data_2Y8L # _model_server_result.job_id YF54NXEt-rcUkw6nH2pqfg _model_server_result.datetime_utc '2024-11-04 20:03:56' _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 2y8l # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1329}' # _entry.id 2Y8L # _exptl.entry_id 2Y8L _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 347.221 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'ADENOSINE MONOPHOSPHATE' _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 2Y8L _cell.length_a 48.567 _cell.length_b 121.464 _cell.length_c 125.922 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2Y8L _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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 5 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C10 H14 N5 O7 P' _chem_comp.formula_weight 347.221 _chem_comp.id AMP _chem_comp.mon_nstd_flag . _chem_comp.name 'ADENOSINE MONOPHOSPHATE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 P O1P AMP doub 57 n n P O2P AMP sing 58 n n P O3P AMP sing 59 n n P O5' AMP sing 60 n n O2P HOP2 AMP sing 61 n n O3P HOP3 AMP sing 62 n n O5' C5' AMP sing 63 n n C5' C4' AMP sing 64 n n C5' "H5'1" AMP sing 65 n n C5' "H5'2" AMP sing 66 n n C4' O4' AMP sing 67 n n C4' C3' AMP sing 68 n n C4' H4' AMP sing 69 n n O4' C1' AMP sing 70 n n C3' O3' AMP sing 71 n n C3' C2' AMP sing 72 n n C3' H3' AMP sing 73 n n O3' HO3' AMP sing 74 n n C2' O2' AMP sing 75 n n C2' C1' AMP sing 76 n n C2' H2' AMP sing 77 n n O2' HO2' AMP sing 78 n n C1' N9 AMP sing 79 n n C1' H1' AMP sing 80 n n N9 C8 AMP sing 81 n y N9 C4 AMP sing 82 n y C8 N7 AMP doub 83 n y C8 H8 AMP sing 84 n n N7 C5 AMP sing 85 n y C5 C6 AMP sing 86 n y C5 C4 AMP doub 87 n y C6 N6 AMP sing 88 n n C6 N1 AMP doub 89 n y N6 HN61 AMP sing 90 n n N6 HN62 AMP sing 91 n n N1 C2 AMP sing 92 n y C2 N3 AMP doub 93 n y C2 H2 AMP sing 94 n n N3 C4 AMP sing 95 n y # _atom_sites.entry_id 2Y8L _atom_sites.fract_transf_matrix[1][1] 0.02059 _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] 0.008233 _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] 0.007941 _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 D 4 ADP E 1 1327 1327 ADP ADP . E 4 ADP E 1 1328 1328 ADP ADP . F 5 AMP E 1 1329 1329 AMP AMP . G 6 HOH A 1 2001 2001 HOH HOH . G 6 HOH A 2 2002 2002 HOH HOH . G 6 HOH A 3 2003 2003 HOH HOH . G 6 HOH A 4 2004 2004 HOH HOH . G 6 HOH A 5 2005 2005 HOH HOH . G 6 HOH A 6 2006 2006 HOH HOH . G 6 HOH A 7 2007 2007 HOH HOH . G 6 HOH A 8 2008 2008 HOH HOH . G 6 HOH A 9 2009 2009 HOH HOH . G 6 HOH A 10 2010 2010 HOH HOH . G 6 HOH A 11 2011 2011 HOH HOH . G 6 HOH A 12 2012 2012 HOH HOH . G 6 HOH A 13 2013 2013 HOH HOH . G 6 HOH A 14 2014 2014 HOH HOH . G 6 HOH A 15 2015 2015 HOH HOH . G 6 HOH A 16 2016 2016 HOH HOH . G 6 HOH A 17 2017 2017 HOH HOH . G 6 HOH A 18 2018 2018 HOH HOH . G 6 HOH A 19 2019 2019 HOH HOH . G 6 HOH A 20 2020 2020 HOH HOH . G 6 HOH A 21 2021 2021 HOH HOH . G 6 HOH A 22 2022 2022 HOH HOH . G 6 HOH A 23 2023 2023 HOH HOH . H 6 HOH B 1 2001 2001 HOH HOH . H 6 HOH B 2 2002 2002 HOH HOH . H 6 HOH B 3 2003 2003 HOH HOH . H 6 HOH B 4 2004 2004 HOH HOH . H 6 HOH B 5 2005 2005 HOH HOH . H 6 HOH B 6 2006 2006 HOH HOH . H 6 HOH B 7 2007 2007 HOH HOH . H 6 HOH B 8 2008 2008 HOH HOH . H 6 HOH B 9 2009 2009 HOH HOH . H 6 HOH B 10 2010 2010 HOH HOH . H 6 HOH B 11 2011 2011 HOH HOH . H 6 HOH B 12 2012 2012 HOH HOH . H 6 HOH B 13 2013 2013 HOH HOH . H 6 HOH B 14 2014 2014 HOH HOH . H 6 HOH B 15 2015 2015 HOH HOH . H 6 HOH B 16 2016 2016 HOH HOH . H 6 HOH B 17 2017 2017 HOH HOH . I 6 HOH E 1 2001 2001 HOH HOH . I 6 HOH E 2 2002 2002 HOH HOH . I 6 HOH E 3 2003 2003 HOH HOH . I 6 HOH E 4 2004 2004 HOH HOH . I 6 HOH E 5 2005 2005 HOH HOH . I 6 HOH E 6 2006 2006 HOH HOH . I 6 HOH E 7 2007 2007 HOH HOH . I 6 HOH E 8 2008 2008 HOH HOH . I 6 HOH E 9 2009 2009 HOH HOH . I 6 HOH E 10 2010 2010 HOH HOH . I 6 HOH E 11 2011 2011 HOH HOH . I 6 HOH E 12 2012 2012 HOH HOH . I 6 HOH E 13 2013 2013 HOH HOH . I 6 HOH E 14 2014 2014 HOH HOH . I 6 HOH E 15 2015 2015 HOH HOH . I 6 HOH E 16 2016 2016 HOH HOH . I 6 HOH E 17 2017 2017 HOH HOH . I 6 HOH E 18 2018 2018 HOH HOH . I 6 HOH E 19 2019 2019 HOH HOH . I 6 HOH E 20 2020 2020 HOH HOH . I 6 HOH E 21 2021 2021 HOH HOH . I 6 HOH E 22 2022 2022 HOH HOH . I 6 HOH E 23 2023 2023 HOH HOH . I 6 HOH E 24 2024 2024 HOH HOH . I 6 HOH E 25 2025 2025 HOH HOH . I 6 HOH E 26 2026 2026 HOH HOH . I 6 HOH E 27 2027 2027 HOH HOH . I 6 HOH E 28 2028 2028 HOH HOH . I 6 HOH E 29 2029 2029 HOH HOH . I 6 HOH E 30 2030 2030 HOH HOH . I 6 HOH E 31 2031 2031 HOH HOH . I 6 HOH E 32 2032 2032 HOH HOH . I 6 HOH E 33 2033 2033 HOH HOH . I 6 HOH E 34 2034 2034 HOH HOH . I 6 HOH E 35 2035 2035 HOH HOH . I 6 HOH E 36 2036 2036 HOH HOH . I 6 HOH E 37 2037 2037 HOH HOH . I 6 HOH E 38 2038 2038 HOH HOH . I 6 HOH E 39 2039 2039 HOH HOH . I 6 HOH E 40 2040 2040 HOH HOH . I 6 HOH E 41 2041 2041 HOH HOH . I 6 HOH E 42 2042 2042 HOH HOH . I 6 HOH E 43 2043 2043 HOH HOH . I 6 HOH E 44 2044 2044 HOH HOH . I 6 HOH E 45 2045 2045 HOH HOH . I 6 HOH E 46 2046 2046 HOH HOH . I 6 HOH E 47 2047 2047 HOH HOH . I 6 HOH E 48 2048 2048 HOH HOH . I 6 HOH E 49 2049 2049 HOH HOH . I 6 HOH E 50 2050 2050 HOH HOH . I 6 HOH E 51 2051 2051 HOH HOH . I 6 HOH E 52 2052 2052 HOH HOH . I 6 HOH E 53 2053 2053 HOH HOH . I 6 HOH E 54 2054 2054 HOH HOH . I 6 HOH E 55 2055 2055 HOH HOH . I 6 HOH E 56 2056 2056 HOH HOH . I 6 HOH E 57 2057 2057 HOH HOH . I 6 HOH E 58 2058 2058 HOH HOH . I 6 HOH E 59 2059 2059 HOH HOH . I 6 HOH E 60 2060 2060 HOH HOH . I 6 HOH E 61 2061 2061 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 P AMP . . . F 5 -0.581 -13.877 -43.908 1 47.8 ? P AMP 1329 E 1 HETATM 2 O O1P AMP . . . F 5 -2.008 -13.621 -43.451 1 47.44 ? O1P AMP 1329 E 1 HETATM 3 O O2P AMP . . . F 5 0.481 -13.998 -42.799 1 46.45 ? O2P AMP 1329 E 1 HETATM 4 O O3P AMP . . . F 5 -0.184 -13.034 -45.096 1 44.11 ? O3P AMP 1329 E 1 HETATM 5 O O5' AMP . . . F 5 -0.721 -15.368 -44.474 1 45.71 ? O5' AMP 1329 E 1 HETATM 6 C C5' AMP . . . F 5 -1.169 -16.406 -43.595 1 44.66 ? C5' AMP 1329 E 1 HETATM 7 C C4' AMP . . . F 5 -1.308 -17.704 -44.39 1 45.34 ? C4' AMP 1329 E 1 HETATM 8 O O4' AMP . . . F 5 -2.355 -17.514 -45.33 1 44.74 ? O4' AMP 1329 E 1 HETATM 9 C C3' AMP . . . F 5 -0.083 -18.061 -45.211 1 46.03 ? C3' AMP 1329 E 1 HETATM 10 O O3' AMP . . . F 5 0.041 -19.48 -45.244 1 49.79 ? O3' AMP 1329 E 1 HETATM 11 C C2' AMP . . . F 5 -0.369 -17.48 -46.581 1 44.04 ? C2' AMP 1329 E 1 HETATM 12 O O2' AMP . . . F 5 0.269 -18.18 -47.656 1 45.52 ? O2' AMP 1329 E 1 HETATM 13 C C1' AMP . . . F 5 -1.888 -17.559 -46.671 1 44.02 ? C1' AMP 1329 E 1 HETATM 14 N N9 AMP . . . F 5 -2.483 -16.433 -47.437 1 41.42 ? N9 AMP 1329 E 1 HETATM 15 C C8 AMP . . . F 5 -2.072 -15.148 -47.459 1 39.06 ? C8 AMP 1329 E 1 HETATM 16 N N7 AMP . . . F 5 -2.839 -14.395 -48.275 1 37.81 ? N7 AMP 1329 E 1 HETATM 17 C C5 AMP . . . F 5 -3.781 -15.207 -48.795 1 39.19 ? C5 AMP 1329 E 1 HETATM 18 C C6 AMP . . . F 5 -4.929 -15.072 -49.721 1 39.32 ? C6 AMP 1329 E 1 HETATM 19 N N6 AMP . . . F 5 -5.234 -13.892 -50.288 1 37.76 ? N6 AMP 1329 E 1 HETATM 20 N N1 AMP . . . F 5 -5.664 -16.171 -49.994 1 44.07 ? N1 AMP 1329 E 1 HETATM 21 C C2 AMP . . . F 5 -5.386 -17.376 -49.447 1 45.87 ? C2 AMP 1329 E 1 HETATM 22 N N3 AMP . . . F 5 -4.368 -17.568 -48.586 1 44.86 ? N3 AMP 1329 E 1 HETATM 23 C C4 AMP . . . F 5 -3.54 -16.551 -48.241 1 41.66 ? C4 AMP 1329 E 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 284 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 23 #