data_5AR3 # _model_server_result.job_id EwGXOpQGXlvNPRToLBHXtg _model_server_result.datetime_utc '2024-11-06 22:40:35' _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 5ar3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1311}' # _entry.id 5AR3 # _exptl.entry_id 5AR3 _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 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 120 _cell.entry_id 5AR3 _cell.length_a 131.566 _cell.length_b 131.566 _cell.length_c 106.582 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5AR3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 ? 2 C N N ? 2 E 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 OD1 ASN 167 A ASN 151 1_555 D MG MG . A MG 1312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.19 ? metalc ? metalc2 A OD2 ASP 180 A ASP 164 1_555 D MG MG . A MG 1312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? metalc ? metalc3 C O1A ACP . A ACP 1311 1_555 D MG MG . A MG 1312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.185 ? metalc ? metalc4 C O2B ACP . A ACP 1311 1_555 D MG MG . A MG 1312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.188 ? metalc ? metalc5 D MG MG . A MG 1312 1_555 G O HOH . A HOH 2023 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? metalc ? metalc6 B OD1 ASN 167 B ASN 151 1_555 F MG MG . B MG 1312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc7 B OD2 ASP 180 B ASP 164 1_555 F MG MG . B MG 1312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.183 ? metalc ? metalc8 E O2B ACP . B ACP 1311 1_555 F MG MG . B MG 1312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.183 ? metalc ? metalc9 E O1A ACP . B ACP 1311 1_555 F MG MG . B MG 1312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.189 ? # _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 5AR3 _atom_sites.fract_transf_matrix[1][1] 0.007601 _atom_sites.fract_transf_matrix[1][2] 0.004388 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008777 _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] 0.009382 _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 C 2 ACP A 1 1311 1311 ACP ACP . D 3 MG A 1 1312 1312 MG MG . E 2 ACP B 1 1311 1311 ACP ACP . F 3 MG B 1 1312 1312 MG MG . G 4 HOH A 1 2001 2001 HOH HOH . G 4 HOH A 2 2002 2002 HOH HOH . G 4 HOH A 3 2003 2003 HOH HOH . G 4 HOH A 4 2004 2004 HOH HOH . G 4 HOH A 5 2005 2005 HOH HOH . G 4 HOH A 6 2006 2006 HOH HOH . G 4 HOH A 7 2007 2007 HOH HOH . G 4 HOH A 8 2008 2008 HOH HOH . G 4 HOH A 9 2009 2009 HOH HOH . G 4 HOH A 10 2010 2010 HOH HOH . G 4 HOH A 11 2011 2011 HOH HOH . G 4 HOH A 12 2012 2012 HOH HOH . G 4 HOH A 13 2013 2013 HOH HOH . G 4 HOH A 14 2014 2014 HOH HOH . G 4 HOH A 15 2015 2015 HOH HOH . G 4 HOH A 16 2016 2016 HOH HOH . G 4 HOH A 17 2017 2017 HOH HOH . G 4 HOH A 18 2018 2018 HOH HOH . G 4 HOH A 19 2019 2019 HOH HOH . G 4 HOH A 20 2020 2020 HOH HOH . G 4 HOH A 21 2021 2021 HOH HOH . G 4 HOH A 22 2022 2022 HOH HOH . G 4 HOH A 23 2023 2023 HOH HOH . G 4 HOH A 24 2024 2024 HOH HOH . G 4 HOH A 25 2025 2025 HOH HOH . G 4 HOH A 26 2026 2026 HOH HOH . G 4 HOH A 27 2027 2027 HOH HOH . G 4 HOH A 28 2028 2028 HOH HOH . G 4 HOH A 29 2029 2029 HOH HOH . G 4 HOH A 30 2030 2030 HOH HOH . G 4 HOH A 31 2031 2031 HOH HOH . G 4 HOH A 32 2032 2032 HOH HOH . G 4 HOH A 33 2033 2033 HOH HOH . G 4 HOH A 34 2034 2034 HOH HOH . G 4 HOH A 35 2035 2035 HOH HOH . G 4 HOH A 36 2036 2036 HOH HOH . G 4 HOH A 37 2037 2037 HOH HOH . G 4 HOH A 38 2038 2038 HOH HOH . G 4 HOH A 39 2039 2039 HOH HOH . G 4 HOH A 40 2040 2040 HOH HOH . G 4 HOH A 41 2041 2041 HOH HOH . G 4 HOH A 42 2042 2042 HOH HOH . G 4 HOH A 43 2043 2043 HOH HOH . G 4 HOH A 44 2044 2044 HOH HOH . G 4 HOH A 45 2045 2045 HOH HOH . H 4 HOH B 1 2001 2001 HOH HOH . H 4 HOH B 2 2002 2002 HOH HOH . H 4 HOH B 3 2003 2003 HOH HOH . H 4 HOH B 4 2004 2004 HOH HOH . H 4 HOH B 5 2005 2005 HOH HOH . H 4 HOH B 6 2006 2006 HOH HOH . H 4 HOH B 7 2007 2007 HOH HOH . H 4 HOH B 8 2008 2008 HOH HOH . H 4 HOH B 9 2009 2009 HOH HOH . H 4 HOH B 10 2010 2010 HOH HOH . H 4 HOH B 11 2011 2011 HOH HOH . H 4 HOH B 12 2012 2012 HOH HOH . H 4 HOH B 13 2013 2013 HOH HOH . H 4 HOH B 14 2014 2014 HOH HOH . H 4 HOH B 15 2015 2015 HOH HOH . H 4 HOH B 16 2016 2016 HOH HOH . H 4 HOH B 17 2017 2017 HOH HOH . H 4 HOH B 18 2018 2018 HOH HOH . H 4 HOH B 19 2019 2019 HOH HOH . H 4 HOH B 20 2020 2020 HOH HOH . H 4 HOH B 21 2021 2021 HOH HOH . H 4 HOH B 22 2022 2022 HOH HOH . H 4 HOH B 23 2023 2023 HOH HOH . H 4 HOH B 24 2024 2024 HOH HOH . H 4 HOH B 25 2025 2025 HOH HOH . H 4 HOH B 26 2026 2026 HOH HOH . H 4 HOH B 27 2027 2027 HOH HOH . H 4 HOH B 28 2028 2028 HOH HOH . H 4 HOH B 29 2029 2029 HOH HOH . H 4 HOH B 30 2030 2030 HOH HOH . H 4 HOH B 31 2031 2031 HOH HOH . H 4 HOH B 32 2032 2032 HOH HOH . H 4 HOH B 33 2033 2033 HOH HOH . H 4 HOH B 34 2034 2034 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 . . . E 2 39.939 56.675 23.714 1 115.95 ? PG ACP 1311 B 1 HETATM 2 O O1G ACP . . . E 2 39.723 56.473 25.196 1 121.3 ? O1G ACP 1311 B 1 HETATM 3 O O2G ACP . . . E 2 39.968 58.166 23.302 1 109.01 ? O2G ACP 1311 B 1 HETATM 4 O O3G ACP . . . E 2 38.92 55.917 22.851 1 116.62 ? O3G ACP 1311 B 1 HETATM 5 P PB ACP . . . E 2 42.899 57.008 23.831 1 100.15 ? PB ACP 1311 B 1 HETATM 6 O O1B ACP . . . E 2 42.752 58.452 23.413 1 95.05 ? O1B ACP 1311 B 1 HETATM 7 O O2B ACP . . . E 2 42.881 56.886 25.397 1 91.91 ? O2B ACP 1311 B 1 HETATM 8 C C3B ACP . . . E 2 41.527 56.044 23.219 1 102.94 ? C3B ACP 1311 B 1 HETATM 9 P PA ACP . . . E 2 45.698 56.235 23.81 1 79.65 ? PA ACP 1311 B 1 HETATM 10 O O1A ACP . . . E 2 45.89 57.116 25.026 1 83.53 ? O1A ACP 1311 B 1 HETATM 11 O O2A ACP . . . E 2 46.592 56.583 22.594 1 77.51 ? O2A ACP 1311 B 1 HETATM 12 O O3A ACP . . . E 2 44.225 56.286 23.235 1 86.45 ? O3A ACP 1311 B 1 HETATM 13 O O5' ACP . . . E 2 45.896 54.691 24.078 1 71.84 ? O5' ACP 1311 B 1 HETATM 14 C C5' ACP . . . E 2 46.38 54.412 25.385 1 70.29 ? C5' ACP 1311 B 1 HETATM 15 C C4' ACP . . . E 2 46.137 52.97 25.766 1 70.11 ? C4' ACP 1311 B 1 HETATM 16 O O4' ACP . . . E 2 46.245 52.12 24.629 1 64.56 ? O4' ACP 1311 B 1 HETATM 17 C C3' ACP . . . E 2 47.093 52.47 26.82 1 74.45 ? C3' ACP 1311 B 1 HETATM 18 O O3' ACP . . . E 2 46.358 51.998 27.939 1 83.74 ? O3' ACP 1311 B 1 HETATM 19 C C2' ACP . . . E 2 47.837 51.319 26.189 1 70.95 ? C2' ACP 1311 B 1 HETATM 20 O O2' ACP . . . E 2 47.41 50.102 26.779 1 72.99 ? O2' ACP 1311 B 1 HETATM 21 C C1' ACP . . . E 2 47.434 51.348 24.73 1 65.22 ? C1' ACP 1311 B 1 HETATM 22 N N9 ACP . . . E 2 48.463 51.904 23.863 1 59.39 ? N9 ACP 1311 B 1 HETATM 23 C C8 ACP . . . E 2 48.437 53.087 23.185 1 55.27 ? C8 ACP 1311 B 1 HETATM 24 N N7 ACP . . . E 2 49.52 53.317 22.479 1 50.23 ? N7 ACP 1311 B 1 HETATM 25 C C5 ACP . . . E 2 50.299 52.216 22.712 1 52.18 ? C5 ACP 1311 B 1 HETATM 26 C C6 ACP . . . E 2 51.555 51.878 22.247 1 48.8 ? C6 ACP 1311 B 1 HETATM 27 N N6 ACP . . . E 2 52.245 52.665 21.423 1 47.2 ? N6 ACP 1311 B 1 HETATM 28 N N1 ACP . . . E 2 52.06 50.715 22.66 1 47.56 ? N1 ACP 1311 B 1 HETATM 29 C C2 ACP . . . E 2 51.331 49.961 23.485 1 50.56 ? C2 ACP 1311 B 1 HETATM 30 N N3 ACP . . . E 2 50.121 50.173 24 1 53.43 ? N3 ACP 1311 B 1 HETATM 31 C C4 ACP . . . E 2 49.664 51.339 23.559 1 55.37 ? C4 ACP 1311 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 227 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #