data_3R8F # _model_server_result.job_id JWNW1CpMn3ttlToRXPgKtg _model_server_result.datetime_utc '2025-01-23 00:10:27' _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 3r8f # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":700}' # _entry.id 3R8F # _exptl.entry_id 3R8F _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 4 _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 3R8F _cell.length_a 99.797 _cell.length_b 114.219 _cell.length_c 201.266 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3R8F _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _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,K,L,M,N,O,P,Q,R _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 ? 4 G N N ? 4 I N N ? 4 K N N ? 4 M 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 51 A THR 126 1_555 F MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.501 ? metalc ? metalc2 F MG MG . A MG 401 1_555 G O3G ACP . A ACP 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? metalc ? metalc3 F MG MG . A MG 401 1_555 G O2B ACP . A ACP 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.73 ? metalc ? metalc4 B OG1 THR 51 B THR 126 1_555 H MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.501 ? metalc ? metalc5 H MG MG . B MG 401 1_555 I O1G ACP . B ACP 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? metalc ? metalc6 H MG MG . B MG 401 1_555 I O1B ACP . B ACP 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.514 ? metalc ? metalc7 C OG1 THR 51 C THR 126 1_555 J MG MG . C MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.501 ? metalc ? metalc8 J MG MG . C MG 401 1_555 K O3G ACP . C ACP 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? metalc ? metalc9 J MG MG . C MG 401 1_555 K O1B ACP . C ACP 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.473 ? metalc ? metalc10 D OG1 THR 51 D THR 126 1_555 L MG MG . D MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.5 ? metalc ? metalc11 L MG MG . D MG 401 1_555 M O3G ACP . D ACP 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.792 ? metalc ? metalc12 L MG MG . D MG 401 1_555 M O1B ACP . D ACP 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.605 ? # _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 3R8F _atom_sites.fract_transf_matrix[1][1] 0.01002 _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] 0.008755 _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] 0.004969 _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 F 3 MG A 1 401 401 MG MG . G 4 ACP A 1 700 700 ACP ABG . H 3 MG B 1 401 401 MG MG . I 4 ACP B 1 700 700 ACP ABG . J 3 MG C 1 401 401 MG MG . K 4 ACP C 1 700 700 ACP ABG . L 3 MG D 1 401 401 MG MG . M 4 ACP D 1 700 700 ACP ABG . N 5 HOH A 1 1 1 HOH HOH . N 5 HOH A 2 2 2 HOH HOH . N 5 HOH A 3 3 3 HOH HOH . N 5 HOH A 4 4 4 HOH HOH . O 5 HOH B 1 6 6 HOH HOH . O 5 HOH B 2 7 7 HOH HOH . O 5 HOH B 3 8 8 HOH HOH . O 5 HOH B 4 9 9 HOH HOH . O 5 HOH B 5 10 10 HOH HOH . P 5 HOH C 1 12 12 HOH HOH . P 5 HOH C 2 13 13 HOH HOH . P 5 HOH C 3 14 14 HOH HOH . P 5 HOH C 4 15 15 HOH HOH . P 5 HOH C 5 16 16 HOH HOH . P 5 HOH C 6 17 17 HOH HOH . Q 5 HOH D 1 5 5 HOH HOH . Q 5 HOH D 2 18 18 HOH HOH . Q 5 HOH D 3 19 19 HOH HOH . Q 5 HOH D 4 20 20 HOH HOH . Q 5 HOH D 5 21 21 HOH HOH . Q 5 HOH D 6 22 22 HOH HOH . R 5 HOH E 1 13 11 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 . . . M 4 -17.816 14.658 80.31 1 74.65 ? PG ACP 700 D 1 HETATM 2 O O1G ACP . . . M 4 -18.884 14.083 79.433 1 93.11 ? O1G ACP 700 D 1 HETATM 3 O O2G ACP . . . M 4 -16.523 13.948 80.053 1 72.92 ? O2G ACP 700 D 1 HETATM 4 O O3G ACP . . . M 4 -17.654 16.114 80.008 1 62.53 ? O3G ACP 700 D 1 HETATM 5 P PB ACP . . . M 4 -19.112 15.965 82.655 1 55.17 ? PB ACP 700 D 1 HETATM 6 O O1B ACP . . . M 4 -18.835 17.105 81.726 1 43.19 ? O1B ACP 700 D 1 HETATM 7 O O2B ACP . . . M 4 -18.639 16.309 84.033 1 52.49 ? O2B ACP 700 D 1 HETATM 8 C C3B ACP . . . M 4 -18.288 14.448 82.061 1 73.91 ? C3B ACP 700 D 1 HETATM 9 P PA ACP . . . M 4 -21.629 16.656 83.313 1 55.15 ? PA ACP 700 D 1 HETATM 10 O O1A ACP . . . M 4 -22.253 17.51 82.254 1 54.65 ? O1A ACP 700 D 1 HETATM 11 O O2A ACP . . . M 4 -20.918 17.52 84.308 1 43.13 ? O2A ACP 700 D 1 HETATM 12 O O3A ACP . . . M 4 -20.636 15.64 82.673 1 59.54 ? O3A ACP 700 D 1 HETATM 13 O O5' ACP . . . M 4 -22.716 15.795 84.024 1 68.24 ? O5' ACP 700 D 1 HETATM 14 C C5' ACP . . . M 4 -23.645 15.116 83.266 1 80.15 ? C5' ACP 700 D 1 HETATM 15 C C4' ACP . . . M 4 -25.012 15.392 83.793 1 84.76 ? C4' ACP 700 D 1 HETATM 16 O O4' ACP . . . M 4 -25.131 14.892 85.081 1 88.44 ? O4' ACP 700 D 1 HETATM 17 C C3' ACP . . . M 4 -25.255 16.855 83.82 1 72.98 ? C3' ACP 700 D 1 HETATM 18 O O3' ACP . . . M 4 -26.359 17.174 83.063 1 80.37 ? O3' ACP 700 D 1 HETATM 19 C C2' ACP . . . M 4 -25.487 17.19 85.233 1 68.73 ? C2' ACP 700 D 1 HETATM 20 O O2' ACP . . . M 4 -26.658 17.897 85.374 1 69.97 ? O2' ACP 700 D 1 HETATM 21 C C1' ACP . . . M 4 -25.578 15.887 85.935 1 80.73 ? C1' ACP 700 D 1 HETATM 22 N N9 ACP . . . M 4 -24.773 15.915 87.117 1 76.57 ? N9 ACP 700 D 1 HETATM 23 C C8 ACP . . . M 4 -23.549 15.306 87.277 1 73.94 ? C8 ACP 700 D 1 HETATM 24 N N7 ACP . . . M 4 -23.093 15.553 88.524 1 72.72 ? N7 ACP 700 D 1 HETATM 25 C C5 ACP . . . M 4 -24.044 16.339 89.187 1 74.9 ? C5 ACP 700 D 1 HETATM 26 C C6 ACP . . . M 4 -24.094 16.877 90.467 1 77.43 ? C6 ACP 700 D 1 HETATM 27 N N6 ACP . . . M 4 -23.014 16.644 91.373 1 77.52 ? N6 ACP 700 D 1 HETATM 28 N N1 ACP . . . M 4 -25.153 17.618 90.867 1 82.2 ? N1 ACP 700 D 1 HETATM 29 C C2 ACP . . . M 4 -26.158 17.82 89.986 1 83.94 ? C2 ACP 700 D 1 HETATM 30 N N3 ACP . . . M 4 -26.126 17.307 88.745 1 81.43 ? N3 ACP 700 D 1 HETATM 31 C C4 ACP . . . M 4 -25.109 16.569 88.295 1 77.24 ? C4 ACP 700 D 1 # _model_server_stats.io_time_ms 25 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 39 _model_server_stats.query_time_ms 321 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #