data_1XR1 # _model_server_result.job_id tC2leYyOUg5OFkM9mtMTsw _model_server_result.datetime_utc '2024-12-02 22:42:25' _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 1xr1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":501}' # _entry.id 1XR1 # _exptl.entry_id 1XR1 _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 1XR1 _cell.length_a 96.68 _cell.length_b 96.68 _cell.length_c 80.02 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1XR1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _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 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 OD1 ASN 159 A ASN 172 1_555 B MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.688 ? metalc ? metalc2 A OD2 ASP 173 A ASP 186 1_555 B MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.608 ? metalc ? metalc3 A OD2 ASP 173 A ASP 186 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.867 ? metalc ? metalc4 A OD1 ASP 173 A ASP 186 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.802 ? metalc ? metalc5 B MG MG . A MG 401 1_555 D O2A ANP . A ANP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? metalc ? metalc6 B MG MG . A MG 401 1_555 D O1G ANP . A ANP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc7 C MG MG . A MG 402 1_555 D O2B ANP . A ANP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? # _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 1XR1 _atom_sites.fract_transf_matrix[1][1] 0.010343 _atom_sites.fract_transf_matrix[1][2] 0.005972 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011944 _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] 0.012497 _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 MG A 1 401 1 MG MG2 . C 2 MG A 1 402 2 MG MG2 . D 3 ANP A 1 501 1 ANP ANP . E 4 HOH A 1 502 1 HOH HOH . E 4 HOH A 2 503 2 HOH HOH . E 4 HOH A 3 504 3 HOH HOH . E 4 HOH A 4 505 4 HOH HOH . E 4 HOH A 5 506 5 HOH HOH . E 4 HOH A 6 507 6 HOH HOH . E 4 HOH A 7 508 7 HOH HOH . E 4 HOH A 8 509 8 HOH HOH . E 4 HOH A 9 510 9 HOH HOH . E 4 HOH A 10 511 10 HOH HOH . E 4 HOH A 11 512 11 HOH HOH . E 4 HOH A 12 513 12 HOH HOH . E 4 HOH A 13 514 13 HOH HOH . E 4 HOH A 14 515 14 HOH HOH . E 4 HOH A 15 516 15 HOH HOH . E 4 HOH A 16 517 16 HOH HOH . E 4 HOH A 17 518 17 HOH HOH . E 4 HOH A 18 519 18 HOH HOH . E 4 HOH A 19 520 19 HOH HOH . E 4 HOH A 20 521 20 HOH HOH . E 4 HOH A 21 522 21 HOH HOH . E 4 HOH A 22 523 22 HOH HOH . E 4 HOH A 23 524 23 HOH HOH . E 4 HOH A 24 525 24 HOH HOH . E 4 HOH A 25 526 25 HOH HOH . E 4 HOH A 26 527 26 HOH HOH . E 4 HOH A 27 528 27 HOH HOH . E 4 HOH A 28 529 28 HOH HOH . E 4 HOH A 29 530 29 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 77.235 27.632 4.271 1 43.67 ? PG ANP 501 A 1 HETATM 2 O O1G ANP . . . D 3 76.032 27.056 3.446 1 44.22 ? O1G ANP 501 A 1 HETATM 3 O O2G ANP . . . D 3 78.025 26.404 4.805 1 42.32 ? O2G ANP 501 A 1 HETATM 4 O O3G ANP . . . D 3 76.69 28.421 5.504 1 44.15 ? O3G ANP 501 A 1 HETATM 5 P PB ANP . . . D 3 78.304 28.555 1.683 1 38.3 ? PB ANP 501 A 1 HETATM 6 O O1B ANP . . . D 3 79.791 28.556 1.225 1 40.7 ? O1B ANP 501 A 1 HETATM 7 O O2B ANP . . . D 3 77.588 27.307 1.071 1 39.59 ? O2B ANP 501 A 1 HETATM 8 N N3B ANP . . . D 3 78.245 28.574 3.342 1 41.25 ? N3B ANP 501 A 1 HETATM 9 P PA ANP . . . D 3 76.265 30.414 1.028 1 35.07 ? PA ANP 501 A 1 HETATM 10 O O1A ANP . . . D 3 75.589 30.497 -0.357 1 35.94 ? O1A ANP 501 A 1 HETATM 11 O O2A ANP . . . D 3 75.456 29.462 1.915 1 33.79 ? O2A ANP 501 A 1 HETATM 12 O O3A ANP . . . D 3 77.687 29.832 0.998 1 38.22 ? O3A ANP 501 A 1 HETATM 13 O O5' ANP . . . D 3 76.09 31.785 1.679 1 35.19 ? O5' ANP 501 A 1 HETATM 14 C C5' ANP . . . D 3 76.759 32.034 2.956 1 32.26 ? C5' ANP 501 A 1 HETATM 15 C C4' ANP . . . D 3 76.252 33.318 3.62 1 32.1 ? C4' ANP 501 A 1 HETATM 16 O O4' ANP . . . D 3 76.589 34.495 2.857 1 31.57 ? O4' ANP 501 A 1 HETATM 17 C C3' ANP . . . D 3 74.739 33.319 3.782 1 30.81 ? C3' ANP 501 A 1 HETATM 18 O O3' ANP . . . D 3 74.238 32.726 4.99 1 35.27 ? O3' ANP 501 A 1 HETATM 19 C C2' ANP . . . D 3 74.378 34.787 3.627 1 30.44 ? C2' ANP 501 A 1 HETATM 20 O O2' ANP . . . D 3 74.384 35.416 4.934 1 29.38 ? O2' ANP 501 A 1 HETATM 21 C C1' ANP . . . D 3 75.477 35.405 2.765 1 28.92 ? C1' ANP 501 A 1 HETATM 22 N N9 ANP . . . D 3 75.078 35.594 1.332 1 25.84 ? N9 ANP 501 A 1 HETATM 23 C C8 ANP . . . D 3 75.26 34.672 0.331 1 23.27 ? C8 ANP 501 A 1 HETATM 24 N N7 ANP . . . D 3 74.795 35.161 -0.843 1 25.09 ? N7 ANP 501 A 1 HETATM 25 C C5 ANP . . . D 3 74.302 36.416 -0.607 1 23.33 ? C5 ANP 501 A 1 HETATM 26 C C6 ANP . . . D 3 73.719 37.41 -1.348 1 23.28 ? C6 ANP 501 A 1 HETATM 27 N N6 ANP . . . D 3 73.509 37.246 -2.665 1 22.81 ? N6 ANP 501 A 1 HETATM 28 N N1 ANP . . . D 3 73.339 38.579 -0.773 1 24.54 ? N1 ANP 501 A 1 HETATM 29 C C2 ANP . . . D 3 73.519 38.815 0.544 1 26.17 ? C2 ANP 501 A 1 HETATM 30 N N3 ANP . . . D 3 74.093 37.885 1.364 1 24.27 ? N3 ANP 501 A 1 HETATM 31 C C4 ANP . . . D 3 74.473 36.709 0.761 1 24.46 ? C4 ANP 501 A 1 # _model_server_stats.io_time_ms 68 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 260 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 31 #