data_1O6Y # _model_server_result.job_id 1W5m3w-P1_fBs9VzkoFjxw _model_server_result.datetime_utc '2024-12-26 15:38:22' _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 1o6y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1279}' # _entry.id 1O6Y # _exptl.entry_id 1O6Y _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 2 _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 1O6Y _cell.length_a 114.607 _cell.length_b 122.088 _cell.length_c 46.975 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1O6Y _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 2 2 21' # _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 _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 2 _struct_asym.id B _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 metalc ? metalc1 A OD1 ASN 163 A ASN 143 1_555 C MG MG . A MG 1280 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.27 ? metalc ? metalc2 A OD1 ASP 176 A ASP 156 1_555 C MG MG . A MG 1280 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? metalc ? metalc3 B O1A ACP . A ACP 1279 1_555 C MG MG . A MG 1280 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? metalc ? metalc4 B O1B ACP . A ACP 1279 1_555 C MG MG . A MG 1280 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? metalc ? metalc5 B O2B ACP . A ACP 1279 1_555 D MG MG . A MG 1281 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.938 ? metalc ? metalc6 B O1G ACP . A ACP 1279 1_555 D MG MG . A MG 1281 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? metalc ? metalc7 C MG MG . A MG 1280 1_555 E O HOH . A HOH 2079 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.125 ? metalc ? metalc8 C MG MG . A MG 1280 1_555 E O HOH . A HOH 2080 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? metalc ? metalc9 D MG MG . A MG 1281 1_555 E O HOH . A HOH 2054 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.919 ? metalc ? metalc10 D MG MG . A MG 1281 1_555 E O HOH . A HOH 2055 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? metalc ? metalc11 D MG MG . A MG 1281 1_555 E O HOH . A HOH 2081 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? metalc ? metalc12 D MG MG . A MG 1281 1_555 E O HOH . A HOH 2082 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? # _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 1O6Y _atom_sites.fract_transf_matrix[1][1] 0.008725 _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] 0.008191 _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] 0.021288 _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 ACP A 1 1279 1279 ACP ACP . C 3 MG A 1 1280 1280 MG MG . D 3 MG A 1 1281 1281 MG MG . E 4 HOH A 1 2001 2001 HOH HOH . E 4 HOH A 2 2002 2002 HOH HOH . E 4 HOH A 3 2003 2003 HOH HOH . E 4 HOH A 4 2004 2004 HOH HOH . E 4 HOH A 5 2005 2005 HOH HOH . E 4 HOH A 6 2006 2006 HOH HOH . E 4 HOH A 7 2007 2007 HOH HOH . E 4 HOH A 8 2008 2008 HOH HOH . E 4 HOH A 9 2009 2009 HOH HOH . E 4 HOH A 10 2010 2010 HOH HOH . E 4 HOH A 11 2011 2011 HOH HOH . E 4 HOH A 12 2012 2012 HOH HOH . E 4 HOH A 13 2013 2013 HOH HOH . E 4 HOH A 14 2014 2014 HOH HOH . E 4 HOH A 15 2015 2015 HOH HOH . E 4 HOH A 16 2016 2016 HOH HOH . E 4 HOH A 17 2017 2017 HOH HOH . E 4 HOH A 18 2018 2018 HOH HOH . E 4 HOH A 19 2019 2019 HOH HOH . E 4 HOH A 20 2020 2020 HOH HOH . E 4 HOH A 21 2021 2021 HOH HOH . E 4 HOH A 22 2022 2022 HOH HOH . E 4 HOH A 23 2023 2023 HOH HOH . E 4 HOH A 24 2024 2024 HOH HOH . E 4 HOH A 25 2025 2025 HOH HOH . E 4 HOH A 26 2026 2026 HOH HOH . E 4 HOH A 27 2027 2027 HOH HOH . E 4 HOH A 28 2028 2028 HOH HOH . E 4 HOH A 29 2029 2029 HOH HOH . E 4 HOH A 30 2030 2030 HOH HOH . E 4 HOH A 31 2031 2031 HOH HOH . E 4 HOH A 32 2032 2032 HOH HOH . E 4 HOH A 33 2033 2033 HOH HOH . E 4 HOH A 34 2034 2034 HOH HOH . E 4 HOH A 35 2035 2035 HOH HOH . E 4 HOH A 36 2036 2036 HOH HOH . E 4 HOH A 37 2037 2037 HOH HOH . E 4 HOH A 38 2038 2038 HOH HOH . E 4 HOH A 39 2039 2039 HOH HOH . E 4 HOH A 40 2040 2040 HOH HOH . E 4 HOH A 41 2041 2041 HOH HOH . E 4 HOH A 42 2042 2042 HOH HOH . E 4 HOH A 43 2043 2043 HOH HOH . E 4 HOH A 44 2044 2044 HOH HOH . E 4 HOH A 45 2045 2045 HOH HOH . E 4 HOH A 46 2046 2046 HOH HOH . E 4 HOH A 47 2047 2047 HOH HOH . E 4 HOH A 48 2048 2048 HOH HOH . E 4 HOH A 49 2049 2049 HOH HOH . E 4 HOH A 50 2050 2050 HOH HOH . E 4 HOH A 51 2051 2051 HOH HOH . E 4 HOH A 52 2052 2052 HOH HOH . E 4 HOH A 53 2053 2053 HOH HOH . E 4 HOH A 54 2054 2054 HOH HOH . E 4 HOH A 55 2055 2055 HOH HOH . E 4 HOH A 56 2056 2056 HOH HOH . E 4 HOH A 57 2057 2057 HOH HOH . E 4 HOH A 58 2058 2058 HOH HOH . E 4 HOH A 59 2059 2059 HOH HOH . E 4 HOH A 60 2060 2060 HOH HOH . E 4 HOH A 61 2061 2061 HOH HOH . E 4 HOH A 62 2062 2062 HOH HOH . E 4 HOH A 63 2063 2063 HOH HOH . E 4 HOH A 64 2064 2064 HOH HOH . E 4 HOH A 65 2065 2065 HOH HOH . E 4 HOH A 66 2066 2066 HOH HOH . E 4 HOH A 67 2067 2067 HOH HOH . E 4 HOH A 68 2068 2068 HOH HOH . E 4 HOH A 69 2069 2069 HOH HOH . E 4 HOH A 70 2070 2070 HOH HOH . E 4 HOH A 71 2071 2071 HOH HOH . E 4 HOH A 72 2072 2072 HOH HOH . E 4 HOH A 73 2073 2073 HOH HOH . E 4 HOH A 74 2074 2074 HOH HOH . E 4 HOH A 75 2075 2075 HOH HOH . E 4 HOH A 76 2076 2076 HOH HOH . E 4 HOH A 77 2077 2077 HOH HOH . E 4 HOH A 78 2078 2078 HOH HOH . E 4 HOH A 79 2079 2079 HOH HOH . E 4 HOH A 80 2080 2080 HOH HOH . E 4 HOH A 81 2081 2081 HOH HOH . E 4 HOH A 82 2082 2082 HOH HOH . E 4 HOH A 83 2083 2083 HOH HOH . E 4 HOH A 84 2084 2084 HOH HOH . E 4 HOH A 85 2085 2085 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 . . . B 2 79.502 82.783 21.991 1 27 ? PG ACP 1279 A 1 HETATM 2 O O1G ACP . . . B 2 79.601 82.281 20.595 1 28.37 ? O1G ACP 1279 A 1 HETATM 3 O O2G ACP . . . B 2 80.095 84.169 22.125 1 29.81 ? O2G ACP 1279 A 1 HETATM 4 O O3G ACP . . . B 2 78.06 82.872 22.311 1 26.96 ? O3G ACP 1279 A 1 HETATM 5 P PB ACP . . . B 2 81.488 80.556 22.538 1 28.6 ? PB ACP 1279 A 1 HETATM 6 O O1B ACP . . . B 2 82.757 81.325 22.19 1 24.4 ? O1B ACP 1279 A 1 HETATM 7 O O2B ACP . . . B 2 80.952 79.824 21.362 1 27.39 ? O2B ACP 1279 A 1 HETATM 8 C C3B ACP . . . B 2 80.273 81.659 23.134 1 25.35 ? C3B ACP 1279 A 1 HETATM 9 P PA ACP . . . B 2 83.008 78.563 23.85 1 26.21 ? PA ACP 1279 A 1 HETATM 10 O O1A ACP . . . B 2 84.325 79.051 23.311 1 22.41 ? O1A ACP 1279 A 1 HETATM 11 O O2A ACP . . . B 2 82.699 77.212 23.358 1 25.79 ? O2A ACP 1279 A 1 HETATM 12 O O3A ACP . . . B 2 81.826 79.516 23.631 1 27.64 ? O3A ACP 1279 A 1 HETATM 13 O O5' ACP . . . B 2 83.179 78.389 25.331 1 25.94 ? O5' ACP 1279 A 1 HETATM 14 C C5' ACP . . . B 2 83.015 79.544 26.136 1 26.8 ? C5' ACP 1279 A 1 HETATM 15 C C4' ACP . . . B 2 83.74 79.302 27.425 1 27.19 ? C4' ACP 1279 A 1 HETATM 16 O O4' ACP . . . B 2 83.034 78.327 28.175 1 27.19 ? O4' ACP 1279 A 1 HETATM 17 C C3' ACP . . . B 2 85.137 78.703 27.239 1 26.9 ? C3' ACP 1279 A 1 HETATM 18 O O3' ACP . . . B 2 86.128 79.708 27.176 1 28.44 ? O3' ACP 1279 A 1 HETATM 19 C C2' ACP . . . B 2 85.296 77.881 28.485 1 28.79 ? C2' ACP 1279 A 1 HETATM 20 O O2' ACP . . . B 2 85.631 78.785 29.527 1 26.78 ? O2' ACP 1279 A 1 HETATM 21 C C1' ACP . . . B 2 83.89 77.343 28.751 1 29.29 ? C1' ACP 1279 A 1 HETATM 22 N N9 ACP . . . B 2 83.776 76.006 28.108 1 27.84 ? N9 ACP 1279 A 1 HETATM 23 C C8 ACP . . . B 2 83.349 75.736 26.861 1 30.71 ? C8 ACP 1279 A 1 HETATM 24 N N7 ACP . . . B 2 83.364 74.418 26.626 1 28.74 ? N7 ACP 1279 A 1 HETATM 25 C C5 ACP . . . B 2 83.829 73.845 27.751 1 26.13 ? C5 ACP 1279 A 1 HETATM 26 C C6 ACP . . . B 2 84.09 72.458 28.158 1 24.65 ? C6 ACP 1279 A 1 HETATM 27 N N6 ACP . . . B 2 83.82 71.444 27.24 1 26.52 ? N6 ACP 1279 A 1 HETATM 28 N N1 ACP . . . B 2 84.506 72.226 29.397 1 27.62 ? N1 ACP 1279 A 1 HETATM 29 C C2 ACP . . . B 2 84.746 73.242 30.287 1 27.24 ? C2 ACP 1279 A 1 HETATM 30 N N3 ACP . . . B 2 84.49 74.532 29.969 1 24.68 ? N3 ACP 1279 A 1 HETATM 31 C C4 ACP . . . B 2 84.063 74.865 28.731 1 26.57 ? C4 ACP 1279 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 247 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 31 #