data_5AUP # _model_server_result.job_id b_2cJz0cJcpRYzbEPPisxg _model_server_result.datetime_utc '2024-11-27 23:06:18' _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 5aup # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":301}' # _entry.id 5AUP # _exptl.entry_id 5AUP _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 90 _cell.angle_gamma 90 _cell.entry_id 5AUP _cell.length_a 121.945 _cell.length_b 123.931 _cell.length_c 55.099 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5AUP _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,J,K,L _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 F N N ? 4 I 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 SG CYS 73 A CYS 73 1_555 E ZN ZN . A ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.285 ? metalc ? metalc2 A SG CYS 76 A CYS 76 1_555 E ZN ZN . A ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.29 ? metalc ? metalc3 A SG CYS 110 A CYS 110 1_555 E ZN ZN . A ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.322 ? metalc ? metalc4 A SG CYS 113 A CYS 113 1_555 E ZN ZN . A ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.281 ? metalc ? metalc5 B OG SER 34 B SER 34 1_555 G MG MG . B MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? metalc ? metalc6 F O3G ACP . B ACP 301 1_555 G MG MG . B MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.927 ? metalc ? metalc7 F O2B ACP . B ACP 301 1_555 G MG MG . B MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? metalc ? metalc8 G MG MG . B MG 302 1_555 K O HOH . B HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? metalc ? metalc9 G MG MG . B MG 302 1_555 K O HOH . B HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? metalc ? metalc10 G MG MG . B MG 302 1_555 K O HOH . B HOH 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? metalc ? metalc11 C SG CYS 73 H CYS 73 1_555 H ZN ZN . H ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? metalc ? metalc12 C SG CYS 76 H CYS 76 1_555 H ZN ZN . H ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.259 ? metalc ? metalc13 C SG CYS 110 H CYS 110 1_555 H ZN ZN . H ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? metalc ? metalc14 C SG CYS 113 H CYS 113 1_555 H ZN ZN . H ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? metalc ? metalc15 D OG SER 34 I SER 34 1_555 J MG MG . I MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? metalc ? metalc16 I O3G ACP . I ACP 301 1_555 J MG MG . I MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? metalc ? metalc17 I O1B ACP . I ACP 301 1_555 J MG MG . I MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? metalc ? metalc18 J MG MG . I MG 302 1_555 L O HOH . I HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? metalc ? metalc19 J MG MG . I MG 302 1_555 L O HOH . I HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? metalc ? metalc20 J MG MG . I MG 302 1_555 L O HOH . I HOH 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? # _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 5AUP _atom_sites.fract_transf_matrix[1][1] 0.0082 _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] 0.008069 _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] 0.018149 _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 E 3 ZN A 1 201 1 ZN ZN . F 4 ACP B 1 301 301 ACP ACP . G 5 MG B 1 302 1 MG MG . H 3 ZN H 1 201 1 ZN ZN . I 4 ACP I 1 301 301 ACP ACP . J 5 MG I 1 302 1 MG MG . K 6 HOH B 1 401 2 HOH HOH . K 6 HOH B 2 402 1 HOH HOH . K 6 HOH B 3 403 3 HOH HOH . K 6 HOH B 4 404 4 HOH HOH . L 6 HOH I 1 401 7 HOH HOH . L 6 HOH I 2 402 6 HOH HOH . L 6 HOH I 3 403 5 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 . . . I 4 -27.895 5.124 23.043 1 54.06 ? PG ACP 301 I 1 HETATM 2 O O1G ACP . . . I 4 -27.824 5.941 21.768 1 67.7 ? O1G ACP 301 I 1 HETATM 3 O O2G ACP . . . I 4 -26.571 5.204 23.781 1 54.14 ? O2G ACP 301 I 1 HETATM 4 O O3G ACP . . . I 4 -28.973 5.658 23.91 1 54.78 ? O3G ACP 301 I 1 HETATM 5 P PB ACP . . . I 4 -28.353 2.397 24.196 1 52.29 ? PB ACP 301 I 1 HETATM 6 O O1B ACP . . . I 4 -29.545 2.845 24.999 1 60.23 ? O1B ACP 301 I 1 HETATM 7 O O2B ACP . . . I 4 -27.082 2.608 25.008 1 49.75 ? O2B ACP 301 I 1 HETATM 8 C C3B ACP . . . I 4 -28.26 3.392 22.627 1 55.41 ? C3B ACP 301 I 1 HETATM 9 P PA ACP . . . I 4 -29.9 0.193 23.399 1 59.44 ? PA ACP 301 I 1 HETATM 10 O O1A ACP . . . I 4 -30.661 1.149 22.557 1 51.38 ? O1A ACP 301 I 1 HETATM 11 O O2A ACP . . . I 4 -30.713 -0.159 24.65 1 55.07 ? O2A ACP 301 I 1 HETATM 12 O O3A ACP . . . I 4 -28.512 0.847 23.833 1 60.53 ? O3A ACP 301 I 1 HETATM 13 O O5' ACP . . . I 4 -29.609 -1.131 22.553 1 57.01 ? O5' ACP 301 I 1 HETATM 14 C C5' ACP . . . I 4 -29.266 -0.972 21.152 1 61.95 ? C5' ACP 301 I 1 HETATM 15 C C4' ACP . . . I 4 -29.59 -2.298 20.383 1 68.7 ? C4' ACP 301 I 1 HETATM 16 O O4' ACP . . . I 4 -28.824 -3.262 20.833 1 66.38 ? O4' ACP 301 I 1 HETATM 17 C C3' ACP . . . I 4 -31.037 -2.711 20.666 1 67.11 ? C3' ACP 301 I 1 HETATM 18 O O3' ACP . . . I 4 -31.683 -3.016 19.505 1 68.05 ? O3' ACP 301 I 1 HETATM 19 C C2' ACP . . . I 4 -30.933 -3.961 21.566 1 65.56 ? C2' ACP 301 I 1 HETATM 20 O O2' ACP . . . I 4 -32.029 -4.93 21.228 1 73.96 ? O2' ACP 301 I 1 HETATM 21 C C1' ACP . . . I 4 -29.78 -4.48 21.286 1 64.91 ? C1' ACP 301 I 1 HETATM 22 N N9 ACP . . . I 4 -29.232 -5.118 22.436 1 63.84 ? N9 ACP 301 I 1 HETATM 23 C C8 ACP . . . I 4 -28.902 -4.532 23.621 1 62.18 ? C8 ACP 301 I 1 HETATM 24 N N7 ACP . . . I 4 -28.413 -5.491 24.446 1 56.76 ? N7 ACP 301 I 1 HETATM 25 C C5 ACP . . . I 4 -28.437 -6.667 23.778 1 64.54 ? C5 ACP 301 I 1 HETATM 26 C C6 ACP . . . I 4 -28.061 -7.941 24.138 1 65.41 ? C6 ACP 301 I 1 HETATM 27 N N6 ACP . . . I 4 -27.531 -8.51 25.272 1 63.55 ? N6 ACP 301 I 1 HETATM 28 N N1 ACP . . . I 4 -28.191 -8.957 23.264 1 66.18 ? N1 ACP 301 I 1 HETATM 29 C C2 ACP . . . I 4 -28.696 -8.725 22.024 1 63.82 ? C2 ACP 301 I 1 HETATM 30 N N3 ACP . . . I 4 -29.074 -7.457 21.658 1 65.73 ? N3 ACP 301 I 1 HETATM 31 C C4 ACP . . . I 4 -28.945 -6.436 22.531 1 65.82 ? C4 ACP 301 I 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 26 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 318 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #