data_5OF3 # _model_server_result.job_id UuBdhwb4ThH16zXPQFIstg _model_server_result.datetime_utc '2025-02-05 09:53:34' _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 5of3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":1001}' # _entry.id 5OF3 # _exptl.entry_id 5OF3 _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 'DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL 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 5OF3 _cell.length_a 104.889 _cell.length_b 104.889 _cell.length_c 229.758 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5OF3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 76 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details software_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 _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 J N N ? 4 M N N ? 4 O 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 disulf ? disulf1 B SG CYS 120 B CYS 120 1_555 B SG CYS 139 B CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf2 C SG CYS 108 D CYS 108 1_555 C SG CYS 145 D CYS 145 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf3 C SG CYS 184 D CYS 184 1_555 C SG CYS 188 D CYS 188 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf4 D SG CYS 120 E CYS 120 1_555 D SG CYS 139 E CYS 139 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.032 ? metalc ? metalc1 A OD1 ASP 101 A ASP 101 1_555 H MN MN . A MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.17 ? metalc ? metalc2 A OD1 ASP 103 A ASP 103 1_555 H MN MN . A MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.143 ? metalc ? metalc3 A SG CYS 116 A CYS 116 1_555 I ZN ZN . A ZN 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.345 ? metalc ? metalc4 A SG CYS 119 A CYS 119 1_555 I ZN ZN . A ZN 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.29 ? metalc ? metalc5 A SG CYS 128 A CYS 128 1_555 I ZN ZN . A ZN 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? metalc ? metalc6 A OD2 ASP 131 A ASP 131 1_555 I ZN ZN . A ZN 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.996 ? metalc ? metalc7 G O1G APC . A APC 1001 1_555 H MN MN . A MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.477 ? metalc ? metalc8 G O1B APC . A APC 1001 1_555 H MN MN . A MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? metalc ? metalc9 G O1A APC . A APC 1001 1_555 H MN MN . A MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.507 ? metalc ? metalc10 C OD1 ASP 101 D ASP 101 1_555 K MN MN . D MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? metalc ? metalc11 C OD1 ASP 103 D ASP 103 1_555 K MN MN . D MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? metalc ? metalc12 C SG CYS 116 D CYS 116 1_555 L ZN ZN . D ZN 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? metalc ? metalc13 C SG CYS 119 D CYS 119 1_555 L ZN ZN . D ZN 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.309 ? metalc ? metalc14 C SG CYS 128 D CYS 128 1_555 L ZN ZN . D ZN 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc15 C OD2 ASP 131 D ASP 131 1_555 L ZN ZN . D ZN 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.992 ? metalc ? metalc16 J O2G APC . D APC 1001 1_555 K MN MN . D MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? metalc ? metalc17 J O2B APC . D APC 1001 1_555 K MN MN . D MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? metalc ? metalc18 J O2A APC . D APC 1001 1_555 K MN MN . D MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.381 ? metalc ? metalc19 E O ASP 70 C ASP 70 1_555 N MN MN . C MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.159 ? metalc ? metalc20 E OD1 ASP 70 C ASP 70 1_555 N MN MN . C MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? metalc ? metalc21 M O2G APC . C APC 1001 1_555 N MN MN . C MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.418 ? metalc ? metalc22 M O2B APC . C APC 1001 1_555 N MN MN . C MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.128 ? metalc ? metalc23 M O2A APC . C APC 1001 1_555 N MN MN . C MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? metalc ? metalc24 F O ASP 70 F ASP 70 1_555 P MN MN . F MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? metalc ? metalc25 F OD1 ASP 70 F ASP 70 1_555 P MN MN . F MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? metalc ? metalc26 O O1G APC . F APC 1001 1_555 P MN MN . F MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.31 ? metalc ? metalc27 O O1B APC . F APC 1001 1_555 P MN MN . F MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.209 ? metalc ? metalc28 O O1A APC . F APC 1001 1_555 P MN MN . F MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? # _chem_comp.formula 'C11 H18 N5 O12 P3' _chem_comp.formula_weight 505.208 _chem_comp.id APC _chem_comp.mon_nstd_flag . _chem_comp.name 'DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ALPHA,BETA-METHYLENEADENOSINE-5'-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 APC doub 13 n n PG O2G APC sing 14 n n PG O3G APC sing 15 n n PG O3B APC sing 16 n n O2G HOG2 APC sing 17 n n O3G HOG3 APC sing 18 n n PB O1B APC doub 19 n n PB O2B APC sing 20 n n PB O3B APC sing 21 n n PB C3A APC sing 22 n n O2B HOB2 APC sing 23 n n PA O1A APC doub 24 n n PA O2A APC sing 25 n n PA C3A APC sing 26 n n PA O5' APC sing 27 n n O2A HOA2 APC sing 28 n n C3A H3A1 APC sing 29 n n C3A H3A2 APC sing 30 n n O5' C5' APC sing 31 n n C5' C4' APC sing 32 n n C5' "H5'1" APC sing 33 n n C5' "H5'2" APC sing 34 n n C4' O4' APC sing 35 n n C4' C3' APC sing 36 n n C4' H4' APC sing 37 n n O4' C1' APC sing 38 n n C3' O3' APC sing 39 n n C3' C2' APC sing 40 n n C3' H3' APC sing 41 n n O3' HO3' APC sing 42 n n C2' O2' APC sing 43 n n C2' C1' APC sing 44 n n C2' H2' APC sing 45 n n O2' HO2' APC sing 46 n n C1' N9 APC sing 47 n n C1' H1' APC sing 48 n n N9 C8 APC sing 49 n y N9 C4 APC sing 50 n y C8 N7 APC doub 51 n y C8 H8 APC sing 52 n n N7 C5 APC sing 53 n y C5 C6 APC sing 54 n y C5 C4 APC doub 55 n y C6 N6 APC sing 56 n n C6 N1 APC doub 57 n y N6 HN61 APC sing 58 n n N6 HN62 APC sing 59 n n N1 C2 APC sing 60 n y C2 N3 APC doub 61 n y C2 H2 APC sing 62 n n N3 C4 APC sing 63 n y # _atom_sites.entry_id 5OF3 _atom_sites.fract_transf_matrix[1][1] 0.009534 _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] 0.009534 _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] 0.004352 _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 4 APC A 1 1001 1001 APC APC . H 5 MN A 1 1002 1002 MN MN . I 6 ZN A 1 1003 1003 ZN ZN . J 4 APC D 1 1001 1001 APC APC . K 5 MN D 1 1002 1002 MN MN . L 6 ZN D 1 1003 1003 ZN ZN . M 4 APC C 1 1001 1001 APC APC . N 5 MN C 1 1002 1002 MN MN . O 4 APC F 1 1001 1001 APC APC . P 5 MN F 1 1002 1002 MN MN . # 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 APC . . . G 4 34.624 18.051 -16.652 0.75 86.33 ? PG APC 1001 A 1 HETATM 2 O O1G APC . . . G 4 35.913 17.746 -17.424 0.75 94 ? O1G APC 1001 A 1 HETATM 3 O O2G APC . . . G 4 34.047 19.394 -16.98 0.75 53.63 ? O2G APC 1001 A 1 HETATM 4 O O3G APC . . . G 4 33.649 16.897 -16.896 0.75 53.08 ? O3G APC 1001 A 1 HETATM 5 P PB APC . . . G 4 36.412 18.136 -14.372 0.75 78.86 ? PB APC 1001 A 1 HETATM 6 O O1B APC . . . G 4 37.319 16.987 -14.9 0.75 80.51 ? O1B APC 1001 A 1 HETATM 7 O O2B APC . . . G 4 36.288 17.969 -12.874 0.75 81.7 ? O2B APC 1001 A 1 HETATM 8 O O3B APC . . . G 4 35.014 17.976 -15.11 0.75 73.27 ? O3B APC 1001 A 1 HETATM 9 P PA APC . . . G 4 38.531 19.48 -16.098 0.75 108.56 ? PA APC 1001 A 1 HETATM 10 O O1A APC . . . G 4 38.456 18.598 -17.329 0.75 94.7 ? O1A APC 1001 A 1 HETATM 11 O O2A APC . . . G 4 38.916 20.917 -16.56 0.75 103.39 ? O2A APC 1001 A 1 HETATM 12 C C3A APC . . . G 4 37.056 19.655 -15.086 0.75 71.65 ? C3A APC 1001 A 1 HETATM 13 O O5' APC . . . G 4 39.628 19.025 -15.066 0.75 85.15 ? O5' APC 1001 A 1 HETATM 14 C C5' APC . . . G 4 40.545 17.946 -15.346 0.75 78.23 ? C5' APC 1001 A 1 HETATM 15 C C4' APC . . . G 4 41.193 17.454 -14.073 0.75 80.69 ? C4' APC 1001 A 1 HETATM 16 O O4' APC . . . G 4 41.635 18.57 -13.273 0.75 87.99 ? O4' APC 1001 A 1 HETATM 17 C C3' APC . . . G 4 40.327 16.604 -13.15 0.75 86.24 ? C3' APC 1001 A 1 HETATM 18 O O3' APC . . . G 4 41.111 15.645 -12.45 0.75 70.32 ? O3' APC 1001 A 1 HETATM 19 C C2' APC . . . G 4 39.717 17.642 -12.203 0.75 86.65 ? C2' APC 1001 A 1 HETATM 20 O O2' APC . . . G 4 39.476 17.09 -10.914 0.75 69.6 ? O2' APC 1001 A 1 HETATM 21 C C1' APC . . . G 4 40.813 18.715 -12.127 0.75 87.91 ? C1' APC 1001 A 1 HETATM 22 N N9 APC . . . G 4 40.299 20.079 -12.118 0.75 95.36 ? N9 APC 1001 A 1 HETATM 23 C C8 APC . . . G 4 39.021 20.478 -12.408 0.75 91.48 ? C8 APC 1001 A 1 HETATM 24 N N7 APC . . . G 4 38.851 21.779 -12.4 0.75 97.82 ? N7 APC 1001 A 1 HETATM 25 C C5 APC . . . G 4 40.106 22.27 -12.075 0.75 85.64 ? C5 APC 1001 A 1 HETATM 26 C C6 APC . . . G 4 40.599 23.579 -11.915 0.75 85.8 ? C6 APC 1001 A 1 HETATM 27 N N6 APC . . . G 4 39.871 24.677 -12.126 0.75 83.08 ? N6 APC 1001 A 1 HETATM 28 N N1 APC . . . G 4 41.897 23.723 -11.569 0.75 98.99 ? N1 APC 1001 A 1 HETATM 29 C C2 APC . . . G 4 42.646 22.627 -11.41 0.75 93.97 ? C2 APC 1001 A 1 HETATM 30 N N3 APC . . . G 4 42.295 21.346 -11.551 0.75 93.28 ? N3 APC 1001 A 1 HETATM 31 C C4 APC . . . G 4 41.006 21.235 -11.887 0.75 88.33 ? C4 APC 1001 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 30 _model_server_stats.query_time_ms 327 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 31 #