data_5YZ8 # _model_server_result.job_id 4VTkcm1E4WPvm59Ie8WHbw _model_server_result.datetime_utc '2024-11-13 04:53:03' _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 5yz8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"W","auth_seq_id":301}' # _entry.id 5YZ8 # _exptl.entry_id 5YZ8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 506.196 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER' _entity.pdbx_number_of_molecules 6 _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 5YZ8 _cell.length_a 108.072 _cell.length_b 108.072 _cell.length_c 224.069 _cell.Z_PDB 36 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YZ8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 G N N ? 2 K N N ? 2 N N N ? 2 Q N N ? 2 T N N ? 2 W 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 53 A THR 53 1_555 H MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.945 ? metalc ? metalc2 G O1G ANP . A ANP 301 1_555 H MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.81 ? metalc ? metalc3 G O1B ANP . A ANP 301 1_555 H MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? metalc ? metalc4 H MG MG . A MG 302 1_555 Y O HOH . A HOH 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.873 ? metalc ? metalc5 H MG MG . A MG 302 1_555 Y O HOH . A HOH 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? metalc ? metalc6 B OG1 THR 53 B THR 53 1_555 L MG MG . B MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.976 ? metalc ? metalc7 K O1G ANP . B ANP 301 1_555 L MG MG . B MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.817 ? metalc ? metalc8 K O1B ANP . B ANP 301 1_555 L MG MG . B MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.49 ? metalc ? metalc9 L MG MG . B MG 302 1_555 Z O HOH . B HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? metalc ? metalc10 L MG MG . B MG 302 1_555 Z O HOH . B HOH 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? metalc ? metalc11 C OG1 THR 53 C THR 53 1_555 O MG MG . C MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? metalc ? metalc12 N O2G ANP . C ANP 301 1_555 O MG MG . C MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.882 ? metalc ? metalc13 N O2B ANP . C ANP 301 1_555 O MG MG . C MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? metalc ? metalc14 O MG MG . C MG 302 1_555 AA O HOH . C HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? metalc ? metalc15 O MG MG . C MG 302 1_555 AA O HOH . C HOH 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? metalc ? metalc16 D OG1 THR 53 D THR 53 1_555 R MG MG . D MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.938 ? metalc ? metalc17 Q O3G ANP . D ANP 301 1_555 R MG MG . D MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.769 ? metalc ? metalc18 Q O2B ANP . D ANP 301 1_555 R MG MG . D MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.248 ? metalc ? metalc19 R MG MG . D MG 302 1_555 BA O HOH . D HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? metalc ? metalc20 R MG MG . D MG 302 1_555 BA O HOH . D HOH 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? metalc ? metalc21 E OG1 THR 53 E THR 53 1_555 U MG MG . E MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? metalc ? metalc22 T O2G ANP . E ANP 301 1_555 U MG MG . E MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.86 ? metalc ? metalc23 T O2B ANP . E ANP 301 1_555 U MG MG . E MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.47 ? metalc ? metalc24 U MG MG . E MG 302 1_555 CA O HOH . E HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? metalc ? metalc25 U MG MG . E MG 302 1_555 CA O HOH . E HOH 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? metalc ? metalc26 F OG1 THR 53 F THR 53 1_555 X MG MG . F MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.953 ? metalc ? metalc27 W O3G ANP . F ANP 301 1_555 X MG MG . F MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.905 ? metalc ? metalc28 W O1B ANP . F ANP 301 1_555 X MG MG . F MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.478 ? metalc ? metalc29 X MG MG . F MG 302 1_555 DA O HOH . F HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.377 ? metalc ? metalc30 X MG MG . F MG 302 1_555 DA O HOH . F HOH 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.218 ? # _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 5YZ8 _atom_sites.fract_transf_matrix[1][1] 0.009253 _atom_sites.fract_transf_matrix[1][2] 0.005342 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010685 _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] 0.004463 _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 2 ANP A 1 301 301 ANP ANP . H 3 MG A 1 302 302 MG MG . I 4 CL A 1 303 303 CL CL . J 4 CL A 1 304 304 CL CL . K 2 ANP B 1 301 301 ANP ANP . L 3 MG B 1 302 302 MG MG . M 4 CL B 1 303 303 CL CL . N 2 ANP C 1 301 301 ANP ANP . O 3 MG C 1 302 302 MG MG . P 4 CL C 1 303 303 CL CL . Q 2 ANP D 1 301 301 ANP ANP . R 3 MG D 1 302 302 MG MG . S 4 CL D 1 303 303 CL CL . T 2 ANP E 1 301 301 ANP ANP . U 3 MG E 1 302 302 MG MG . V 4 CL E 1 303 303 CL CL . W 2 ANP F 1 301 301 ANP ANP . X 3 MG F 1 302 302 MG MG . Y 5 HOH A 1 401 401 HOH HOH . Y 5 HOH A 2 402 402 HOH HOH . Y 5 HOH A 3 403 403 HOH HOH . Y 5 HOH A 4 404 404 HOH HOH . Y 5 HOH A 5 405 405 HOH HOH . Y 5 HOH A 6 406 406 HOH HOH . Y 5 HOH A 7 407 407 HOH HOH . Z 5 HOH B 1 401 401 HOH HOH . Z 5 HOH B 2 402 402 HOH HOH . Z 5 HOH B 3 403 403 HOH HOH . Z 5 HOH B 4 404 404 HOH HOH . Z 5 HOH B 5 405 405 HOH HOH . Z 5 HOH B 6 406 406 HOH HOH . AA 5 HOH C 1 401 401 HOH HOH . AA 5 HOH C 2 402 402 HOH HOH . AA 5 HOH C 3 403 403 HOH HOH . AA 5 HOH C 4 404 404 HOH HOH . AA 5 HOH C 5 405 405 HOH HOH . AA 5 HOH C 6 406 406 HOH HOH . BA 5 HOH D 1 401 401 HOH HOH . BA 5 HOH D 2 402 402 HOH HOH . BA 5 HOH D 3 403 403 HOH HOH . BA 5 HOH D 4 404 404 HOH HOH . BA 5 HOH D 5 405 405 HOH HOH . BA 5 HOH D 6 406 406 HOH HOH . BA 5 HOH D 7 407 407 HOH HOH . CA 5 HOH E 1 401 401 HOH HOH . CA 5 HOH E 2 402 402 HOH HOH . CA 5 HOH E 3 403 403 HOH HOH . CA 5 HOH E 4 404 404 HOH HOH . CA 5 HOH E 5 405 405 HOH HOH . DA 5 HOH F 1 401 401 HOH HOH . DA 5 HOH F 2 402 402 HOH HOH . DA 5 HOH F 3 403 403 HOH HOH . DA 5 HOH F 4 404 404 HOH HOH . DA 5 HOH F 5 405 405 HOH HOH . DA 5 HOH F 6 406 406 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 ANP . . . W 2 -54.274 22.945 -37.538 1 43.88 ? PG ANP 301 F 1 HETATM 2 O O1G ANP . . . W 2 -53.414 23.467 -38.667 1 42.9 ? O1G ANP 301 F 1 HETATM 3 O O2G ANP . . . W 2 -53.469 22.592 -36.305 1 43.53 ? O2G ANP 301 F 1 HETATM 4 O O3G ANP . . . W 2 -55.5 23.786 -37.261 1 44.67 ? O3G ANP 301 F 1 HETATM 5 P PB ANP . . . W 2 -55.981 20.429 -37.202 1 35.52 ? PB ANP 301 F 1 HETATM 6 O O1B ANP . . . W 2 -56.973 21.333 -36.512 1 35.06 ? O1B ANP 301 F 1 HETATM 7 O O2B ANP . . . W 2 -55.177 19.476 -36.361 1 33.37 ? O2B ANP 301 F 1 HETATM 8 N N3B ANP . . . W 2 -54.954 21.458 -38.163 1 39.3 ? N3B ANP 301 F 1 HETATM 9 P PA ANP . . . W 2 -58.343 19.777 -38.571 1 39.64 ? PA ANP 301 F 1 HETATM 10 O O1A ANP . . . W 2 -58.469 21.12 -39.246 1 40.11 ? O1A ANP 301 F 1 HETATM 11 O O2A ANP . . . W 2 -59.146 19.507 -37.315 1 39.08 ? O2A ANP 301 F 1 HETATM 12 O O3A ANP . . . W 2 -56.777 19.525 -38.269 1 37.84 ? O3A ANP 301 F 1 HETATM 13 O O5' ANP . . . W 2 -58.661 18.613 -39.613 1 38.61 ? O5' ANP 301 F 1 HETATM 14 C C5' ANP . . . W 2 -58.622 18.881 -41.001 1 40.64 ? C5' ANP 301 F 1 HETATM 15 C C4' ANP . . . W 2 -58.062 17.662 -41.707 1 41.23 ? C4' ANP 301 F 1 HETATM 16 O O4' ANP . . . W 2 -59.105 16.703 -41.86 1 41.61 ? O4' ANP 301 F 1 HETATM 17 C C3' ANP . . . W 2 -57.526 18.028 -43.08 1 41.29 ? C3' ANP 301 F 1 HETATM 18 O O3' ANP . . . W 2 -56.105 17.873 -43.121 1 42.74 ? O3' ANP 301 F 1 HETATM 19 C C2' ANP . . . W 2 -58.249 17.112 -44.04 1 41.82 ? C2' ANP 301 F 1 HETATM 20 O O2' ANP . . . W 2 -57.347 16.223 -44.7 1 42.52 ? O2' ANP 301 F 1 HETATM 21 C C1' ANP . . . W 2 -59.26 16.316 -43.221 1 42.85 ? C1' ANP 301 F 1 HETATM 22 N N9 ANP . . . W 2 -60.655 16.56 -43.687 1 43.97 ? N9 ANP 301 F 1 HETATM 23 C C8 ANP . . . W 2 -61.322 17.728 -43.628 1 44.94 ? C8 ANP 301 F 1 HETATM 24 N N7 ANP . . . W 2 -62.571 17.599 -44.146 1 45.75 ? N7 ANP 301 F 1 HETATM 25 C C5 ANP . . . W 2 -62.715 16.328 -44.548 1 45.63 ? C5 ANP 301 F 1 HETATM 26 C C6 ANP . . . W 2 -63.789 15.519 -45.179 1 47.2 ? C6 ANP 301 F 1 HETATM 27 N N6 ANP . . . W 2 -64.985 16.074 -45.488 1 47.62 ? N6 ANP 301 F 1 HETATM 28 N N1 ANP . . . W 2 -63.539 14.207 -45.429 1 47.91 ? N1 ANP 301 F 1 HETATM 29 C C2 ANP . . . W 2 -62.358 13.634 -45.118 1 47.1 ? C2 ANP 301 F 1 HETATM 30 N N3 ANP . . . W 2 -61.336 14.319 -44.551 1 47.06 ? N3 ANP 301 F 1 HETATM 31 C C4 ANP . . . W 2 -61.45 15.642 -44.242 1 45.19 ? C4 ANP 301 F 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 252 _model_server_stats.encode_time_ms 17 _model_server_stats.element_count 31 #