data_5AUP # _model_server_result.job_id 3bF4bZK43dCq92o7lxRQDQ _model_server_result.datetime_utc '2024-11-24 05:21:13' _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":"F","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 . . . F 4 -20.903 6.196 19.381 1 57.41 ? PG ACP 301 B 1 HETATM 2 O O1G ACP . . . F 4 -22.229 6.636 18.795 1 63.57 ? O1G ACP 301 B 1 HETATM 3 O O2G ACP . . . F 4 -20.973 6.222 20.896 1 59.27 ? O2G ACP 301 B 1 HETATM 4 O O3G ACP . . . F 4 -19.827 7.103 18.915 1 62.96 ? O3G ACP 301 B 1 HETATM 5 P PB ACP . . . F 4 -20.546 4.479 16.956 1 61.36 ? PB ACP 301 B 1 HETATM 6 O O1B ACP . . . F 4 -21.902 4.922 16.422 1 63.81 ? O1B ACP 301 B 1 HETATM 7 O O2B ACP . . . F 4 -19.48 5.413 16.446 1 60.88 ? O2B ACP 301 B 1 HETATM 8 C C3B ACP . . . F 4 -20.56 4.505 18.817 1 68.72 ? C3B ACP 301 B 1 HETATM 9 P PA ACP . . . F 4 -18.786 2.321 16.538 1 65.52 ? PA ACP 301 B 1 HETATM 10 O O1A ACP . . . F 4 -18.032 2.646 15.244 1 56.75 ? O1A ACP 301 B 1 HETATM 11 O O2A ACP . . . F 4 -18.028 2.842 17.704 1 66.85 ? O2A ACP 301 B 1 HETATM 12 O O3A ACP . . . F 4 -20.236 2.984 16.477 1 66.45 ? O3A ACP 301 B 1 HETATM 13 O O5' ACP . . . F 4 -18.944 0.738 16.682 1 61.11 ? O5' ACP 301 B 1 HETATM 14 C C5' ACP . . . F 4 -19.659 0.215 17.832 1 62.51 ? C5' ACP 301 B 1 HETATM 15 C C4' ACP . . . F 4 -19.402 -1.328 17.917 1 75.8 ? C4' ACP 301 B 1 HETATM 16 O O4' ACP . . . F 4 -20.08 -1.935 16.976 1 77.02 ? O4' ACP 301 B 1 HETATM 17 C C3' ACP . . . F 4 -17.92 -1.609 17.649 1 77.53 ? C3' ACP 301 B 1 HETATM 18 O O3' ACP . . . F 4 -17.406 -2.421 18.614 1 82.72 ? O3' ACP 301 B 1 HETATM 19 C C2' ACP . . . F 4 -17.88 -2.332 16.288 1 84.17 ? C2' ACP 301 B 1 HETATM 20 O O2' ACP . . . F 4 -16.82 -3.397 16.298 1 91.87 ? O2' ACP 301 B 1 HETATM 21 C C1' ACP . . . F 4 -19.049 -2.87 16.166 1 82.43 ? C1' ACP 301 B 1 HETATM 22 N N9 ACP . . . F 4 -19.422 -2.89 14.798 1 79.36 ? N9 ACP 301 B 1 HETATM 23 C C8 ACP . . . F 4 -19.585 -1.817 13.975 1 77.35 ? C8 ACP 301 B 1 HETATM 24 N N7 ACP . . . F 4 -19.942 -2.282 12.753 1 77.49 ? N7 ACP 301 B 1 HETATM 25 C C5 ACP . . . F 4 -20 -3.632 12.821 1 82.19 ? C5 ACP 301 B 1 HETATM 26 C C6 ACP . . . F 4 -20.309 -4.59 11.885 1 82.03 ? C6 ACP 301 B 1 HETATM 27 N N6 ACP . . . F 4 -20.667 -4.566 10.559 1 76.13 ? N6 ACP 301 B 1 HETATM 28 N N1 ACP . . . F 4 -20.292 -5.893 12.222 1 87.17 ? N1 ACP 301 B 1 HETATM 29 C C2 ACP . . . F 4 -19.97 -6.264 13.489 1 89.19 ? C2 ACP 301 B 1 HETATM 30 N N3 ACP . . . F 4 -19.66 -5.315 14.428 1 86.03 ? N3 ACP 301 B 1 HETATM 31 C C4 ACP . . . F 4 -19.677 -4.01 14.091 1 82.11 ? C4 ACP 301 B 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 44 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 31 #