data_1U54 # _model_server_result.job_id DoXVL-RwcLIFdM1tw_Gypw _model_server_result.datetime_utc '2024-12-02 17:02:36' _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 1u54 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":101}' # _entry.id 1U54 # _exptl.entry_id 1U54 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOMETHYLPHOSPHONIC 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 96.28 _cell.angle_gamma 90 _cell.entry_id 1U54 _cell.length_a 200.384 _cell.length_b 42.332 _cell.length_c 70.848 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1U54 _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 ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,I 1 1 B,F,G,H,J 2 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 ? 4 E N N ? 4 H 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 covale ? covale1 A C HIS 177 A HIS 283 1_555 A N PTR 178 A PTR 284 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale2 A C PTR 178 A PTR 284 1_555 A N VAL 179 A VAL 285 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? metalc ? metalc1 E O2G ACP . A ACP 101 1_555 C MG MG . A MG 398 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? metalc ? metalc2 E O2B ACP . A ACP 101 1_555 C MG MG . A MG 398 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.439 ? metalc ? metalc3 E O1G ACP . A ACP 101 1_555 D MG MG . A MG 399 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.546 ? metalc ? metalc4 E O2G ACP . A ACP 101 1_555 D MG MG . A MG 399 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.533 ? metalc ? metalc5 E O3A ACP . A ACP 101 1_555 D MG MG . A MG 399 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.332 ? metalc ? metalc6 E O2A ACP . A ACP 101 1_555 D MG MG . A MG 399 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.644 ? metalc ? metalc7 A ND2 ASN 151 A ASN 257 1_555 D MG MG . A MG 399 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.909 ? metalc ? metalc8 A OD1 ASP 164 A ASP 270 1_555 C MG MG . A MG 398 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.421 ? metalc ? metalc9 A OD2 ASP 164 A ASP 270 1_555 C MG MG . A MG 398 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.095 ? metalc ? metalc10 A OD1 ASP 164 A ASP 270 1_555 D MG MG . A MG 399 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.357 ? metalc ? metalc11 C MG MG . A MG 398 1_555 D MG MG . A MG 399 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.962 ? metalc ? metalc12 B OD1 ASN 151 B ASN 257 1_555 G MG MG . B MG 399 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.491 ? metalc ? metalc13 B OD2 ASP 164 B ASP 270 1_555 F MG MG . B MG 398 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.653 ? metalc ? metalc14 B OD1 ASP 164 B ASP 270 1_555 F MG MG . B MG 398 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.597 ? metalc ? metalc15 B OD1 ASP 164 B ASP 270 1_555 G MG MG . B MG 399 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.485 ? metalc ? metalc16 F MG MG . B MG 398 1_555 H O1G ACP . B ACP 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.899 ? metalc ? metalc17 F MG MG . B MG 398 1_555 H O2B ACP . B ACP 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.977 ? metalc ? metalc18 G MG MG . B MG 399 1_555 H O3G ACP . B ACP 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.907 ? metalc ? metalc19 G MG MG . B MG 399 1_555 H O2A ACP . B ACP 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.565 ? metalc ? metalc20 G MG MG . B MG 399 1_555 H O1G ACP . B ACP 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.717 ? # _chem_comp.formula 'C11 H18 N5 O12 P3' _chem_comp.formula_weight 505.208 _chem_comp.id ACP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE" # 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 ACP doub 1 n n PG O2G ACP sing 2 n n PG O3G ACP sing 3 n n PG C3B ACP sing 4 n n O2G HOG2 ACP sing 5 n n O3G HOG3 ACP sing 6 n n PB O1B ACP doub 7 n n PB O2B ACP sing 8 n n PB C3B ACP sing 9 n n PB O3A ACP sing 10 n n O2B HOB2 ACP sing 11 n n C3B H3B1 ACP sing 12 n n C3B H3B2 ACP sing 13 n n PA O1A ACP doub 14 n n PA O2A ACP sing 15 n n PA O3A ACP sing 16 n n PA O5' ACP sing 17 n n O2A HOA2 ACP sing 18 n n O5' C5' ACP sing 19 n n C5' C4' ACP sing 20 n n C5' "H5'1" ACP sing 21 n n C5' "H5'2" ACP sing 22 n n C4' O4' ACP sing 23 n n C4' C3' ACP sing 24 n n C4' H4' ACP sing 25 n n O4' C1' ACP sing 26 n n C3' O3' ACP sing 27 n n C3' C2' ACP sing 28 n n C3' H3' ACP sing 29 n n O3' HO3' ACP sing 30 n n C2' O2' ACP sing 31 n n C2' C1' ACP sing 32 n n C2' H2' ACP sing 33 n n O2' HO2' ACP sing 34 n n C1' N9 ACP sing 35 n n C1' H1' ACP sing 36 n n N9 C8 ACP sing 37 n y N9 C4 ACP sing 38 n y C8 N7 ACP doub 39 n y C8 H8 ACP sing 40 n n N7 C5 ACP sing 41 n y C5 C6 ACP sing 42 n y C5 C4 ACP doub 43 n y C6 N6 ACP sing 44 n n C6 N1 ACP doub 45 n y N6 HN61 ACP sing 46 n n N6 HN62 ACP sing 47 n n N1 C2 ACP sing 48 n y C2 N3 ACP doub 49 n y C2 H2 ACP sing 50 n n N3 C4 ACP sing 51 n y # _atom_sites.entry_id 1U54 _atom_sites.fract_transf_matrix[1][1] 0.00499 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000549 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.023623 _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] 0.0142 _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 MG A 1 398 1 MG MG . D 3 MG A 1 399 2 MG MG . E 4 ACP A 1 101 1 ACP ACP . F 3 MG B 1 398 3 MG MG . G 3 MG B 1 399 4 MG MG . H 4 ACP B 1 400 1 ACP ACP . I 5 HOH A 1 5 5 HOH HOH . I 5 HOH A 2 6 6 HOH HOH . I 5 HOH A 3 10 10 HOH HOH . I 5 HOH A 4 11 11 HOH HOH . I 5 HOH A 5 12 12 HOH HOH . I 5 HOH A 6 13 13 HOH HOH . J 5 HOH B 1 1 1 HOH HOH . J 5 HOH B 2 7 7 HOH HOH . J 5 HOH B 3 8 8 HOH HOH . J 5 HOH B 4 9 9 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 ACP . . . E 4 30.04 14.372 61.856 1 56.85 ? PG ACP 101 A 1 HETATM 2 O O1G ACP . . . E 4 30.067 15.939 61.743 1 43.54 ? O1G ACP 101 A 1 HETATM 3 O O2G ACP . . . E 4 29.628 13.555 60.573 1 49.78 ? O2G ACP 101 A 1 HETATM 4 O O3G ACP . . . E 4 29.412 13.817 63.153 1 48.96 ? O3G ACP 101 A 1 HETATM 5 P PB ACP . . . E 4 32.57 15.529 61 1 56.14 ? PB ACP 101 A 1 HETATM 6 O O1B ACP . . . E 4 33.164 16.62 61.922 1 57.44 ? O1B ACP 101 A 1 HETATM 7 O O2B ACP . . . E 4 33.269 14.768 59.832 1 51.52 ? O2B ACP 101 A 1 HETATM 8 C C3B ACP . . . E 4 31.888 14.145 62.031 1 53.13 ? C3B ACP 101 A 1 HETATM 9 P PA ACP . . . E 4 31.815 17.71 59.283 1 54.36 ? PA ACP 101 A 1 HETATM 10 O O1A ACP . . . E 4 32.912 17.327 58.303 1 51.48 ? O1A ACP 101 A 1 HETATM 11 O O2A ACP . . . E 4 30.477 18.119 58.624 1 56 ? O2A ACP 101 A 1 HETATM 12 O O3A ACP . . . E 4 31.438 16.541 60.381 1 50.28 ? O3A ACP 101 A 1 HETATM 13 O O5' ACP . . . E 4 32.292 19.018 60.188 1 53.46 ? O5' ACP 101 A 1 HETATM 14 C C5' ACP . . . E 4 31.377 19.676 61.104 1 50.64 ? C5' ACP 101 A 1 HETATM 15 C C4' ACP . . . E 4 31.203 21.221 60.829 1 51.55 ? C4' ACP 101 A 1 HETATM 16 O O4' ACP . . . E 4 32.384 22.05 60.575 1 49.82 ? O4' ACP 101 A 1 HETATM 17 C C3' ACP . . . E 4 30.242 21.448 59.656 1 50.44 ? C3' ACP 101 A 1 HETATM 18 O O3' ACP . . . E 4 29.009 21.961 60.133 1 51.18 ? O3' ACP 101 A 1 HETATM 19 C C2' ACP . . . E 4 30.871 22.495 58.767 1 51.93 ? C2' ACP 101 A 1 HETATM 20 O O2' ACP . . . E 4 30.062 23.654 58.583 1 55.11 ? O2' ACP 101 A 1 HETATM 21 C C1' ACP . . . E 4 32.216 22.877 59.39 1 51.78 ? C1' ACP 101 A 1 HETATM 22 N N9 ACP . . . E 4 32.991 22.567 58.149 1 53.73 ? N9 ACP 101 A 1 HETATM 23 C C8 ACP . . . E 4 33.402 21.311 57.681 1 55.75 ? C8 ACP 101 A 1 HETATM 24 N N7 ACP . . . E 4 34.06 21.398 56.429 1 53.91 ? N7 ACP 101 A 1 HETATM 25 C C5 ACP . . . E 4 34.041 22.687 56.089 1 50.88 ? C5 ACP 101 A 1 HETATM 26 C C6 ACP . . . E 4 34.472 23.498 54.961 1 51.39 ? C6 ACP 101 A 1 HETATM 27 N N6 ACP . . . E 4 35.113 22.921 53.922 1 51 ? N6 ACP 101 A 1 HETATM 28 N N1 ACP . . . E 4 34.19 24.827 54.988 1 52.75 ? N1 ACP 101 A 1 HETATM 29 C C2 ACP . . . E 4 33.567 25.438 56.028 1 54.27 ? C2 ACP 101 A 1 HETATM 30 N N3 ACP . . . E 4 33.116 24.788 57.133 1 52.96 ? N3 ACP 101 A 1 HETATM 31 C C4 ACP . . . E 4 33.339 23.391 57.172 1 51.6 ? C4 ACP 101 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 333 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 31 #