data_3KEX # _model_server_result.job_id df0pKqfM0xBzSX68q3cwDA _model_server_result.datetime_utc '2024-12-23 07:19:10' _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 3kex # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1}' # _entry.id 3KEX # _exptl.entry_id 3KEX _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 108.04 _cell.angle_gamma 90 _cell.entry_id 3KEX _cell.length_a 194.164 _cell.length_b 47.637 _cell.length_c 81.281 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3KEX _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 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 software_defined_assembly 1 PISA dimeric 2 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,C,D,E,F,G,H 1 1 A,C,D,G 2 1 B,E,F,H 2 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' 3_555 x+1/2,y+1/2,z 1 0 0 0 1 0 0 0 1 97.082 23.8185 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 C O2A ANP . A ANP 1 1_555 D MG MG . A MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.233 ? metalc ? metalc2 G O HOH . A HOH 17 1_555 D MG MG . A MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.607 ? metalc ? metalc3 A OD1 ASN 145 A ASN 820 1_555 D MG MG . A MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? metalc ? metalc4 E O2A ANP . B ANP 2 1_555 F MG MG . B MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? metalc ? metalc5 E O3G ANP . B ANP 2 1_555 F MG MG . B MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.88 ? metalc ? metalc6 H O HOH . B HOH 21 1_555 F MG MG . B MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.542 ? metalc ? metalc7 H O HOH . B HOH 22 1_555 F MG MG . B MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.591 ? metalc ? metalc8 B OD1 ASN 145 B ASN 820 1_555 F MG MG . B MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? metalc ? metalc9 B OD2 ASP 158 B ASP 833 1_555 F MG MG . B MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.891 ? # _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 3KEX _atom_sites.fract_transf_matrix[1][1] 0.00515 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001678 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.020992 _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] 0.012939 _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 1 1 ANP ANP . D 3 MG A 1 1001 1 MG MG . E 2 ANP B 1 2 2 ANP ANP . F 3 MG B 1 1001 2 MG MG . G 4 HOH A 1 4 4 HOH HOH . G 4 HOH A 2 5 5 HOH HOH . G 4 HOH A 3 10 10 HOH HOH . G 4 HOH A 4 11 11 HOH HOH . G 4 HOH A 5 14 14 HOH HOH . G 4 HOH A 6 15 15 HOH HOH . G 4 HOH A 7 17 17 HOH HOH . G 4 HOH A 8 18 18 HOH HOH . G 4 HOH A 9 27 27 HOH HOH . G 4 HOH A 10 28 28 HOH HOH . G 4 HOH A 11 30 30 HOH HOH . G 4 HOH A 12 31 31 HOH HOH . G 4 HOH A 13 32 32 HOH HOH . G 4 HOH A 14 33 33 HOH HOH . G 4 HOH A 15 1002 1 HOH HOH . H 4 HOH B 1 3 3 HOH HOH . H 4 HOH B 2 6 6 HOH HOH . H 4 HOH B 3 9 9 HOH HOH . H 4 HOH B 4 12 12 HOH HOH . H 4 HOH B 5 13 13 HOH HOH . H 4 HOH B 6 16 16 HOH HOH . H 4 HOH B 7 21 21 HOH HOH . H 4 HOH B 8 22 22 HOH HOH . H 4 HOH B 9 25 25 HOH HOH . H 4 HOH B 10 26 26 HOH HOH . H 4 HOH B 11 34 34 HOH HOH . H 4 HOH B 12 35 35 HOH HOH . H 4 HOH B 13 36 36 HOH HOH . H 4 HOH B 14 37 37 HOH HOH . H 4 HOH B 15 1002 2 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 . . . C 2 26.715 -0.06 -12.747 1 50.82 ? PG ANP 1 A 1 HETATM 2 O O1G ANP . . . C 2 27.601 -0.962 -11.685 1 58.94 ? O1G ANP 1 A 1 HETATM 3 O O2G ANP . . . C 2 26.062 -1.11 -13.831 1 45.62 ? O2G ANP 1 A 1 HETATM 4 O O3G ANP . . . C 2 27.544 0.903 -13.44 1 56.61 ? O3G ANP 1 A 1 HETATM 5 P PB ANP . . . C 2 24.981 0.014 -10.589 1 49.21 ? PB ANP 1 A 1 HETATM 6 O O1B ANP . . . C 2 23.336 0.045 -10.519 1 72.64 ? O1B ANP 1 A 1 HETATM 7 O O2B ANP . . . C 2 25.453 -1.376 -10.674 1 57.11 ? O2B ANP 1 A 1 HETATM 8 N N3B ANP . . . C 2 25.53 0.847 -11.955 1 44.95 ? N3B ANP 1 A 1 HETATM 9 P PA ANP . . . C 2 27.068 1.158 -8.962 1 49.22 ? PA ANP 1 A 1 HETATM 10 O O1A ANP . . . C 2 28.055 -0.162 -9.024 1 55 ? O1A ANP 1 A 1 HETATM 11 O O2A ANP . . . C 2 27.49 2.133 -9.946 1 50.98 ? O2A ANP 1 A 1 HETATM 12 O O3A ANP . . . C 2 25.493 0.778 -9.224 1 63.65 ? O3A ANP 1 A 1 HETATM 13 O O5' ANP . . . C 2 27.113 1.841 -7.454 1 48.33 ? O5' ANP 1 A 1 HETATM 14 C C5' ANP . . . C 2 26.079 1.554 -6.559 1 52.56 ? C5' ANP 1 A 1 HETATM 15 C C4' ANP . . . C 2 25.11 2.736 -6.323 1 57.97 ? C4' ANP 1 A 1 HETATM 16 O O4' ANP . . . C 2 25.717 4.02 -6.328 1 59.36 ? O4' ANP 1 A 1 HETATM 17 C C3' ANP . . . C 2 23.913 2.888 -7.358 1 61.39 ? C3' ANP 1 A 1 HETATM 18 O O3' ANP . . . C 2 22.708 2.214 -7.129 1 90.61 ? O3' ANP 1 A 1 HETATM 19 C C2' ANP . . . C 2 23.907 4.409 -7.753 1 55.04 ? C2' ANP 1 A 1 HETATM 20 O O2' ANP . . . C 2 22.693 5.035 -8.072 1 72.18 ? O2' ANP 1 A 1 HETATM 21 C C1' ANP . . . C 2 24.787 4.992 -6.681 1 59.07 ? C1' ANP 1 A 1 HETATM 22 N N9 ANP . . . C 2 25.533 6.145 -7.203 1 44.8 ? N9 ANP 1 A 1 HETATM 23 C C8 ANP . . . C 2 26.552 6.136 -8.114 1 41.97 ? C8 ANP 1 A 1 HETATM 24 N N7 ANP . . . C 2 26.997 7.496 -8.268 1 56.3 ? N7 ANP 1 A 1 HETATM 25 C C5 ANP . . . C 2 26.209 8.322 -7.414 1 43.03 ? C5 ANP 1 A 1 HETATM 26 C C6 ANP . . . C 2 26.223 9.669 -7.181 1 46.75 ? C6 ANP 1 A 1 HETATM 27 N N6 ANP . . . C 2 27.184 10.514 -7.85 1 57.89 ? N6 ANP 1 A 1 HETATM 28 N N1 ANP . . . C 2 25.296 10.232 -6.251 1 46.95 ? N1 ANP 1 A 1 HETATM 29 C C2 ANP . . . C 2 24.424 9.443 -5.614 1 52.33 ? C2 ANP 1 A 1 HETATM 30 N N3 ANP . . . C 2 24.411 8.061 -5.853 1 45.78 ? N3 ANP 1 A 1 HETATM 31 C C4 ANP . . . C 2 25.314 7.518 -6.755 1 42.65 ? C4 ANP 1 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 226 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #