data_4YXW # _model_server_result.job_id 2r7xDQbbVv06-cugt8bwNw _model_server_result.datetime_utc '2024-11-21 18:33:19' _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 4yxw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"T","auth_seq_id":600}' # _entry.id 4YXW # _exptl.entry_id 4YXW _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 506.196 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER' _entity.pdbx_number_of_molecules 5 _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 4YXW _cell.length_a 105.353 _cell.length_b 123.052 _cell.length_c 261.276 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YXW _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 PISA _pdbx_struct_assembly.oligomeric_details nonameric _pdbx_struct_assembly.oligomeric_count 9 _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 _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 ? 6 J N N ? 6 L N N ? 6 N N N ? 6 P N N ? 6 T 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 176 A THR 176 1_555 K MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc2 J O1G ANP . A ANP 600 1_555 K MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc3 J O1B ANP . A ANP 600 1_555 K MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc4 K MG MG . A MG 601 1_555 W O HOH . A HOH 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc5 K MG MG . A MG 601 1_555 W O HOH . A HOH 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc6 K MG MG . A MG 601 1_555 W O HOH . A HOH 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc7 B OG1 THR 176 B THR 176 1_555 M MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc8 L O1G ANP . B ANP 600 1_555 M MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc9 L O1B ANP . B ANP 600 1_555 M MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc10 M MG MG . B MG 601 1_555 X O HOH . B HOH 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc11 M MG MG . B MG 601 1_555 X O HOH . B HOH 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc12 M MG MG . B MG 601 1_555 X O HOH . B HOH 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc13 C OG1 THR 176 C THR 176 1_555 O MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc14 N O1G ANP . C ANP 600 1_555 O MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc15 N O1B ANP . C ANP 600 1_555 O MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? metalc ? metalc16 O MG MG . C MG 601 1_555 Y O HOH . C HOH 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc17 O MG MG . C MG 601 1_555 Y O HOH . C HOH 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc18 O MG MG . C MG 601 1_555 Y O HOH . C HOH 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc19 D OG1 THR 167 D THR 163 1_555 Q MG MG . D MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc20 P O1G ANP . D ANP 600 1_555 Q MG MG . D MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? metalc ? metalc21 P O1B ANP . D ANP 600 1_555 Q MG MG . D MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc22 Q MG MG . D MG 601 1_555 Z O HOH . D HOH 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc23 Q MG MG . D MG 601 1_555 Z O HOH . D HOH 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc24 Q MG MG . D MG 601 1_555 Z O HOH . D HOH 707 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc25 F OG1 THR 167 F THR 163 1_555 U MG MG . F MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc26 F O LEU 418 F LEU 414 1_555 V NA NA . F NA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.399 ? metalc ? metalc27 T O1G ANP . F ANP 600 1_555 U MG MG . F MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc28 T O1B ANP . F ANP 600 1_555 U MG MG . F MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc29 U MG MG . F MG 601 1_555 BA O HOH . F HOH 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc30 U MG MG . F MG 601 1_555 BA O HOH . F HOH 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc31 U MG MG . F MG 601 1_555 BA O HOH . F HOH 708 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? # _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 4YXW _atom_sites.fract_transf_matrix[1][1] 0.009492 _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] 0.008127 _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] 0.003827 _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 J 6 ANP A 1 600 600 ANP ANP . K 7 MG A 1 601 601 MG MG . L 6 ANP B 1 600 600 ANP ANP . M 7 MG B 1 601 601 MG MG . N 6 ANP C 1 600 600 ANP ANP . O 7 MG C 1 601 601 MG MG . P 6 ANP D 1 600 600 ANP ANP . Q 7 MG D 1 601 601 MG MG . R 8 CL D 1 503 1 CL CL . S 9 TS6 E 1 603 1 TS6 TS6 . T 6 ANP F 1 600 600 ANP ANP . U 7 MG F 1 601 601 MG MG . V 10 NA F 1 503 1 NA NA . W 11 HOH A 1 701 247 HOH HOH . W 11 HOH A 2 702 242 HOH HOH . W 11 HOH A 3 703 703 HOH HOH . W 11 HOH A 4 704 701 HOH HOH . W 11 HOH A 5 705 702 HOH HOH . W 11 HOH A 6 706 13 HOH HOH . X 11 HOH B 1 701 276 HOH HOH . X 11 HOH B 2 702 269 HOH HOH . X 11 HOH B 3 703 330 HOH HOH . X 11 HOH B 4 704 701 HOH HOH . X 11 HOH B 5 705 703 HOH HOH . X 11 HOH B 6 706 702 HOH HOH . X 11 HOH B 7 707 261 HOH HOH . Y 11 HOH C 1 701 425 HOH HOH . Y 11 HOH C 2 702 701 HOH HOH . Y 11 HOH C 3 703 702 HOH HOH . Y 11 HOH C 4 704 703 HOH HOH . Z 11 HOH D 1 701 346 HOH HOH . Z 11 HOH D 2 702 173 HOH HOH . Z 11 HOH D 3 703 63 HOH HOH . Z 11 HOH D 4 704 703 HOH HOH . Z 11 HOH D 5 705 701 HOH HOH . Z 11 HOH D 6 706 125 HOH HOH . Z 11 HOH D 7 707 702 HOH HOH . Z 11 HOH D 8 708 74 HOH HOH . AA 11 HOH E 1 701 139 HOH HOH . AA 11 HOH E 2 702 166 HOH HOH . AA 11 HOH E 3 703 13 HOH HOH . BA 11 HOH F 1 701 427 HOH HOH . BA 11 HOH F 2 702 703 HOH HOH . BA 11 HOH F 3 703 424 HOH HOH . BA 11 HOH F 4 704 69 HOH HOH . BA 11 HOH F 5 705 702 HOH HOH . BA 11 HOH F 6 706 423 HOH HOH . BA 11 HOH F 7 707 426 HOH HOH . BA 11 HOH F 8 708 701 HOH HOH . BA 11 HOH F 9 709 207 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 . . . T 6 26.869 96.652 29.338 1 48.42 ? PG ANP 600 F 1 HETATM 2 O O1G ANP . . . T 6 26.337 95.633 28.363 1 48.81 ? O1G ANP 600 F 1 HETATM 3 O O2G ANP . . . T 6 28.348 96.891 29.208 1 48.78 ? O2G ANP 600 F 1 HETATM 4 O O3G ANP . . . T 6 26.027 97.896 29.462 1 47.89 ? O3G ANP 600 F 1 HETATM 5 P PB ANP . . . T 6 25.22 95.387 31.524 1 50.42 ? PB ANP 600 F 1 HETATM 6 O O1B ANP . . . T 6 24.739 94.257 30.656 1 49.41 ? O1B ANP 600 F 1 HETATM 7 O O2B ANP . . . T 6 24.34 96.6 31.7 1 49.48 ? O2B ANP 600 F 1 HETATM 8 N N3B ANP . . . T 6 26.761 95.893 30.901 1 49.52 ? N3B ANP 600 F 1 HETATM 9 P PA ANP . . . T 6 26.441 93.492 33.209 1 52.93 ? PA ANP 600 F 1 HETATM 10 O O1A ANP . . . T 6 27.476 93.469 32.116 1 54.33 ? O1A ANP 600 F 1 HETATM 11 O O2A ANP . . . T 6 25.575 92.278 33.414 1 52.16 ? O2A ANP 600 F 1 HETATM 12 O O3A ANP . . . T 6 25.482 94.772 32.992 1 51.55 ? O3A ANP 600 F 1 HETATM 13 O O5' ANP . . . T 6 27.176 93.829 34.602 1 54.14 ? O5' ANP 600 F 1 HETATM 14 C C5' ANP . . . T 6 28.465 94.441 34.645 1 56.35 ? C5' ANP 600 F 1 HETATM 15 C C4' ANP . . . T 6 29.164 94.137 35.962 1 58.39 ? C4' ANP 600 F 1 HETATM 16 O O4' ANP . . . T 6 28.373 94.558 37.077 1 60.72 ? O4' ANP 600 F 1 HETATM 17 C C3' ANP . . . T 6 29.443 92.657 36.175 1 59.28 ? C3' ANP 600 F 1 HETATM 18 O O3' ANP . . . T 6 30.669 92.231 35.572 1 58.04 ? O3' ANP 600 F 1 HETATM 19 C C2' ANP . . . T 6 29.469 92.545 37.683 1 60.99 ? C2' ANP 600 F 1 HETATM 20 O O2' ANP . . . T 6 30.774 92.823 38.201 1 62.08 ? O2' ANP 600 F 1 HETATM 21 C C1' ANP . . . T 6 28.484 93.613 38.151 1 62.24 ? C1' ANP 600 F 1 HETATM 22 N N9 ANP . . . T 6 27.173 92.986 38.472 1 64.21 ? N9 ANP 600 F 1 HETATM 23 C C8 ANP . . . T 6 26.017 93.126 37.792 1 65.21 ? C8 ANP 600 F 1 HETATM 24 N N7 ANP . . . T 6 25.017 92.404 38.364 1 66.29 ? N7 ANP 600 F 1 HETATM 25 C C5 ANP . . . T 6 25.536 91.78 39.435 1 67.13 ? C5 ANP 600 F 1 HETATM 26 C C6 ANP . . . T 6 25.044 90.859 40.49 1 68.74 ? C6 ANP 600 F 1 HETATM 27 N N6 ANP . . . T 6 23.751 90.45 40.512 1 69.49 ? N6 ANP 600 F 1 HETATM 28 N N1 ANP . . . T 6 25.935 90.45 41.432 1 68.87 ? N1 ANP 600 F 1 HETATM 29 C C2 ANP . . . T 6 27.229 90.847 41.429 1 68.7 ? C2 ANP 600 F 1 HETATM 30 N N3 ANP . . . T 6 27.736 91.681 40.498 1 67.03 ? N3 ANP 600 F 1 HETATM 31 C C4 ANP . . . T 6 26.956 92.171 39.501 1 66.01 ? C4 ANP 600 F 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 293 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 31 #