data_8P53 # _model_server_result.job_id Fi6bJty7G4GjaLJ1jtMTRA _model_server_result.datetime_utc '2024-11-13 07:18:04' _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 8p53 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":302}' # _entry.id 8P53 # _exptl.entry_id 8P53 _exptl.method 'ELECTRON MICROSCOPY' # _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 90 _cell.angle_gamma 90 _cell.entry_id 8P53 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8P53 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J _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 ? _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 H N N ? 4 J 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 A OG1 THR 52 A THR 25 1_555 G MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.943 ? metalc ? metalc2 G MG MG . A MG 301 1_555 H O3G ACP . A ACP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? metalc ? metalc3 G MG MG . A MG 301 1_555 H O1B ACP . A ACP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.883 ? metalc ? metalc4 B OG1 THR 52 B THR 25 1_555 I MG MG . B MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.998 ? metalc ? metalc5 I MG MG . B MG 301 1_555 J O2G ACP . B ACP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.36 ? metalc ? metalc6 I MG MG . B MG 301 1_555 J O1B ACP . B ACP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.412 ? # _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 8P53 _atom_sites.fract_transf_matrix[1][1] 1 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 1 _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] 1 _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 G 3 MG A 1 301 502 MG MG . H 4 ACP A 1 302 301 ACP ACP . I 3 MG B 1 301 303 MG MG . J 4 ACP B 1 302 301 ACP ACP . # 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 . . . J 4 185.649 188.884 218.901 1 47.61 ? PG ACP 302 B 1 HETATM 2 O O1G ACP . . . J 4 186.982 188.427 218.38 1 51.87 ? O1G ACP 302 B 1 HETATM 3 O O2G ACP . . . J 4 185.331 190.296 218.494 1 51.69 ? O2G ACP 302 B 1 HETATM 4 O O3G ACP . . . J 4 184.547 187.93 218.544 1 52.87 ? O3G ACP 302 B 1 HETATM 5 P PB ACP . . . J 4 187.27 189.705 221.308 1 35.23 ? PB ACP 302 B 1 HETATM 6 O O1B ACP . . . J 4 187.427 191.008 220.575 1 53.52 ? O1B ACP 302 B 1 HETATM 7 O O2B ACP . . . J 4 188.409 188.734 221.186 1 52.12 ? O2B ACP 302 B 1 HETATM 8 C C3B ACP . . . J 4 185.776 188.881 220.69 1 42.03 ? C3B ACP 302 B 1 HETATM 9 P PA ACP . . . J 4 186.586 191.389 223.572 1 39.11 ? PA ACP 302 B 1 HETATM 10 O O1A ACP . . . J 4 185.352 191.922 222.925 1 54.78 ? O1A ACP 302 B 1 HETATM 11 O O2A ACP . . . J 4 187.784 192.276 223.651 1 58.97 ? O2A ACP 302 B 1 HETATM 12 O O3A ACP . . . J 4 187.006 190.029 222.839 1 26.98 ? O3A ACP 302 B 1 HETATM 13 O O5' ACP . . . J 4 186.227 190.851 225.038 1 46.04 ? O5' ACP 302 B 1 HETATM 14 C C5' ACP . . . J 4 185.178 189.865 225.174 1 49.22 ? C5' ACP 302 B 1 HETATM 15 C C4' ACP . . . J 4 184.85 189.675 226.634 1 43.58 ? C4' ACP 302 B 1 HETATM 16 O O4' ACP . . . J 4 186.053 189.266 227.336 1 46.69 ? O4' ACP 302 B 1 HETATM 17 C C3' ACP . . . J 4 184.335 190.91 227.391 1 42.03 ? C3' ACP 302 B 1 HETATM 18 O O3' ACP . . . J 4 183.351 190.517 228.337 1 51.09 ? O3' ACP 302 B 1 HETATM 19 C C2' ACP . . . J 4 185.579 191.356 228.16 1 50.17 ? C2' ACP 302 B 1 HETATM 20 O O2' ACP . . . J 4 185.321 192.179 229.277 1 59.31 ? O2' ACP 302 B 1 HETATM 21 C C1' ACP . . . J 4 186.142 189.994 228.536 1 45.32 ? C1' ACP 302 B 1 HETATM 22 N N9 ACP . . . J 4 187.539 190.037 228.946 1 44.92 ? N9 ACP 302 B 1 HETATM 23 C C8 ACP . . . J 4 188.635 190.064 228.122 1 46.98 ? C8 ACP 302 B 1 HETATM 24 N N7 ACP . . . J 4 189.77 190.098 228.77 1 43.11 ? N7 ACP 302 B 1 HETATM 25 C C5 ACP . . . J 4 189.403 190.094 230.107 1 39.07 ? C5 ACP 302 B 1 HETATM 26 C C6 ACP . . . J 4 190.156 190.122 231.294 1 44.75 ? C6 ACP 302 B 1 HETATM 27 N N6 ACP . . . J 4 191.484 190.158 231.327 1 48.76 ? N6 ACP 302 B 1 HETATM 28 N N1 ACP . . . J 4 189.476 190.108 232.464 1 48.68 ? N1 ACP 302 B 1 HETATM 29 C C2 ACP . . . J 4 188.14 190.07 232.426 1 45.4 ? C2 ACP 302 B 1 HETATM 30 N N3 ACP . . . J 4 187.33 190.042 231.373 1 44.69 ? N3 ACP 302 B 1 HETATM 31 C C4 ACP . . . J 4 188.029 190.054 230.228 1 39.99 ? C4 ACP 302 B 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 36 _model_server_stats.query_time_ms 269 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #