data_5UPK # _model_server_result.job_id zfOoCi14XbRMIaIh9aj5uA _model_server_result.datetime_utc '2024-11-22 14:12:53' _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":"D","auth_seq_id":600}' # _entry.id 5UPK # _exptl.entry_id 5UPK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 506.196 _entity.id 4 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 'PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE 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 4 _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 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 O12 P3' _chem_comp.formula_weight 506.196 _chem_comp.id ANP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE 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 ANP doub 13 n n PG O2G ANP sing 14 n n PG O3G ANP sing 15 n n PG N3B ANP sing 16 n n O2G HOG2 ANP sing 17 n n O3G HOG3 ANP sing 18 n n PB O1B ANP doub 19 n n PB O2B ANP sing 20 n n PB N3B ANP sing 21 n n PB O3A ANP sing 22 n n O2B HOB2 ANP sing 23 n n N3B HNB1 ANP sing 24 n n PA O1A ANP doub 25 n n PA O2A ANP sing 26 n n PA O3A ANP sing 27 n n PA O5' ANP sing 28 n n O2A HOA2 ANP sing 29 n n O5' C5' ANP sing 30 n n C5' C4' ANP sing 31 n n C5' "H5'1" ANP sing 32 n n C5' "H5'2" ANP sing 33 n n C4' O4' ANP sing 34 n n C4' C3' ANP sing 35 n n C4' H4' ANP sing 36 n n O4' C1' ANP sing 37 n n C3' O3' ANP sing 38 n n C3' C2' ANP sing 39 n n C3' H3' ANP sing 40 n n O3' HO3' ANP sing 41 n n C2' O2' ANP sing 42 n n C2' C1' ANP sing 43 n n C2' H2' ANP sing 44 n n O2' HO2' ANP sing 45 n n C1' N9 ANP sing 46 n n C1' H1' ANP sing 47 n n N9 C8 ANP sing 48 n y N9 C4 ANP sing 49 n y C8 N7 ANP doub 50 n y C8 H8 ANP sing 51 n n N7 C5 ANP sing 52 n y C5 C6 ANP sing 53 n y C5 C4 ANP doub 54 n y C6 N6 ANP sing 55 n n C6 N1 ANP doub 56 n y N6 HN61 ANP sing 57 n n N6 HN62 ANP sing 58 n n N1 C2 ANP sing 59 n y C2 N3 ANP doub 60 n y C2 H2 ANP sing 61 n n N3 C4 ANP sing 62 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 PA ANP . . . D 4 2.269 8.46 10.043 1 88.02 ? PA ANP 600 B 1 HETATM 2 O O1A ANP . . . D 4 3.217 9.448 9.395 1 86.23 ? O1A ANP 600 B 1 HETATM 3 O O2A ANP . . . D 4 2.299 8.273 11.546 1 87.63 ? O2A ANP 600 B 1 HETATM 4 O O3A ANP . . . D 4 0.765 8.849 9.609 1 88.33 ? O3A ANP 600 B 1 HETATM 5 O O5' ANP . . . D 4 2.475 7.016 9.355 1 76.73 ? O5' ANP 600 B 1 HETATM 6 C C5' ANP . . . D 4 1.616 5.916 9.656 1 69.32 ? C5' ANP 600 B 1 HETATM 7 C C4' ANP . . . D 4 2.319 4.6 9.334 1 65.41 ? C4' ANP 600 B 1 HETATM 8 O O4' ANP . . . D 4 2.82 4.626 7.994 1 61.39 ? O4' ANP 600 B 1 HETATM 9 C C3' ANP . . . D 4 3.51 4.315 10.241 1 63.59 ? C3' ANP 600 B 1 HETATM 10 O O3' ANP . . . D 4 3.499 2.936 10.638 1 64.46 ? O3' ANP 600 B 1 HETATM 11 C C2' ANP . . . D 4 4.729 4.639 9.402 1 59.86 ? C2' ANP 600 B 1 HETATM 12 O O2' ANP . . . D 4 5.839 3.784 9.692 1 60.67 ? O2' ANP 600 B 1 HETATM 13 C C1' ANP . . . D 4 4.237 4.419 7.982 1 57.88 ? C1' ANP 600 B 1 HETATM 14 N N9 ANP . . . D 4 4.906 5.332 7.02 1 52.75 ? N9 ANP 600 B 1 HETATM 15 C C8 ANP . . . D 4 4.735 6.669 6.879 1 50.96 ? C8 ANP 600 B 1 HETATM 16 N N7 ANP . . . D 4 5.522 7.159 5.887 1 48.09 ? N7 ANP 600 B 1 HETATM 17 C C5 ANP . . . D 4 6.207 6.124 5.378 1 47.85 ? C5 ANP 600 B 1 HETATM 18 C C6 ANP . . . D 4 7.21 5.927 4.313 1 48.24 ? C6 ANP 600 B 1 HETATM 19 N N6 ANP . . . D 4 7.644 6.974 3.571 1 49.41 ? N6 ANP 600 B 1 HETATM 20 N N1 ANP . . . D 4 7.676 4.669 4.11 1 48.38 ? N1 ANP 600 B 1 HETATM 21 C C2 ANP . . . D 4 7.249 3.615 4.839 1 47.77 ? C2 ANP 600 B 1 HETATM 22 N N3 ANP . . . D 4 6.34 3.728 5.82 1 47.99 ? N3 ANP 600 B 1 HETATM 23 C C4 ANP . . . D 4 5.795 4.926 6.126 1 49.33 ? C4 ANP 600 B 1 # _model_server_stats.io_time_ms 32 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 303 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 23 #