data_2Y8L # _model_server_result.job_id pHR6kCP2YI7yEKftuF47tg _model_server_result.datetime_utc '2024-11-04 20:01:27' _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":"E","auth_seq_id":1328}' # _entry.id 2Y8L # _exptl.entry_id 2Y8L _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _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 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 D N N ? 4 E N N # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id ADP _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-5'-DIPHOSPHATE" _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 PB O1B ADP doub 1 n n PB O2B ADP sing 2 n n PB O3B ADP sing 3 n n PB O3A ADP sing 4 n n O2B HOB2 ADP sing 5 n n O3B HOB3 ADP sing 6 n n PA O1A ADP doub 7 n n PA O2A ADP sing 8 n n PA O3A ADP sing 9 n n PA O5' ADP sing 10 n n O2A HOA2 ADP sing 11 n n O5' C5' ADP sing 12 n n C5' C4' ADP sing 13 n n C5' "H5'1" ADP sing 14 n n C5' "H5'2" ADP sing 15 n n C4' O4' ADP sing 16 n n C4' C3' ADP sing 17 n n C4' H4' ADP sing 18 n n O4' C1' ADP sing 19 n n C3' O3' ADP sing 20 n n C3' C2' ADP sing 21 n n C3' H3' ADP sing 22 n n O3' HO3' ADP sing 23 n n C2' O2' ADP sing 24 n n C2' C1' ADP sing 25 n n C2' H2' ADP sing 26 n n O2' HO2' ADP sing 27 n n C1' N9 ADP sing 28 n n C1' H1' ADP sing 29 n n N9 C8 ADP sing 30 n y N9 C4 ADP sing 31 n y C8 N7 ADP doub 32 n y C8 H8 ADP sing 33 n n N7 C5 ADP sing 34 n y C5 C6 ADP sing 35 n y C5 C4 ADP doub 36 n y C6 N6 ADP sing 37 n n C6 N1 ADP doub 38 n y N6 HN61 ADP sing 39 n n N6 HN62 ADP sing 40 n n N1 C2 ADP sing 41 n y C2 N3 ADP doub 42 n y C2 H2 ADP sing 43 n n N3 C4 ADP sing 44 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 PB ADP . . . E 4 3.015 -4.427 -43.26 1 72.07 ? PB ADP 1328 E 1 HETATM 2 O O1B ADP . . . E 4 3.196 -5.547 -42.25 1 70.44 ? O1B ADP 1328 E 1 HETATM 3 O O2B ADP . . . E 4 2.519 -3.149 -42.631 1 71.77 ? O2B ADP 1328 E 1 HETATM 4 O O3B ADP . . . E 4 4.125 -4.248 -44.278 1 73.09 ? O3B ADP 1328 E 1 HETATM 5 P PA ADP . . . E 4 1.761 -4.955 -45.756 1 66.16 ? PA ADP 1328 E 1 HETATM 6 O O1A ADP . . . E 4 0.456 -5.61 -46.133 1 65.87 ? O1A ADP 1328 E 1 HETATM 7 O O2A ADP . . . E 4 3.078 -5.551 -46.184 1 67.28 ? O2A ADP 1328 E 1 HETATM 8 O O3A ADP . . . E 4 1.761 -4.896 -44.153 1 68.93 ? O3A ADP 1328 E 1 HETATM 9 O O5' ADP . . . E 4 1.646 -3.416 -46.213 1 66.43 ? O5' ADP 1328 E 1 HETATM 10 C C5' ADP . . . E 4 2.693 -2.743 -46.915 1 65.36 ? C5' ADP 1328 E 1 HETATM 11 C C4' ADP . . . E 4 2.145 -1.914 -48.079 1 65.2 ? C4' ADP 1328 E 1 HETATM 12 O O4' ADP . . . E 4 2.645 -2.455 -49.306 1 64.3 ? O4' ADP 1328 E 1 HETATM 13 C C3' ADP . . . E 4 0.623 -1.905 -48.195 1 64.5 ? C3' ADP 1328 E 1 HETATM 14 O O3' ADP . . . E 4 0.167 -0.581 -48.502 1 67.89 ? O3' ADP 1328 E 1 HETATM 15 C C2' ADP . . . E 4 0.303 -2.834 -49.35 1 62.09 ? C2' ADP 1328 E 1 HETATM 16 O O2' ADP . . . E 4 -0.777 -2.348 -50.153 1 62.72 ? O2' ADP 1328 E 1 HETATM 17 C C1' ADP . . . E 4 1.593 -2.91 -50.151 1 61.42 ? C1' ADP 1328 E 1 HETATM 18 N N9 ADP . . . E 4 1.87 -4.315 -50.528 1 58.28 ? N9 ADP 1328 E 1 HETATM 19 C C8 ADP . . . E 4 1.795 -5.39 -49.717 1 56.29 ? C8 ADP 1328 E 1 HETATM 20 N N7 ADP . . . E 4 2.109 -6.529 -50.383 1 54.83 ? N7 ADP 1328 E 1 HETATM 21 C C5 ADP . . . E 4 2.391 -6.18 -51.65 1 54.57 ? C5 ADP 1328 E 1 HETATM 22 C C6 ADP . . . E 4 2.788 -6.888 -52.883 1 54.37 ? C6 ADP 1328 E 1 HETATM 23 N N6 ADP . . . E 4 2.959 -8.227 -52.875 1 52.39 ? N6 ADP 1328 E 1 HETATM 24 N N1 ADP . . . E 4 2.97 -6.142 -54.007 1 56.41 ? N1 ADP 1328 E 1 HETATM 25 C C2 ADP . . . E 4 2.808 -4.796 -54.023 1 56.35 ? C2 ADP 1328 E 1 HETATM 26 N N3 ADP . . . E 4 2.444 -4.097 -52.935 1 56.16 ? N3 ADP 1328 E 1 HETATM 27 C C4 ADP . . . E 4 2.229 -4.721 -51.748 1 56.4 ? C4 ADP 1328 E 1 # _model_server_stats.io_time_ms 26 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 252 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 27 #