data_6AGG # _model_server_result.job_id bmZ6nEct_I6K3P2Mg2tOPA _model_server_result.datetime_utc '2024-12-26 17:51:29' _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 6agg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":502}' # _entry.id 6AGG # _exptl.entry_id 6AGG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER' _entity.pdbx_number_of_molecules 1 _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 6AGG _cell.length_a 69.786 _cell.length_b 69.786 _cell.length_c 210.822 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6AGG _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 covale ? covale1 A C CYS 17 Z CYS 17 1_555 A N TPO 18 Z TPO 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale2 A C TPO 18 Z TPO 18 1_555 A N THR 19 Z THR 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? metalc ? metalc1 A OD2 ASP 8 Z ASP 8 1_555 I MG MG . Z MG 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.53 ? metalc ? metalc2 A OD2 ASP 11 Z ASP 11 1_555 H MG MG . Z MG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.536 ? metalc ? metalc3 A O1P TPO 18 Z TPO 18 1_555 H MG MG . Z MG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.279 ? metalc ? metalc4 A O2P TPO 18 Z TPO 18 1_555 H MG MG . Z MG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.946 ? metalc ? metalc5 A O2P TPO 18 Z TPO 18 1_555 I MG MG . Z MG 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.368 ? metalc ? metalc6 A O GLY 57 Z GLY 57 1_555 I MG MG . Z MG 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.674 ? metalc ? metalc7 A SG CYS 352 Z CYS 352 1_555 B ZN ZN . Z ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.568 ? metalc ? metalc8 A SG CYS 355 Z CYS 355 1_555 B ZN ZN . Z ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.6 ? metalc ? metalc9 A SG CYS 370 Z CYS 370 1_555 B ZN ZN . Z ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.375 ? metalc ? metalc10 A SG CYS 373 Z CYS 373 1_555 B ZN ZN . Z ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.66 ? metalc ? metalc11 C O1A ACP . Z ACP 502 1_555 H MG MG . Z MG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.482 ? metalc ? metalc12 C O2A ACP . Z ACP 502 1_555 H MG MG . Z MG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.869 ? metalc ? metalc13 C O1B ACP . Z ACP 502 1_555 I MG MG . Z MG 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.502 ? metalc ? metalc14 C O2A ACP . Z ACP 502 1_555 I MG MG . Z MG 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.848 ? # _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 6AGG _atom_sites.fract_transf_matrix[1][1] 0.01433 _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] 0.01433 _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] 0.004743 _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 B 2 ZN Z 1 501 1 ZN ZN . C 3 ACP Z 1 502 1 ACP ACP . D 4 AG2 Z 1 503 1 AG2 AG2 . E 5 ACT Z 1 504 2 ACT ACT . F 5 ACT Z 1 505 3 ACT ACT . G 6 NH4 Z 1 506 1 NH4 NH4 . H 7 MG Z 1 507 1 MG MG . I 7 MG Z 1 508 2 MG MG . J 8 HOH Z 1 601 5 HOH HOH . J 8 HOH Z 2 602 7 HOH HOH . J 8 HOH Z 3 603 6 HOH HOH . J 8 HOH Z 4 604 1 HOH HOH . J 8 HOH Z 5 605 2 HOH HOH . J 8 HOH Z 6 606 8 HOH HOH . J 8 HOH Z 7 607 9 HOH HOH . J 8 HOH Z 8 608 10 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 . . . C 3 20.584 7.663 36.701 1 218.52 ? PG ACP 502 Z 1 HETATM 2 O O1G ACP . . . C 3 20.177 8.505 35.414 1 112.62 ? O1G ACP 502 Z 1 HETATM 3 O O2G ACP . . . C 3 22.04 7.846 35.907 1 210.32 ? O2G ACP 502 Z 1 HETATM 4 O O3G ACP . . . C 3 20.615 9.263 37.382 1 208.15 ? O3G ACP 502 Z 1 HETATM 5 P PB ACP . . . C 3 18.472 4.571 38.086 1 151.79 ? PB ACP 502 Z 1 HETATM 6 O O1B ACP . . . C 3 17.925 5.347 38.734 1 143.35 ? O1B ACP 502 Z 1 HETATM 7 O O2B ACP . . . C 3 19.505 4.063 38.874 1 160.24 ? O2B ACP 502 Z 1 HETATM 8 C C3B ACP . . . C 3 19.566 6.038 37.35 1 104.03 ? C3B ACP 502 Z 1 HETATM 9 P PA ACP . . . C 3 18.765 2.728 36.017 1 96.9 ? PA ACP 502 Z 1 HETATM 10 O O1A ACP . . . C 3 19.362 2.759 34.787 1 116.96 ? O1A ACP 502 Z 1 HETATM 11 O O2A ACP . . . C 3 17.356 3.01 35.881 1 96.78 ? O2A ACP 502 Z 1 HETATM 12 O O3A ACP . . . C 3 19.441 3.798 36.946 1 75.7 ? O3A ACP 502 Z 1 HETATM 13 O O5' ACP . . . C 3 18.925 1.097 36.659 1 109.54 ? O5' ACP 502 Z 1 HETATM 14 C C5' ACP . . . C 3 17.811 0.623 37.492 1 101.52 ? C5' ACP 502 Z 1 HETATM 15 C C4' ACP . . . C 3 16.995 -0.531 36.987 1 90.28 ? C4' ACP 502 Z 1 HETATM 16 O O4' ACP . . . C 3 16.868 -1.434 38.031 1 81.81 ? O4' ACP 502 Z 1 HETATM 17 C C3' ACP . . . C 3 15.628 -0.06 36.672 1 86.42 ? C3' ACP 502 Z 1 HETATM 18 O O3' ACP . . . C 3 15.13 -0.853 35.613 1 72.23 ? O3' ACP 502 Z 1 HETATM 19 C C2' ACP . . . C 3 14.882 -0.295 37.833 1 91.07 ? C2' ACP 502 Z 1 HETATM 20 O O2' ACP . . . C 3 13.478 -0.428 37.531 1 73.93 ? O2' ACP 502 Z 1 HETATM 21 C C1' ACP . . . C 3 15.427 -1.453 38.392 1 88.76 ? C1' ACP 502 Z 1 HETATM 22 N N9 ACP . . . C 3 15.253 -1.533 39.886 1 97.92 ? N9 ACP 502 Z 1 HETATM 23 C C8 ACP . . . C 3 15.193 -0.495 40.72 1 92.8 ? C8 ACP 502 Z 1 HETATM 24 N N7 ACP . . . C 3 15.062 -0.983 41.979 1 91.99 ? N7 ACP 502 Z 1 HETATM 25 C C5 ACP . . . C 3 15.047 -2.342 41.93 1 93.79 ? C5 ACP 502 Z 1 HETATM 26 C C6 ACP . . . C 3 14.931 -3.367 42.916 1 89.36 ? C6 ACP 502 Z 1 HETATM 27 N N6 ACP . . . C 3 14.798 -3.084 44.241 1 73.23 ? N6 ACP 502 Z 1 HETATM 28 N N1 ACP . . . C 3 14.956 -4.655 42.483 1 87.69 ? N1 ACP 502 Z 1 HETATM 29 C C2 ACP . . . C 3 15.086 -4.975 41.19 1 83.52 ? C2 ACP 502 Z 1 HETATM 30 N N3 ACP . . . C 3 15.196 -4.023 40.257 1 100.01 ? N3 ACP 502 Z 1 HETATM 31 C C4 ACP . . . C 3 15.178 -2.709 40.594 1 101.11 ? C4 ACP 502 Z 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 327 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 31 #