data_5UPK # _model_server_result.job_id LZZZhH1h2A52-xuYd-BKxA _model_server_result.datetime_utc '2024-11-22 13:51:55' _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 5upk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":200}' # _entry.id 5UPK # _exptl.entry_id 5UPK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 522.196 _entity.id 5 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 'PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER' _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 91.57 _cell.angle_gamma 90 _cell.entry_id 5UPK _cell.length_a 58.465 _cell.length_b 61.621 _cell.length_c 85.791 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5UPK _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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 5 _struct_asym.id E _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 covale ? covale1 B C LYS 228 B LYS 473 1_555 B N SEP 229 B SEP 474 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale2 B C SEP 229 B SEP 474 1_555 B N LEU 230 B LEU 475 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? metalc ? metalc1 C OG1 THR 17 C THR 17 1_555 F MG MG . C MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.64 ? metalc ? metalc2 C O VAL 33 C VAL 33 1_555 F MG MG . C MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.948 ? metalc ? metalc3 C OG1 THR 35 C THR 35 1_555 F MG MG . C MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.432 ? metalc ? metalc4 E O1G GNP . C GNP 200 1_555 F MG MG . C MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.75 ? metalc ? metalc5 E O1B GNP . C GNP 200 1_555 F MG MG . C MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.604 ? metalc ? metalc6 E O2A GNP . C GNP 200 1_555 F MG MG . C MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? # _chem_comp.formula 'C10 H17 N6 O13 P3' _chem_comp.formula_weight 522.196 _chem_comp.id GNP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER' _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 PG O1G GNP doub 179 n n PG O2G GNP sing 180 n n PG O3G GNP sing 181 n n PG N3B GNP sing 182 n n O2G HOG2 GNP sing 183 n n O3G HOG3 GNP sing 184 n n N3B PB GNP sing 185 n n N3B HNB3 GNP sing 186 n n PB O1B GNP doub 187 n n PB O2B GNP sing 188 n n PB O3A GNP sing 189 n n O2B HOB2 GNP sing 190 n n O3A PA GNP sing 191 n n PA O1A GNP doub 192 n n PA O2A GNP sing 193 n n PA O5' GNP sing 194 n n O2A HOA2 GNP sing 195 n n O5' C5' GNP sing 196 n n C5' C4' GNP sing 197 n n C5' "H5'2" GNP sing 198 n n C5' "H5'1" GNP sing 199 n n C4' O4' GNP sing 200 n n C4' C3' GNP sing 201 n n C4' H4' GNP sing 202 n n O4' C1' GNP sing 203 n n C3' O3' GNP sing 204 n n C3' C2' GNP sing 205 n n C3' H3' GNP sing 206 n n O3' HO3' GNP sing 207 n n C2' O2' GNP sing 208 n n C2' C1' GNP sing 209 n n C2' H2' GNP sing 210 n n O2' HO2' GNP sing 211 n n C1' N9 GNP sing 212 n n C1' H1' GNP sing 213 n n N9 C8 GNP sing 214 n y N9 C4 GNP sing 215 n y C8 N7 GNP doub 216 n y C8 H8 GNP sing 217 n n N7 C5 GNP sing 218 n y C5 C6 GNP sing 219 n y C5 C4 GNP doub 220 n y C6 O6 GNP doub 221 n n C6 N1 GNP sing 222 n y N1 C2 GNP sing 223 n y N1 HN1 GNP sing 224 n n C2 N2 GNP sing 225 n n C2 N3 GNP doub 226 n y N2 HN21 GNP sing 227 n n N2 HN22 GNP sing 228 n n N3 C4 GNP sing 229 n y # _atom_sites.entry_id 5UPK _atom_sites.fract_transf_matrix[1][1] 0.017104 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00047 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016228 _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] 0.011661 _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 D 4 ANP B 1 600 600 ANP ANP . E 5 GNP C 1 200 200 GNP GNP . F 6 MG C 1 201 201 MG MG . G 7 HOH B 1 701 25 HOH HOH . G 7 HOH B 2 702 4 HOH HOH . G 7 HOH B 3 703 9 HOH HOH . G 7 HOH B 4 704 13 HOH HOH . G 7 HOH B 5 705 3 HOH HOH . G 7 HOH B 6 706 20 HOH HOH . G 7 HOH B 7 707 7 HOH HOH . G 7 HOH B 8 708 6 HOH HOH . G 7 HOH B 9 709 1 HOH HOH . G 7 HOH B 10 710 15 HOH HOH . G 7 HOH B 11 711 11 HOH HOH . G 7 HOH B 12 712 23 HOH HOH . G 7 HOH B 13 713 12 HOH HOH . G 7 HOH B 14 714 21 HOH HOH . G 7 HOH B 15 715 5 HOH HOH . G 7 HOH B 16 716 24 HOH HOH . G 7 HOH B 17 717 16 HOH HOH . G 7 HOH B 18 718 10 HOH HOH . G 7 HOH B 19 719 14 HOH HOH . G 7 HOH B 20 720 22 HOH HOH . G 7 HOH B 21 721 8 HOH HOH . G 7 HOH B 22 722 19 HOH HOH . G 7 HOH B 23 723 2 HOH HOH . H 7 HOH C 1 301 18 HOH HOH . H 7 HOH C 2 302 17 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 PG GNP . . . E 5 -25.769 37.708 34.533 1 71.28 ? PG GNP 200 C 1 HETATM 2 O O1G GNP . . . E 5 -26.58 36.575 34.052 1 76.11 ? O1G GNP 200 C 1 HETATM 3 O O2G GNP . . . E 5 -24.57 37.18 35.461 1 72.99 ? O2G GNP 200 C 1 HETATM 4 O O3G GNP . . . E 5 -26.728 38.716 35.346 1 75.73 ? O3G GNP 200 C 1 HETATM 5 N N3B GNP . . . E 5 -25.095 38.49 33.14 1 70.77 ? N3B GNP 200 C 1 HETATM 6 P PB GNP . . . E 5 -24.1 37.607 32.021 1 68.23 ? PB GNP 200 C 1 HETATM 7 O O1B GNP . . . E 5 -24.686 36.109 31.877 1 68.94 ? O1B GNP 200 C 1 HETATM 8 O O2B GNP . . . E 5 -22.701 37.559 32.495 1 66.84 ? O2B GNP 200 C 1 HETATM 9 O O3A GNP . . . E 5 -24.107 38.404 30.619 1 70.98 ? O3A GNP 200 C 1 HETATM 10 P PA GNP . . . E 5 -24.991 37.887 29.379 1 71.85 ? PA GNP 200 C 1 HETATM 11 O O1A GNP . . . E 5 -24.137 36.891 28.627 1 73.33 ? O1A GNP 200 C 1 HETATM 12 O O2A GNP . . . E 5 -26.348 37.469 29.904 1 65.77 ? O2A GNP 200 C 1 HETATM 13 O O5' GNP . . . E 5 -25.199 39.188 28.458 1 75.4 ? O5' GNP 200 C 1 HETATM 14 C C5' GNP . . . E 5 -24.443 40.392 28.604 1 80.74 ? C5' GNP 200 C 1 HETATM 15 C C4' GNP . . . E 5 -24.721 41.384 27.468 1 83.83 ? C4' GNP 200 C 1 HETATM 16 O O4' GNP . . . E 5 -23.495 42 27.055 1 83.71 ? O4' GNP 200 C 1 HETATM 17 C C3' GNP . . . E 5 -25.349 40.781 26.207 1 85.82 ? C3' GNP 200 C 1 HETATM 18 O O3' GNP . . . E 5 -26.772 40.935 26.173 1 85.38 ? O3' GNP 200 C 1 HETATM 19 C C2' GNP . . . E 5 -24.669 41.476 25.05 1 86.28 ? C2' GNP 200 C 1 HETATM 20 O O2' GNP . . . E 5 -25.434 42.582 24.565 1 89 ? O2' GNP 200 C 1 HETATM 21 C C1' GNP . . . E 5 -23.346 41.943 25.632 1 87.28 ? C1' GNP 200 C 1 HETATM 22 N N9 GNP . . . E 5 -22.293 40.963 25.266 1 89.44 ? N9 GNP 200 C 1 HETATM 23 C C8 GNP . . . E 5 -22.098 39.749 25.821 1 90.91 ? C8 GNP 200 C 1 HETATM 24 N N7 GNP . . . E 5 -21.047 39.115 25.239 1 92.61 ? N7 GNP 200 C 1 HETATM 25 C C5 GNP . . . E 5 -20.561 39.928 24.286 1 91.99 ? C5 GNP 200 C 1 HETATM 26 C C6 GNP . . . E 5 -19.453 39.889 23.297 1 93.3 ? C6 GNP 200 C 1 HETATM 27 O O6 GNP . . . E 5 -18.706 38.893 23.22 1 93.9 ? O6 GNP 200 C 1 HETATM 28 N N1 GNP . . . E 5 -19.279 40.953 22.49 1 94.28 ? N1 GNP 200 C 1 HETATM 29 C C2 GNP . . . E 5 -20.08 42.044 22.562 1 92.87 ? C2 GNP 200 C 1 HETATM 30 N N2 GNP . . . E 5 -19.866 43.087 21.728 1 94.92 ? N2 GNP 200 C 1 HETATM 31 N N3 GNP . . . E 5 -21.108 42.148 23.445 1 91.7 ? N3 GNP 200 C 1 HETATM 32 C C4 GNP . . . E 5 -21.385 41.148 24.314 1 91.04 ? C4 GNP 200 C 1 # _model_server_stats.io_time_ms 261 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 299 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 32 #