data_3AKL # _model_server_result.job_id lk4rwXVSpsGkY3sZ6w0cxg _model_server_result.datetime_utc '2025-08-31 12:24:12' _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 3akl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":601}' # _entry.id 3AKL # _exptl.entry_id 3AKL _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 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 78.84 _cell.angle_beta 71.36 _cell.angle_gamma 85.44 _cell.entry_id 3AKL _cell.length_a 60.133 _cell.length_b 74.835 _cell.length_c 75.815 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3AKL _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,G,H,I,J,P,Q 1 1 C,D,K,L,M,N,O,R,S 2 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 E N N ? 2 H N N ? 2 M 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 disulf ? disulf1 A SG CYS 61 A CYS 61 1_555 A SG CYS 180 A CYS 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? metalc ? metalc1 A OD1 ASN 160 A ASN 160 1_555 G MG MG . A MG 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.696 ? metalc ? metalc2 A OD2 ASP 179 A ASP 179 1_555 F MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.565 ? metalc ? metalc3 A OD1 ASP 179 A ASP 179 1_555 F MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.609 ? metalc ? metalc4 G MG MG . A MG 405 1_555 E O1G ANP . A ANP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? metalc ? metalc5 G MG MG . A MG 405 1_555 E O3A ANP . A ANP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? metalc ? metalc6 G MG MG . A MG 405 1_555 E O2A ANP . A ANP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.951 ? metalc ? metalc7 B OD1 ASN 160 B ASN 160 1_555 J MG MG . B MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.535 ? metalc ? metalc8 B OD1 ASP 179 B ASP 179 1_555 I MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.581 ? metalc ? metalc9 B OD2 ASP 179 B ASP 179 1_555 J MG MG . B MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.949 ? metalc ? metalc10 B OG SER 182 B SER 182 1_555 I MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.852 ? metalc ? metalc11 I MG MG . B MG 401 1_555 H O1G ANP . B ANP 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.632 ? metalc ? metalc12 I MG MG . B MG 401 1_555 H O2B ANP . B ANP 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.912 ? metalc ? metalc13 J MG MG . B MG 404 1_555 H O2A ANP . B ANP 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.274 ? metalc ? metalc14 J MG MG . B MG 404 1_555 H O3G ANP . B ANP 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.735 ? metalc ? metalc15 J MG MG . B MG 404 1_555 H O3' ANP . B ANP 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.914 ? metalc ? metalc16 C OD1 ASN 160 C ASN 160 1_555 L MG MG . C MG 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.547 ? metalc ? metalc17 C OD2 ASP 179 C ASP 179 1_555 L MG MG . C MG 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.271 ? metalc ? metalc18 L MG MG . C MG 400 1_555 K O3B ADP . C ADP 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.4 ? metalc ? metalc19 L MG MG . C MG 400 1_555 K O2A ADP . C ADP 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.441 ? metalc ? metalc20 D OD2 ASP 179 D ASP 179 1_555 O MG MG . D MG 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.952 ? metalc ? metalc21 O MG MG . D MG 406 1_555 M O2G ANP . D ANP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.268 ? # _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 57 n n PG O2G ANP sing 58 n n PG O3G ANP sing 59 n n PG N3B ANP sing 60 n n O2G HOG2 ANP sing 61 n n O3G HOG3 ANP sing 62 n n PB O1B ANP doub 63 n n PB O2B ANP sing 64 n n PB N3B ANP sing 65 n n PB O3A ANP sing 66 n n O2B HOB2 ANP sing 67 n n N3B HNB1 ANP sing 68 n n PA O1A ANP doub 69 n n PA O2A ANP sing 70 n n PA O3A ANP sing 71 n n PA O5' ANP sing 72 n n O2A HOA2 ANP sing 73 n n O5' C5' ANP sing 74 n n C5' C4' ANP sing 75 n n C5' "H5'1" ANP sing 76 n n C5' "H5'2" ANP sing 77 n n C4' O4' ANP sing 78 n n C4' C3' ANP sing 79 n n C4' H4' ANP sing 80 n n O4' C1' ANP sing 81 n n C3' O3' ANP sing 82 n n C3' C2' ANP sing 83 n n C3' H3' ANP sing 84 n n O3' HO3' ANP sing 85 n n C2' O2' ANP sing 86 n n C2' C1' ANP sing 87 n n C2' H2' ANP sing 88 n n O2' HO2' ANP sing 89 n n C1' N9 ANP sing 90 n n C1' H1' ANP sing 91 n n N9 C8 ANP sing 92 n y N9 C4 ANP sing 93 n y C8 N7 ANP doub 94 n y C8 H8 ANP sing 95 n n N7 C5 ANP sing 96 n y C5 C6 ANP sing 97 n y C5 C4 ANP doub 98 n y C6 N6 ANP sing 99 n n C6 N1 ANP doub 100 n y N6 HN61 ANP sing 101 n n N6 HN62 ANP sing 102 n n N1 C2 ANP sing 103 n y C2 N3 ANP doub 104 n y C2 H2 ANP sing 105 n n N3 C4 ANP sing 106 n y # _atom_sites.entry_id 3AKL _atom_sites.fract_transf_matrix[1][1] 0.01663 _atom_sites.fract_transf_matrix[1][2] -0.001327 _atom_sites.fract_transf_matrix[1][3] -0.005462 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013405 _atom_sites.fract_transf_matrix[2][3] -0.002425 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.014147 _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 E 2 ANP A 1 601 601 ANP ANP . F 3 MG A 1 402 402 MG MG . G 3 MG A 1 405 405 MG MG . H 2 ANP B 1 600 600 ANP ANP . I 3 MG B 1 401 401 MG MG . J 3 MG B 1 404 404 MG MG . K 4 ADP C 1 500 500 ADP ADP . L 3 MG C 1 400 400 MG MG . M 2 ANP D 1 602 602 ANP ANP . N 3 MG D 1 403 403 MG MG . O 3 MG D 1 406 406 MG MG . P 5 HOH A 1 326 6 HOH HOH . P 5 HOH A 2 327 9 HOH HOH . P 5 HOH A 3 328 13 HOH HOH . P 5 HOH A 4 329 15 HOH HOH . P 5 HOH A 5 330 16 HOH HOH . P 5 HOH A 6 331 20 HOH HOH . P 5 HOH A 7 332 21 HOH HOH . P 5 HOH A 8 333 29 HOH HOH . P 5 HOH A 9 334 31 HOH HOH . P 5 HOH A 10 335 36 HOH HOH . P 5 HOH A 11 336 37 HOH HOH . P 5 HOH A 12 337 41 HOH HOH . P 5 HOH A 13 338 56 HOH HOH . Q 5 HOH B 1 326 2 HOH HOH . Q 5 HOH B 2 327 7 HOH HOH . Q 5 HOH B 3 328 11 HOH HOH . Q 5 HOH B 4 329 14 HOH HOH . Q 5 HOH B 5 330 17 HOH HOH . Q 5 HOH B 6 331 27 HOH HOH . Q 5 HOH B 7 332 30 HOH HOH . Q 5 HOH B 8 333 39 HOH HOH . Q 5 HOH B 9 334 42 HOH HOH . Q 5 HOH B 10 335 43 HOH HOH . Q 5 HOH B 11 336 46 HOH HOH . Q 5 HOH B 12 337 49 HOH HOH . Q 5 HOH B 13 338 51 HOH HOH . Q 5 HOH B 14 339 54 HOH HOH . Q 5 HOH B 15 340 58 HOH HOH . Q 5 HOH B 16 341 59 HOH HOH . R 5 HOH C 1 326 19 HOH HOH . R 5 HOH C 2 327 22 HOH HOH . R 5 HOH C 3 328 25 HOH HOH . R 5 HOH C 4 329 32 HOH HOH . R 5 HOH C 5 330 33 HOH HOH . R 5 HOH C 6 331 40 HOH HOH . R 5 HOH C 7 332 44 HOH HOH . R 5 HOH C 8 333 50 HOH HOH . R 5 HOH C 9 334 55 HOH HOH . R 5 HOH C 10 335 57 HOH HOH . S 5 HOH D 1 326 1 HOH HOH . S 5 HOH D 2 327 3 HOH HOH . S 5 HOH D 3 328 4 HOH HOH . S 5 HOH D 4 329 5 HOH HOH . S 5 HOH D 5 330 8 HOH HOH . S 5 HOH D 6 331 10 HOH HOH . S 5 HOH D 7 332 12 HOH HOH . S 5 HOH D 8 333 18 HOH HOH . S 5 HOH D 9 334 23 HOH HOH . S 5 HOH D 10 335 24 HOH HOH . S 5 HOH D 11 336 26 HOH HOH . S 5 HOH D 12 337 28 HOH HOH . S 5 HOH D 13 338 34 HOH HOH . S 5 HOH D 14 339 35 HOH HOH . S 5 HOH D 15 340 38 HOH HOH . S 5 HOH D 16 341 45 HOH HOH . S 5 HOH D 17 342 47 HOH HOH . S 5 HOH D 18 343 48 HOH HOH . S 5 HOH D 19 344 52 HOH HOH . S 5 HOH D 20 345 53 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 . . . E 2 14.52 2.895 34.813 1 71.99 ? PG ANP 601 A 1 HETATM 2 O O1G ANP . . . E 2 14.685 2.119 36.06 1 49.55 ? O1G ANP 601 A 1 HETATM 3 O O2G ANP . . . E 2 14.239 4.474 35.143 1 56.02 ? O2G ANP 601 A 1 HETATM 4 O O3G ANP . . . E 2 13.181 2.425 33.916 1 61.19 ? O3G ANP 601 A 1 HETATM 5 P PB ANP . . . E 2 17.263 2.475 34.336 1 49.61 ? PB ANP 601 A 1 HETATM 6 O O1B ANP . . . E 2 18.217 2.182 33.241 1 42.49 ? O1B ANP 601 A 1 HETATM 7 O O2B ANP . . . E 2 17.583 3.561 35.285 1 54.65 ? O2B ANP 601 A 1 HETATM 8 N N3B ANP . . . E 2 15.783 2.76 33.733 1 53.23 ? N3B ANP 601 A 1 HETATM 9 P PA ANP . . . E 2 18.079 -0.13 35.039 1 40.32 ? PA ANP 601 A 1 HETATM 10 O O1A ANP . . . E 2 19.445 0.394 35.15 1 51.04 ? O1A ANP 601 A 1 HETATM 11 O O2A ANP . . . E 2 17.729 -1.272 35.852 1 46.27 ? O2A ANP 601 A 1 HETATM 12 O O3A ANP . . . E 2 17.059 1.111 35.223 1 51.24 ? O3A ANP 601 A 1 HETATM 13 O O5' ANP . . . E 2 17.756 -0.502 33.55 1 46.43 ? O5' ANP 601 A 1 HETATM 14 C C5' ANP . . . E 2 18.22 -1.73 33.071 1 44.5 ? C5' ANP 601 A 1 HETATM 15 C C4' ANP . . . E 2 17.072 -2.628 32.631 1 45.24 ? C4' ANP 601 A 1 HETATM 16 O O4' ANP . . . E 2 17.707 -3.849 32.162 1 50.6 ? O4' ANP 601 A 1 HETATM 17 C C3' ANP . . . E 2 16.115 -3.023 33.763 1 45.85 ? C3' ANP 601 A 1 HETATM 18 O O3' ANP . . . E 2 14.801 -2.502 33.509 1 37.97 ? O3' ANP 601 A 1 HETATM 19 C C2' ANP . . . E 2 16.067 -4.541 33.688 1 45.09 ? C2' ANP 601 A 1 HETATM 20 O O2' ANP . . . E 2 15.033 -4.904 32.783 1 41.19 ? O2' ANP 601 A 1 HETATM 21 C C1' ANP . . . E 2 17.392 -4.96 33.055 1 42.49 ? C1' ANP 601 A 1 HETATM 22 N N9 ANP . . . E 2 18.528 -5.251 34.002 1 46.03 ? N9 ANP 601 A 1 HETATM 23 C C8 ANP . . . E 2 18.984 -4.465 34.98 1 42.98 ? C8 ANP 601 A 1 HETATM 24 N N7 ANP . . . E 2 20.01 -5.058 35.588 1 41.79 ? N7 ANP 601 A 1 HETATM 25 C C5 ANP . . . E 2 20.227 -6.233 34.999 1 45.28 ? C5 ANP 601 A 1 HETATM 26 C C6 ANP . . . E 2 21.138 -7.271 35.203 1 46.1 ? C6 ANP 601 A 1 HETATM 27 N N6 ANP . . . E 2 22.05 -7.196 36.164 1 47.33 ? N6 ANP 601 A 1 HETATM 28 N N1 ANP . . . E 2 21.08 -8.357 34.416 1 46.18 ? N1 ANP 601 A 1 HETATM 29 C C2 ANP . . . E 2 20.169 -8.44 33.459 1 47.82 ? C2 ANP 601 A 1 HETATM 30 N N3 ANP . . . E 2 19.282 -7.475 33.231 1 46.36 ? N3 ANP 601 A 1 HETATM 31 C C4 ANP . . . E 2 19.285 -6.356 33.983 1 49.53 ? C4 ANP 601 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 400 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 31 #