GP sing 57 n n O3' HO3' 5GP sing 58 n n C2' O2' 5GP sing 59 n n C2' C1' 5GP sing 60 n n C2' H2' 5GP sing 61 n n O2' HO2' 5GP sing 62 n n C1' N9 5GP sing 63 n n C1' H1' 5GP sing 64 n n N9 C8 5GP sing 65 n y N9 C4 5GP sing 66 n y C8 N7 5GP doub 67 n y C8 H8 5GP sing 68 n n N7 C5 5GP sing 69 n y C5 C6 5GP sing 70 n n C5 C4 5GP doub 71 n y C6 O6 5GP doub 72 n n C6 N1 5GP sing 73 n n N1 C2 5GP sing 74 n n N1 HN1 5GP sing 75 n n C2 N2 5GP sing 76 n n C2 N3 5GP doub 77 n n N2 HN21 5GP sing 78 n n N2 HN22 5GP sing 79 n n N3 C4 5GP sing 80 n n # _atom_sites.entry_id 1XZ8 _atom_sites.fract_transf_matrix[1][1] 0.00778 _atom_sites.fract_transf_matrix[1][2] 0.004492 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008983 _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] 0.007766 _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 MG A 1 180 100 MG MG . D 3 5GP A 1 200 200 5GP 5GP . E 4 3GP A 1 300 300 3GP 3GP . F 2 MG B 1 180 101 MG MG . G 5 U5P B 1 400 400 U5P U5P . H 6 HOH A 1 301 5 HOH HOH . H 6 HOH A 2 302 6 HOH HOH . H 6 HOH A 3 303 7 HOH HOH . H 6 HOH A 4 304 8 HOH HOH . H 6 HOH A 5 305 10 HOH HOH . H 6 HOH A 6 306 12 HOH HOH . H 6 HOH A 7 307 14 HOH HOH . H 6 HOH A 8 308 17 HOH HOH . H 6 HOH A 9 309 19 HOH HOH . H 6 HOH A 10 310 20 HOH HOH . H 6 HOH A 11 311 22 HOH HOH . H 6 HOH A 12 312 23 HOH HOH . H 6 HOH A 13 313 24 HOH HOH . H 6 HOH A 14 314 30 HOH HOH . H 6 HOH A 15 315 32 HOH HOH . H 6 HOH A 16 316 34 HOH HOH . H 6 HOH A 17 317 35 HOH HOH . H 6 HOH A 18 318 37 HOH HOH . H 6 HOH A 19 319 39 HOH HOH . H 6 HOH A 20 320 41 HOH HOH . H 6 HOH A 21 321 45 HOH HOH . H 6 HOH A 22 322 46 HOH HOH . H 6 HOH A 23 323 47 HOH HOH . H 6 HOH A 24 324 48 HOH HOH . H 6 HOH A 25 325 51 HOH HOH . H 6 HOH A 26 326 52 HOH HOH . H 6 HOH A 27 327 53 HOH HOH . H 6 HOH A 28 328 54 HOH HOH . I 6 HOH B 1 401 1 HOH HOH . I 6 HOH B 2 402 2 HOH HOH . I 6 HOH B 3 403 3 HOH HOH . I 6 HOH B 4 404 4 HOH HOH . I 6 HOH B 5 405 9 HOH HOH . I 6 HOH B 6 406 11 HOH HOH . I 6 HOH B 7 407 13 HOH HOH . I 6 HOH B 8 408 15 HOH HOH . I 6 HOH B 9 409 16 HOH HOH . I 6 HOH B 10 410 18 HOH HOH . I 6 HOH B 11 411 21 HOH HOH . I 6 HOH B 12 412 25 HOH HOH . I 6 HOH B 13 413 26 HOH HOH . I 6 HOH B 14 414 27 HOH HOH . I 6 HOH B 15 415 28 HOH HOH . I 6 HOH B 16 416 31 HOH HOH . I 6 HOH B 17 417 33 HOH HOH . I 6 HOH B 18 418 36 HOH HOH . I 6 HOH B 19 419 38 HOH HOH . I 6 HOH B 20 420 40 HOH HOH . I 6 HOH B 21 421 42 HOH HOH . I 6 HOH B 22 422 43 HOH HOH . I 6 HOH B 23 423 44 HOH HOH . I 6 HOH B 24 424 49 HOH HOH . I 6 HOH B 25 425 50 HOH HOH . I 6 HOH B 26 426 55 HOH HOH . I 6 HOH B 27 427 56 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 P 5GP . . . D 3 27.236 1.709 9.937 1 46.37 ? P 5GP 200 A 1 HETATM 2 O O1P 5GP . . . D 3 26.423 2.443 8.961 1 48.75 ? O1P 5GP 200 A 1 HETATM 3 O O2P 5GP . . . D 3 28.668 1.495 9.536 1 46.35 ? O2P 5GP 200 A 1 HETATM 4 O O3P 5GP . . . D 3 27.146 2.361 11.353 1 46.06 ? O3P 5GP 200 A 1 HETATM 5 O O5' 5GP . . . D 3 26.701 0.285 10.097 1 48.17 ? O5' 5GP 200 A 1 HETATM 6 C C5' 5GP . . . D 3 25.467 0.026 10.708 1 52.67 ? C5' 5GP 200 A 1 HETATM 7 C C4' 5GP . . . D 3 25.251 -1.435 10.67 1 53.04 ? C4' 5GP 200 A 1 HETATM 8 O O4' 5GP . . . D 3 26.637 -1.916 10.54 1 52.33 ? O4' 5GP 200 A 1 HETATM 9 C C3' 5GP . . . D 3 24.746 -2.089 11.9 1 55.83 ? C3' 5GP 200 A 1 HETATM 10 O O3' 5GP . . . D 3 23.33 -2.246 11.895 1 58.6 ? O3' 5GP 200 A 1 HETATM 11 C C2' 5GP . . . D 3 25.472 -3.412 11.907 1 53.9 ? C2' 5GP 200 A 1 HETATM 12 O O2' 5GP . . . D 3 24.758 -4.426 11.146 1 55.54 ? O2' 5GP 200 A 1 HETATM 13 C C1' 5GP . . . D 3 26.805 -3.092 11.277 1 50.27 ? C1' 5GP 200 A 1 HETATM 14 N N9 5GP . . . D 3 28.045 -2.865 12.124 1 47.48 ? N9 5GP 200 A 1 HETATM 15 C C8 5GP . . . D 3 29.265 -2.4 11.698 1 45.71 ? C8 5GP 200 A 1 HETATM 16 N N7 5GP . . . D 3 30.2 -2.308 12.602 1 43.58 ? N7 5GP 200 A 1 HETATM 17 C C5 5GP . . . D 3 29.542 -2.76 13.756 1 44.33 ? C5 5GP 200 A 1 HETATM 18 C C6 5GP . . . D 3 30.08 -2.899 15.076 1 44.4 ? C6 5GP 200 A 1 HETATM 19 O O6 5GP . . . D 3 31.206 -2.659 15.456 1 44.55 ? O6 5GP 200 A 1 HETATM 20 N N1 5GP . . . D 3 29.12 -3.388 15.99 1 44.93 ? N1 5GP 200 A 1 HETATM 21 C C2 5GP . . . D 3 27.816 -3.694 15.652 1 45.49 ? C2 5GP 200 A 1 HETATM 22 N N2 5GP . . . D 3 27.076 -4.146 16.696 1 45.31 ? N2 5GP 200 A 1 HETATM 23 N N3 5GP . . . D 3 27.296 -3.569 14.404 1 45.55 ? N3 5GP 200 A 1 HETATM 24 C C4 5GP . . . D 3 28.222 -3.096 13.498 1 45.81 ? C4 5GP 200 A 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 81 _model_server_stats.query_time_ms 624 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 24 #