data_5VK4 # _model_server_result.job_id bA7Z-Iap3_HQEMMWiiI54w _model_server_result.datetime_utc '2024-11-05 00:38:43' _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 5vk4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":401}' # _entry.id 5VK4 # _exptl.entry_id 5VK4 _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 2 _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 5VK4 _cell.length_a 54.25 _cell.length_b 79.61 _cell.length_c 150.07 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VK4 _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 C N N ? 2 E 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 OD2 ASP 71 A ASP 63 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.689 ? metalc ? metalc2 A OD2 ASP 100 A ASP 92 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.341 ? metalc ? metalc3 D MG MG . A MG 402 1_555 E O3G ANP . B ANP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.365 ? metalc ? metalc4 B OE1 GLU 147 B GLU 139 1_555 F MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.739 ? metalc ? metalc5 E O1A ANP . B ANP 401 1_555 F MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.381 ? # _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 5VK4 _atom_sites.fract_transf_matrix[1][1] 0.018433 _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] 0.012561 _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] 0.006664 _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 C 2 ANP A 1 401 401 ANP ANP . D 3 MG A 1 402 402 MG MG . E 2 ANP B 1 401 401 ANP ANP . F 3 MG B 1 402 403 MG MG . G 4 HOH A 1 501 57 HOH HOH . G 4 HOH A 2 502 23 HOH HOH . G 4 HOH A 3 503 22 HOH HOH . G 4 HOH A 4 504 6 HOH HOH . G 4 HOH A 5 505 20 HOH HOH . G 4 HOH A 6 506 44 HOH HOH . G 4 HOH A 7 507 27 HOH HOH . G 4 HOH A 8 508 1 HOH HOH . G 4 HOH A 9 509 45 HOH HOH . G 4 HOH A 10 510 49 HOH HOH . G 4 HOH A 11 511 5 HOH HOH . G 4 HOH A 12 512 10 HOH HOH . G 4 HOH A 13 513 56 HOH HOH . G 4 HOH A 14 514 42 HOH HOH . G 4 HOH A 15 515 28 HOH HOH . G 4 HOH A 16 516 43 HOH HOH . G 4 HOH A 17 517 3 HOH HOH . G 4 HOH A 18 518 31 HOH HOH . G 4 HOH A 19 519 2 HOH HOH . G 4 HOH A 20 520 32 HOH HOH . G 4 HOH A 21 521 14 HOH HOH . G 4 HOH A 22 522 30 HOH HOH . G 4 HOH A 23 523 25 HOH HOH . G 4 HOH A 24 524 24 HOH HOH . G 4 HOH A 25 525 19 HOH HOH . G 4 HOH A 26 526 34 HOH HOH . G 4 HOH A 27 527 46 HOH HOH . G 4 HOH A 28 528 33 HOH HOH . G 4 HOH A 29 529 17 HOH HOH . G 4 HOH A 30 530 58 HOH HOH . G 4 HOH A 31 531 18 HOH HOH . H 4 HOH B 1 501 54 HOH HOH . H 4 HOH B 2 502 55 HOH HOH . H 4 HOH B 3 503 51 HOH HOH . H 4 HOH B 4 504 37 HOH HOH . H 4 HOH B 5 505 48 HOH HOH . H 4 HOH B 6 506 40 HOH HOH . H 4 HOH B 7 507 47 HOH HOH . H 4 HOH B 8 508 11 HOH HOH . H 4 HOH B 9 509 8 HOH HOH . H 4 HOH B 10 510 9 HOH HOH . H 4 HOH B 11 511 53 HOH HOH . H 4 HOH B 12 512 50 HOH HOH . H 4 HOH B 13 513 16 HOH HOH . H 4 HOH B 14 514 7 HOH HOH . H 4 HOH B 15 515 52 HOH HOH . H 4 HOH B 16 516 39 HOH HOH . H 4 HOH B 17 517 38 HOH HOH . H 4 HOH B 18 518 15 HOH HOH . H 4 HOH B 19 519 4 HOH HOH . H 4 HOH B 20 520 36 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 4.165 3.945 6.259 1 129.62 ? PG ANP 401 B 1 HETATM 2 O O1G ANP . . . E 2 5.475 3.42 5.686 1 130.94 ? O1G ANP 401 B 1 HETATM 3 O O2G ANP . . . E 2 4.464 4.943 7.33 1 130.34 ? O2G ANP 401 B 1 HETATM 4 O O3G ANP . . . E 2 3.375 2.773 6.869 1 130.04 ? O3G ANP 401 B 1 HETATM 5 P PB ANP . . . E 2 2.31 6.056 5.141 1 102.03 ? PB ANP 401 B 1 HETATM 6 O O1B ANP . . . E 2 1.114 5.949 4.231 1 94.35 ? O1B ANP 401 B 1 HETATM 7 O O2B ANP . . . E 2 1.785 6.177 6.558 1 104.86 ? O2B ANP 401 B 1 HETATM 8 N N3B ANP . . . E 2 3.239 4.654 4.98 1 119.63 ? N3B ANP 401 B 1 HETATM 9 P PA ANP . . . E 2 4.813 7.53 4.376 1 79.12 ? PA ANP 401 B 1 HETATM 10 O O1A ANP . . . E 2 5.18 6.693 3.161 1 76.6 ? O1A ANP 401 B 1 HETATM 11 O O2A ANP . . . E 2 5.666 7.093 5.537 1 84.65 ? O2A ANP 401 B 1 HETATM 12 O O3A ANP . . . E 2 3.19 7.398 4.719 1 86.88 ? O3A ANP 401 B 1 HETATM 13 O O5' ANP . . . E 2 5.147 9.104 4.094 1 68.44 ? O5' ANP 401 B 1 HETATM 14 C C5' ANP . . . E 2 5.416 9.532 2.787 1 61.94 ? C5' ANP 401 B 1 HETATM 15 C C4' ANP . . . E 2 4.399 10.632 2.305 1 65.63 ? C4' ANP 401 B 1 HETATM 16 O O4' ANP . . . E 2 4.861 11.249 1.232 1 63.13 ? O4' ANP 401 B 1 HETATM 17 C C3' ANP . . . E 2 3.067 10.025 1.846 1 71.23 ? C3' ANP 401 B 1 HETATM 18 O O3' ANP . . . E 2 2.049 10.902 2.06 1 75.8 ? O3' ANP 401 B 1 HETATM 19 C C2' ANP . . . E 2 3.269 9.752 0.313 1 68.64 ? C2' ANP 401 B 1 HETATM 20 O O2' ANP . . . E 2 2.019 10.017 -0.451 1 74.23 ? O2' ANP 401 B 1 HETATM 21 C C1' ANP . . . E 2 4.216 10.547 -0.089 1 58.52 ? C1' ANP 401 B 1 HETATM 22 N N9 ANP . . . E 2 5.253 9.762 -0.778 1 46.8 ? N9 ANP 401 B 1 HETATM 23 C C8 ANP . . . E 2 6.19 9.025 -0.192 1 43.82 ? C8 ANP 401 B 1 HETATM 24 N N7 ANP . . . E 2 6.963 8.44 -1.129 1 41.95 ? N7 ANP 401 B 1 HETATM 25 C C5 ANP . . . E 2 6.481 8.827 -2.317 1 39.63 ? C5 ANP 401 B 1 HETATM 26 C C6 ANP . . . E 2 6.896 8.52 -3.59 1 33.54 ? C6 ANP 401 B 1 HETATM 27 N N6 ANP . . . E 2 7.991 7.687 -4.127 1 26.34 ? N6 ANP 401 B 1 HETATM 28 N N1 ANP . . . E 2 6.242 9.047 -4.623 1 29.81 ? N1 ANP 401 B 1 HETATM 29 C C2 ANP . . . E 2 5.181 9.862 -4.426 1 28.42 ? C2 ANP 401 B 1 HETATM 30 N N3 ANP . . . E 2 4.77 10.166 -3.167 1 38.77 ? N3 ANP 401 B 1 HETATM 31 C C4 ANP . . . E 2 5.433 9.64 -2.119 1 43.46 ? C4 ANP 401 B 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #