data_5IUM # _model_server_result.job_id VaPd3IKOQZXJBPwbxiLPhQ _model_server_result.datetime_utc '2025-07-31 04:41:56' _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 5ium # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":401}' # _entry.id 5IUM # _exptl.entry_id 5IUM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 2 _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 90 _cell.angle_gamma 120 _cell.entry_id 5IUM _cell.length_a 94.443 _cell.length_b 94.443 _cell.length_c 161.848 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5IUM _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 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,I _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 ? 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 covale ? covale1 A C LEU 35 A LEU 187 1_555 A N NEP 36 A NEP 188 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.315 ? covale ? covale2 A C NEP 36 A NEP 188 1_555 A N ASP 37 A ASP 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.318 ? covale ? covale3 B C LEU 35 B LEU 187 1_555 B N NEP 36 B NEP 188 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.342 ? covale ? covale4 B C NEP 36 B NEP 188 1_555 B N ASP 37 B ASP 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? metalc ? metalc1 A OE2 GLU 137 A GLU 289 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? metalc ? metalc2 A OD1 ASN 141 A ASN 293 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc3 C O3G ACP . A ACP 401 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? metalc ? metalc4 C O1B ACP . A ACP 401 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? metalc ? metalc5 C O1A ACP . A ACP 401 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.117 ? metalc ? metalc6 D MG MG . A MG 402 1_555 H O HOH . A HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.151 ? metalc ? metalc7 B OE2 GLU 137 B GLU 289 1_555 F MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? metalc ? metalc8 B OD1 ASN 141 B ASN 293 1_555 F MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.111 ? metalc ? metalc9 E O3G ACP . B ACP 401 1_555 F MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? metalc ? metalc10 E O1B ACP . B ACP 401 1_555 F MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? metalc ? metalc11 E O1A ACP . B ACP 401 1_555 F MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? metalc ? metalc12 F MG MG . B MG 402 1_555 I O HOH . B HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.121 ? # _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 5IUM _atom_sites.fract_transf_matrix[1][1] 0.010588 _atom_sites.fract_transf_matrix[1][2] 0.006113 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012226 _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] 0.006179 _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 ACP A 1 401 1303 ACP ACP . D 3 MG A 1 402 1 MG MG . E 2 ACP B 1 401 1303 ACP ACP . F 3 MG B 1 402 1 MG MG . G 4 GOL B 1 403 1 GOL GOL . H 5 HOH A 1 501 2 HOH HOH . H 5 HOH A 2 502 9 HOH HOH . I 5 HOH B 1 501 8 HOH HOH . I 5 HOH B 2 502 3 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 2 -80.105 113.946 40.099 1 162.58 ? PG ACP 401 B 1 HETATM 2 O O1G ACP . . . E 2 -80.413 113.541 38.643 1 162.05 ? O1G ACP 401 B 1 HETATM 3 O O2G ACP . . . E 2 -81.275 114.587 40.765 1 160.31 ? O2G ACP 401 B 1 HETATM 4 O O3G ACP . . . E 2 -79.593 112.689 40.837 1 160.68 ? O3G ACP 401 B 1 HETATM 5 P PB ACP . . . E 2 -77.126 114.379 40.538 1 174.97 ? PB ACP 401 B 1 HETATM 6 O O1B ACP . . . E 2 -76.888 113.159 39.595 1 175.77 ? O1B ACP 401 B 1 HETATM 7 O O2B ACP . . . E 2 -75.93 115.308 40.481 1 176.26 ? O2B ACP 401 B 1 HETATM 8 C C3B ACP . . . E 2 -78.703 115.064 40.018 1 168.79 ? C3B ACP 401 B 1 HETATM 9 P PA ACP . . . E 2 -76.836 112.389 42.655 1 179.65 ? PA ACP 401 B 1 HETATM 10 O O1A ACP . . . E 2 -77.236 111.266 41.78 1 178.83 ? O1A ACP 401 B 1 HETATM 11 O O2A ACP . . . E 2 -77.485 112.213 44.03 1 180.25 ? O2A ACP 401 B 1 HETATM 12 O O3A ACP . . . E 2 -77.323 113.764 42.007 1 176.85 ? O3A ACP 401 B 1 HETATM 13 O O5' ACP . . . E 2 -75.241 112.41 42.901 1 181.72 ? O5' ACP 401 B 1 HETATM 14 C C5' ACP . . . E 2 -74.647 113.359 43.816 1 183.41 ? C5' ACP 401 B 1 HETATM 15 C C4' ACP . . . E 2 -73.248 113.717 43.378 1 184.23 ? C4' ACP 401 B 1 HETATM 16 O O4' ACP . . . E 2 -72.376 112.575 43.526 1 184.39 ? O4' ACP 401 B 1 HETATM 17 C C3' ACP . . . E 2 -73.106 114.139 41.921 1 184.61 ? C3' ACP 401 B 1 HETATM 18 O O3' ACP . . . E 2 -73.407 115.522 41.757 1 184 ? O3' ACP 401 B 1 HETATM 19 C C2' ACP . . . E 2 -71.644 113.801 41.621 1 185.17 ? C2' ACP 401 B 1 HETATM 20 O O2' ACP . . . E 2 -70.78 114.861 42.015 1 185.88 ? O2' ACP 401 B 1 HETATM 21 C C1' ACP . . . E 2 -71.416 112.552 42.482 1 184.52 ? C1' ACP 401 B 1 HETATM 22 N N9 ACP . . . E 2 -71.52 111.278 41.766 1 184.28 ? N9 ACP 401 B 1 HETATM 23 C C8 ACP . . . E 2 -72.585 110.414 41.777 1 184.19 ? C8 ACP 401 B 1 HETATM 24 N N7 ACP . . . E 2 -72.388 109.311 41.096 1 184.12 ? N7 ACP 401 B 1 HETATM 25 C C5 ACP . . . E 2 -71.104 109.459 40.594 1 183.76 ? C5 ACP 401 B 1 HETATM 26 C C6 ACP . . . E 2 -70.29 108.62 39.802 1 182.88 ? C6 ACP 401 B 1 HETATM 27 N N6 ACP . . . E 2 -70.68 107.433 39.329 1 182.27 ? N6 ACP 401 B 1 HETATM 28 N N1 ACP . . . E 2 -69.044 109.051 39.503 1 182.97 ? N1 ACP 401 B 1 HETATM 29 C C2 ACP . . . E 2 -68.65 110.247 39.957 1 183.5 ? C2 ACP 401 B 1 HETATM 30 N N3 ACP . . . E 2 -69.329 111.128 40.704 1 183.91 ? N3 ACP 401 B 1 HETATM 31 C C4 ACP . . . E 2 -70.556 110.67 40.996 1 184.06 ? C4 ACP 401 B 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 285 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 31 #