data_5B4E # _model_server_result.job_id fMIEEK1Ypp0TnD_mLY_Tjg _model_server_result.datetime_utc '2025-03-09 05:55:18' _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 5b4e # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":403}' # _entry.id 5B4E # _exptl.entry_id 5B4E _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 506.196 _entity.id 3 _entity.src_method syn _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 90 _cell.angle_gamma 120 _cell.entry_id 5B4E _cell.length_a 92.911 _cell.length_b 92.911 _cell.length_c 266.854 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5B4E _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # _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,I,J,K,L,M _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 12_555 x,x-y,-z+1/6 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 0 0 44.475667 # _struct_asym.details ? _struct_asym.entity_id 3 _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 metalc ? metalc1 A SG CYS 3 A CYS 3 1_555 B ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.19 ? metalc ? metalc2 A SG CYS 6 A CYS 6 1_555 B ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.206 ? metalc ? metalc3 A SG CYS 22 A CYS 22 1_555 B ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.214 ? metalc ? metalc4 A ND1 HIS 25 A HIS 25 1_555 B ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.195 ? metalc ? metalc5 A SG CYS 130 A CYS 130 1_555 E FE2 SF4 . A SF4 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? metalc ? metalc6 A SG CYS 133 A CYS 133 1_555 E FE4 SF4 . A SF4 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? metalc ? metalc7 A SG CYS 222 A CYS 222 1_555 E FE1 SF4 . A SF4 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? metalc ? metalc8 A SG CYS 274 A CYS 274 1_555 C ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.494 ? metalc ? metalc9 A SG CYS 277 A CYS 277 1_555 C ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.361 ? metalc ? metalc10 A SG CYS 286 A CYS 286 1_555 C ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? metalc ? metalc11 A SG CYS 289 A CYS 289 1_555 C ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? # _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 5B4E _atom_sites.fract_transf_matrix[1][1] 0.010763 _atom_sites.fract_transf_matrix[1][2] 0.006214 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012428 _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] 0.003747 _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 B 2 ZN A 1 401 1 ZN ZN . C 2 ZN A 1 402 2 ZN ZN . D 3 ANP A 1 403 1 ANP ANP . E 4 SF4 A 1 404 1 SF4 SF4 . F 5 SO4 A 1 405 1 SO4 SO4 . G 5 SO4 A 1 406 2 SO4 SO4 . H 5 SO4 A 1 407 3 SO4 SO4 . I 5 SO4 A 1 408 5 SO4 SO4 . J 5 SO4 A 1 409 6 SO4 SO4 . K 5 SO4 A 1 410 7 SO4 SO4 . L 6 IPA A 1 411 1 IPA IPA . M 7 HOH A 1 501 39 HOH HOH . M 7 HOH A 2 502 1 HOH HOH . M 7 HOH A 3 503 33 HOH HOH . M 7 HOH A 4 504 37 HOH HOH . M 7 HOH A 5 505 3 HOH HOH . M 7 HOH A 6 506 18 HOH HOH . M 7 HOH A 7 507 17 HOH HOH . M 7 HOH A 8 508 25 HOH HOH . M 7 HOH A 9 509 10 HOH HOH . M 7 HOH A 10 510 16 HOH HOH . M 7 HOH A 11 511 38 HOH HOH . M 7 HOH A 12 512 6 HOH HOH . M 7 HOH A 13 513 14 HOH HOH . M 7 HOH A 14 514 8 HOH HOH . M 7 HOH A 15 515 4 HOH HOH . M 7 HOH A 16 516 5 HOH HOH . M 7 HOH A 17 517 13 HOH HOH . M 7 HOH A 18 518 7 HOH HOH . M 7 HOH A 19 519 11 HOH HOH . M 7 HOH A 20 520 31 HOH HOH . M 7 HOH A 21 521 12 HOH HOH . M 7 HOH A 22 522 2 HOH HOH . M 7 HOH A 23 523 9 HOH HOH . M 7 HOH A 24 524 26 HOH HOH . M 7 HOH A 25 525 40 HOH HOH . M 7 HOH A 26 526 30 HOH HOH . M 7 HOH A 27 527 28 HOH HOH . M 7 HOH A 28 528 32 HOH HOH . M 7 HOH A 29 529 24 HOH HOH . M 7 HOH A 30 530 27 HOH HOH . M 7 HOH A 31 531 35 HOH HOH . M 7 HOH A 32 532 20 HOH HOH . M 7 HOH A 33 533 36 HOH HOH . M 7 HOH A 34 534 34 HOH HOH . M 7 HOH A 35 535 19 HOH HOH . M 7 HOH A 36 536 21 HOH HOH . M 7 HOH A 37 537 29 HOH HOH . M 7 HOH A 38 538 22 HOH HOH . M 7 HOH A 39 539 23 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 . . . D 3 26.558 35.692 8.867 1 48.72 ? PG ANP 403 A 1 HETATM 2 O O1G ANP . . . D 3 25.467 34.833 8.467 1 51.58 ? O1G ANP 403 A 1 HETATM 3 O O2G ANP . . . D 3 26.271 37.068 8.601 1 64.51 ? O2G ANP 403 A 1 HETATM 4 O O3G ANP . . . D 3 27.909 35.399 8.498 1 60.42 ? O3G ANP 403 A 1 HETATM 5 P PB ANP . . . D 3 26.884 34.044 11.463 1 94.94 ? PB ANP 403 A 1 HETATM 6 O O1B ANP . . . D 3 26.774 32.882 10.544 1 57.02 ? O1B ANP 403 A 1 HETATM 7 O O2B ANP . . . D 3 28.206 34.234 12.115 1 90.59 ? O2B ANP 403 A 1 HETATM 8 N N3B ANP . . . D 3 26.578 35.542 10.595 1 80.55 ? N3B ANP 403 A 1 HETATM 9 P PA ANP . . . D 3 24.846 34.992 13.089 1 77.13 ? PA ANP 403 A 1 HETATM 10 O O1A ANP . . . D 3 25.632 36.198 12.774 1 65.75 ? O1A ANP 403 A 1 HETATM 11 O O2A ANP . . . D 3 24.297 34.754 14.443 1 65.59 ? O2A ANP 403 A 1 HETATM 12 O O3A ANP . . . D 3 25.788 33.821 12.611 1 79.92 ? O3A ANP 403 A 1 HETATM 13 O O5' ANP . . . D 3 23.647 35.059 12.087 1 57.34 ? O5' ANP 403 A 1 HETATM 14 C C5' ANP . . . D 3 22.812 33.995 11.742 1 47 ? C5' ANP 403 A 1 HETATM 15 C C4' ANP . . . D 3 21.911 34.455 10.624 1 47.74 ? C4' ANP 403 A 1 HETATM 16 O O4' ANP . . . D 3 20.954 35.381 11.093 1 52.25 ? O4' ANP 403 A 1 HETATM 17 C C3' ANP . . . D 3 22.658 35.228 9.581 1 53.37 ? C3' ANP 403 A 1 HETATM 18 O O3' ANP . . . D 3 23.075 34.378 8.554 1 56.89 ? O3' ANP 403 A 1 HETATM 19 C C2' ANP . . . D 3 21.638 36.13 9.005 1 43.88 ? C2' ANP 403 A 1 HETATM 20 O O2' ANP . . . D 3 20.983 35.359 8.031 1 42.43 ? O2' ANP 403 A 1 HETATM 21 C C1' ANP . . . D 3 20.694 36.392 10.136 1 48.48 ? C1' ANP 403 A 1 HETATM 22 N N9 ANP . . . D 3 21.033 37.709 10.695 1 49.37 ? N9 ANP 403 A 1 HETATM 23 C C8 ANP . . . D 3 21.898 37.9 11.668 1 38.51 ? C8 ANP 403 A 1 HETATM 24 N N7 ANP . . . D 3 22.03 39.18 11.968 1 46.42 ? N7 ANP 403 A 1 HETATM 25 C C5 ANP . . . D 3 21.221 39.854 11.173 1 36.74 ? C5 ANP 403 A 1 HETATM 26 C C6 ANP . . . D 3 20.866 41.264 10.973 1 44.43 ? C6 ANP 403 A 1 HETATM 27 N N6 ANP . . . D 3 21.402 42.247 11.694 1 47.9 ? N6 ANP 403 A 1 HETATM 28 N N1 ANP . . . D 3 19.985 41.554 10.041 1 39.92 ? N1 ANP 403 A 1 HETATM 29 C C2 ANP . . . D 3 19.432 40.602 9.324 1 38.64 ? C2 ANP 403 A 1 HETATM 30 N N3 ANP . . . D 3 19.704 39.322 9.451 1 40.97 ? N3 ANP 403 A 1 HETATM 31 C C4 ANP . . . D 3 20.575 38.88 10.337 1 36.98 ? C4 ANP 403 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 278 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #