data_5OFA # _model_server_result.job_id T0cOkmzX4Sb8U9RJHu4GJA _model_server_result.datetime_utc '2024-10-11 00:28:34' _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 5ofa # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":702}' # _entry.id 5OFA # _exptl.entry_id 5OFA _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 97.91 _cell.angle_gamma 90 _cell.entry_id 5OFA _cell.length_a 69.61 _cell.length_b 125.73 _cell.length_c 81.53 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5OFA _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details 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 _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 ? 3 D N N ? 3 G 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 OD1 ASN 42 B ASN 39 1_555 E MG MG . B MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2 ? metalc ? metalc2 A SG CYS 502 B CYS 499 1_555 C ZN ZN . B ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? metalc ? metalc3 A SG CYS 505 B CYS 502 1_555 C ZN ZN . B ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.529 ? metalc ? metalc4 A SG CYS 528 B CYS 525 1_555 C ZN ZN . B ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.944 ? metalc ? metalc5 A SG CYS 539 B CYS 536 1_555 C ZN ZN . B ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.731 ? metalc ? metalc6 D O1G ANP . B ANP 702 1_555 E MG MG . B MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.944 ? metalc ? metalc7 D O2B ANP . B ANP 702 1_555 E MG MG . B MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.285 ? metalc ? metalc8 D O2A ANP . B ANP 702 1_555 E MG MG . B MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? metalc ? metalc9 E MG MG . B MG 703 1_555 I O HOH . B HOH 806 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.231 ? metalc ? metalc10 B OD1 ASN 42 A ASN 39 1_555 H MG MG . A MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.102 ? metalc ? metalc11 B SG CYS 502 A CYS 499 1_555 F ZN ZN . A ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.613 ? metalc ? metalc12 B SG CYS 505 A CYS 502 1_555 F ZN ZN . A ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.605 ? metalc ? metalc13 B SG CYS 528 A CYS 525 1_555 F ZN ZN . A ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.13 ? metalc ? metalc14 B SG CYS 539 A CYS 536 1_555 F ZN ZN . A ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.952 ? metalc ? metalc15 G O2G ANP . A ANP 702 1_555 H MG MG . A MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? metalc ? metalc16 G O2B ANP . A ANP 702 1_555 H MG MG . A MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.829 ? metalc ? metalc17 G O2A ANP . A ANP 702 1_555 H MG MG . A MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? metalc ? metalc18 H MG MG . A MG 703 1_555 J O HOH . A HOH 808 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? metalc ? metalc19 H MG MG . A MG 703 1_555 J O HOH . A HOH 810 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? # _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 5OFA _atom_sites.fract_transf_matrix[1][1] 0.014366 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001995 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007954 _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] 0.012383 _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 ZN B 1 701 591 ZN ZN . D 3 ANP B 1 702 1 ANP ANP . E 4 MG B 1 703 1 MG MG . F 2 ZN A 1 701 591 ZN ZN . G 3 ANP A 1 702 2 ANP ANP . H 4 MG A 1 703 2 MG MG . I 5 HOH B 1 801 34 HOH HOH . I 5 HOH B 2 802 8 HOH HOH . I 5 HOH B 3 803 19 HOH HOH . I 5 HOH B 4 804 4 HOH HOH . I 5 HOH B 5 805 13 HOH HOH . I 5 HOH B 6 806 37 HOH HOH . I 5 HOH B 7 807 29 HOH HOH . I 5 HOH B 8 808 20 HOH HOH . I 5 HOH B 9 809 25 HOH HOH . I 5 HOH B 10 810 9 HOH HOH . I 5 HOH B 11 811 11 HOH HOH . I 5 HOH B 12 812 2 HOH HOH . I 5 HOH B 13 813 15 HOH HOH . I 5 HOH B 14 814 5 HOH HOH . I 5 HOH B 15 815 21 HOH HOH . I 5 HOH B 16 816 1 HOH HOH . I 5 HOH B 17 817 24 HOH HOH . I 5 HOH B 18 818 6 HOH HOH . I 5 HOH B 19 819 18 HOH HOH . I 5 HOH B 20 820 10 HOH HOH . I 5 HOH B 21 821 14 HOH HOH . I 5 HOH B 22 822 17 HOH HOH . I 5 HOH B 23 823 31 HOH HOH . I 5 HOH B 24 824 23 HOH HOH . I 5 HOH B 25 825 16 HOH HOH . I 5 HOH B 26 826 40 HOH HOH . I 5 HOH B 27 827 38 HOH HOH . J 5 HOH A 1 801 27 HOH HOH . J 5 HOH A 2 802 33 HOH HOH . J 5 HOH A 3 803 22 HOH HOH . J 5 HOH A 4 804 39 HOH HOH . J 5 HOH A 5 805 35 HOH HOH . J 5 HOH A 6 806 12 HOH HOH . J 5 HOH A 7 807 3 HOH HOH . J 5 HOH A 8 808 26 HOH HOH . J 5 HOH A 9 809 7 HOH HOH . J 5 HOH A 10 810 36 HOH HOH . J 5 HOH A 11 811 30 HOH HOH . J 5 HOH A 12 812 28 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 -12.577 -21.585 -28.506 1 41.36 ? PG ANP 702 B 1 HETATM 2 O O1G ANP . . . D 3 -13.777 -20.76 -28.966 1 33.66 ? O1G ANP 702 B 1 HETATM 3 O O2G ANP . . . D 3 -12.944 -23.03 -28.253 1 38.74 ? O2G ANP 702 B 1 HETATM 4 O O3G ANP . . . D 3 -11.511 -21.12 -27.525 1 34.34 ? O3G ANP 702 B 1 HETATM 5 P PB ANP . . . D 3 -12.47 -21.418 -31.47 1 44.23 ? PB ANP 702 B 1 HETATM 6 O O1B ANP . . . D 3 -11.498 -21.82 -32.583 1 58.83 ? O1B ANP 702 B 1 HETATM 7 O O2B ANP . . . D 3 -13.219 -20.132 -31.725 1 46.54 ? O2B ANP 702 B 1 HETATM 8 N N3B ANP . . . D 3 -11.616 -21.502 -30.002 1 39.82 ? N3B ANP 702 B 1 HETATM 9 P PA ANP . . . D 3 -15.126 -22.138 -31.818 1 46.37 ? PA ANP 702 B 1 HETATM 10 O O1A ANP . . . D 3 -15.949 -23.402 -31.748 1 43.11 ? O1A ANP 702 B 1 HETATM 11 O O2A ANP . . . D 3 -15.44 -20.869 -30.933 1 37.49 ? O2A ANP 702 B 1 HETATM 12 O O3A ANP . . . D 3 -13.638 -22.553 -31.369 1 39.92 ? O3A ANP 702 B 1 HETATM 13 O O5' ANP . . . D 3 -15.112 -21.807 -33.362 1 38.9 ? O5' ANP 702 B 1 HETATM 14 C C5' ANP . . . D 3 -14.376 -22.653 -34.239 1 41.82 ? C5' ANP 702 B 1 HETATM 15 C C4' ANP . . . D 3 -14.091 -21.88 -35.519 1 41.56 ? C4' ANP 702 B 1 HETATM 16 O O4' ANP . . . D 3 -15.268 -21.404 -36.17 1 43.87 ? O4' ANP 702 B 1 HETATM 17 C C3' ANP . . . D 3 -13.326 -20.622 -35.197 1 43.66 ? C3' ANP 702 B 1 HETATM 18 O O3' ANP . . . D 3 -11.955 -20.957 -34.98 1 47.39 ? O3' ANP 702 B 1 HETATM 19 C C2' ANP . . . D 3 -13.608 -19.764 -36.388 1 42.42 ? C2' ANP 702 B 1 HETATM 20 O O2' ANP . . . D 3 -12.731 -20.195 -37.431 1 48.95 ? O2' ANP 702 B 1 HETATM 21 C C1' ANP . . . D 3 -15.008 -20.121 -36.776 1 42.37 ? C1' ANP 702 B 1 HETATM 22 N N9 ANP . . . D 3 -15.976 -19.1 -36.353 1 47.27 ? N9 ANP 702 B 1 HETATM 23 C C8 ANP . . . D 3 -16.913 -19.211 -35.378 1 50.71 ? C8 ANP 702 B 1 HETATM 24 N N7 ANP . . . D 3 -17.681 -18.08 -35.305 1 48.63 ? N7 ANP 702 B 1 HETATM 25 C C5 ANP . . . D 3 -17.244 -17.214 -36.228 1 48.1 ? C5 ANP 702 B 1 HETATM 26 C C6 ANP . . . D 3 -17.565 -15.83 -36.663 1 50.58 ? C6 ANP 702 B 1 HETATM 27 N N6 ANP . . . D 3 -18.541 -15.091 -36.125 1 52.47 ? N6 ANP 702 B 1 HETATM 28 N N1 ANP . . . D 3 -16.852 -15.309 -37.675 1 47.53 ? N1 ANP 702 B 1 HETATM 29 C C2 ANP . . . D 3 -15.858 -16.023 -38.243 1 50.99 ? C2 ANP 702 B 1 HETATM 30 N N3 ANP . . . D 3 -15.485 -17.27 -37.897 1 44.19 ? N3 ANP 702 B 1 HETATM 31 C C4 ANP . . . D 3 -16.127 -17.909 -36.918 1 49.57 ? C4 ANP 702 B 1 # _model_server_stats.io_time_ms 59 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 544 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 31 #