data_3PVB # _model_server_result.job_id A6UgysTWnJYnHo6-jqfJpg _model_server_result.datetime_utc '2024-11-22 00:35:59' _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 3pvb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":400}' # _entry.id 3PVB # _exptl.entry_id 3PVB _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 3PVB _cell.length_a 116.667 _cell.length_b 116.667 _cell.length_c 140.103 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3PVB _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _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 covale ? covale1 A C GLY 4 A GLY 9 1_555 A N SEP 5 A SEP 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale2 A C SEP 5 A SEP 10 1_555 A N GLU 6 A GLU 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale3 A C PHE 133 A PHE 138 1_555 A N SEP 134 A SEP 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale4 A C SEP 134 A SEP 139 1_555 A N GLU 135 A GLU 140 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale5 A C TRP 191 A TRP 196 1_555 A N TPO 192 A TPO 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale6 A C TPO 192 A TPO 197 1_555 A N LEU 193 A LEU 198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale7 A C VAL 332 A VAL 337 1_555 A N SEP 333 A SEP 338 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale8 A C SEP 333 A SEP 338 1_555 A N ILE 334 A ILE 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? metalc ? metalc1 A OD1 ASN 166 A ASN 171 1_555 D MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.769 ? metalc ? metalc2 A OD1 ASP 179 A ASP 184 1_555 E MN MN . A MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.224 ? metalc ? metalc3 A OD2 ASP 179 A ASP 184 1_555 E MN MN . A MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.613 ? metalc ? metalc4 C N3B ANP . A ANP 400 1_555 D MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? metalc ? metalc5 C O2A ANP . A ANP 400 1_555 D MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.201 ? metalc ? metalc6 C O2G ANP . A ANP 400 1_555 D MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.488 ? metalc ? metalc7 C O1G ANP . A ANP 400 1_555 E MN MN . A MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? # _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 3PVB _atom_sites.fract_transf_matrix[1][1] 0.008571 _atom_sites.fract_transf_matrix[1][2] 0.004949 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009897 _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] 0.007138 _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 3 ANP A 1 400 400 ANP ANP . D 4 MN A 1 401 401 MN MN . E 4 MN A 1 402 402 MN MN . F 5 GOL B 1 1 1 GOL GOL . G 6 HOH A 1 2 2 HOH WAT . G 6 HOH A 2 3 3 HOH WAT . G 6 HOH A 3 4 4 HOH WAT . G 6 HOH A 4 5 5 HOH WAT . G 6 HOH A 5 351 6 HOH WAT . G 6 HOH A 6 352 7 HOH WAT . G 6 HOH A 7 353 8 HOH WAT . G 6 HOH A 8 354 9 HOH WAT . G 6 HOH A 9 355 10 HOH WAT . G 6 HOH A 10 356 11 HOH WAT . G 6 HOH A 11 357 12 HOH WAT . G 6 HOH A 12 358 13 HOH WAT . G 6 HOH A 13 359 15 HOH WAT . H 6 HOH B 1 14 14 HOH WAT . H 6 HOH B 2 16 16 HOH WAT . # 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 3 73.609 37.611 29.496 1 31.87 ? PG ANP 400 A 1 HETATM 2 O O1G ANP . . . C 3 72.219 37.412 30.094 1 33.05 ? O1G ANP 400 A 1 HETATM 3 O O2G ANP . . . C 3 73.845 39.077 29.17 1 30.76 ? O2G ANP 400 A 1 HETATM 4 O O3G ANP . . . C 3 74.659 37.161 30.499 1 31.65 ? O3G ANP 400 A 1 HETATM 5 P PB ANP . . . C 3 73.359 35.202 28.346 1 28.63 ? PB ANP 400 A 1 HETATM 6 O O1B ANP . . . C 3 73.593 34.77 29.753 1 28.12 ? O1B ANP 400 A 1 HETATM 7 O O2B ANP . . . C 3 71.943 34.944 27.986 1 31.31 ? O2B ANP 400 A 1 HETATM 8 N N3B ANP . . . C 3 73.712 36.767 28.134 1 29.65 ? N3B ANP 400 A 1 HETATM 9 P PA ANP . . . C 3 74.265 34.891 25.854 1 25.61 ? PA ANP 400 A 1 HETATM 10 O O1A ANP . . . C 3 72.945 34.662 25.222 1 23.54 ? O1A ANP 400 A 1 HETATM 11 O O2A ANP . . . C 3 74.583 36.342 25.778 1 25.51 ? O2A ANP 400 A 1 HETATM 12 O O3A ANP . . . C 3 74.33 34.383 27.392 1 26.84 ? O3A ANP 400 A 1 HETATM 13 O O5' ANP . . . C 3 75.348 34.046 25.072 1 24.51 ? O5' ANP 400 A 1 HETATM 14 C C5' ANP . . . C 3 76.704 34.086 25.532 1 23.73 ? C5' ANP 400 A 1 HETATM 15 C C4' ANP . . . C 3 77.616 34.68 24.488 1 23.2 ? C4' ANP 400 A 1 HETATM 16 O O4' ANP . . . C 3 77.742 33.768 23.372 1 24.71 ? O4' ANP 400 A 1 HETATM 17 C C3' ANP . . . C 3 77.199 36.002 23.87 1 22.09 ? C3' ANP 400 A 1 HETATM 18 O O3' ANP . . . C 3 77.579 37.084 24.719 1 17.44 ? O3' ANP 400 A 1 HETATM 19 C C2' ANP . . . C 3 77.964 35.994 22.548 1 22.38 ? C2' ANP 400 A 1 HETATM 20 O O2' ANP . . . C 3 79.306 36.405 22.724 1 21.84 ? O2' ANP 400 A 1 HETATM 21 C C1' ANP . . . C 3 77.955 34.503 22.182 1 25.08 ? C1' ANP 400 A 1 HETATM 22 N N9 ANP . . . C 3 76.98 34.043 21.186 1 29.09 ? N9 ANP 400 A 1 HETATM 23 C C8 ANP . . . C 3 75.658 33.725 21.394 1 30.19 ? C8 ANP 400 A 1 HETATM 24 N N7 ANP . . . C 3 75.043 33.288 20.325 1 31.62 ? N7 ANP 400 A 1 HETATM 25 C C5 ANP . . . C 3 76.014 33.337 19.337 1 32.02 ? C5 ANP 400 A 1 HETATM 26 C C6 ANP . . . C 3 75.985 33.016 17.969 1 32.75 ? C6 ANP 400 A 1 HETATM 27 N N6 ANP . . . C 3 74.889 32.589 17.33 1 33.48 ? N6 ANP 400 A 1 HETATM 28 N N1 ANP . . . C 3 77.13 33.154 17.267 1 33.02 ? N1 ANP 400 A 1 HETATM 29 C C2 ANP . . . C 3 78.212 33.602 17.897 1 31.21 ? C2 ANP 400 A 1 HETATM 30 N N3 ANP . . . C 3 78.361 33.96 19.17 1 32 ? N3 ANP 400 A 1 HETATM 31 C C4 ANP . . . C 3 77.212 33.8 19.849 1 31.15 ? C4 ANP 400 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 311 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #