data_2YBE # _model_server_result.job_id 8Y5SgEGE1iVkYibIVyLo5w _model_server_result.datetime_utc '2024-11-05 04:51:49' _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 2ybe # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1419}' # _entry.id 2YBE # _exptl.entry_id 2YBE _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 "L-ADENOSINE-5'-DIPHOSPHATE" _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 2YBE _cell.length_a 39.202 _cell.length_b 91.03 _cell.length_c 108.807 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2YBE _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 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 _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 4 _struct_asym.id D _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 OD2 ASP 375 A ASP 374 1_555 B MG MG . A MG 1417 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.996 ? metalc ? metalc2 B MG MG . A MG 1417 1_555 D O3B LA8 . A LA8 1419 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.819 ? metalc ? metalc3 B MG MG . A MG 1417 1_555 D O1A LA8 . A LA8 1419 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.866 ? metalc ? metalc4 B MG MG . A MG 1417 1_555 G O HOH . A HOH 2112 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? metalc ? metalc5 B MG MG . A MG 1417 1_555 G O HOH . A HOH 2115 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.225 ? metalc ? metalc6 D O1B LA8 . A LA8 1419 1_555 E AL ALF . A ALF 1420 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.953 ? metalc ? metalc7 E AL ALF . A ALF 1420 1_555 F O2 3PG . A 3PG 1421 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.953 ? # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id LA8 _chem_comp.mon_nstd_flag . _chem_comp.name "L-ADENOSINE-5'-DIPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms L-ADP # 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 C2 N1 LA8 doub 194 n y N1 C6 LA8 sing 195 n y C2 N3 LA8 sing 196 n y C2 H2 LA8 sing 197 n n N3 C4 LA8 doub 198 n y C4 N9 LA8 sing 199 n y C4 C5 LA8 sing 200 n y C6 C5 LA8 doub 201 n y C5 N7 LA8 sing 202 n y C6 N6 LA8 sing 203 n n N6 HN6 LA8 sing 204 n n N6 HN6A LA8 sing 205 n n C8 N7 LA8 doub 206 n y N9 C8 LA8 sing 207 n y C8 H8 LA8 sing 208 n n C1' N9 LA8 sing 209 n n O1A PA LA8 doub 210 n n PA O5' LA8 sing 211 n n PA O3A LA8 sing 212 n n PA O2A LA8 sing 213 n n O2B PB LA8 doub 214 n n O1B PB LA8 sing 215 n n PB O3A LA8 sing 216 n n PB O3B LA8 sing 217 n n C3' C1' LA8 sing 218 n n O4' C1' LA8 sing 219 n n C1' H1' LA8 sing 220 n n O1B HO1B LA8 sing 221 n n O2' C2' LA8 sing 222 n n C2' C4' LA8 sing 223 n n C2' C3' LA8 sing 224 n n C2' H2' LA8 sing 225 n n O2' HO2' LA8 sing 226 n n O2A HO2A LA8 sing 227 n n C3' O3' LA8 sing 228 n n C3' H3' LA8 sing 229 n n O3' HO3' LA8 sing 230 n n O3B HO3B LA8 sing 231 n n C5' C4' LA8 sing 232 n n C4' O4' LA8 sing 233 n n C4' H4' LA8 sing 234 n n C5' O5' LA8 sing 235 n n C5' H5' LA8 sing 236 n n C5' "H5'A" LA8 sing 237 n n # _atom_sites.entry_id 2YBE _atom_sites.fract_transf_matrix[1][1] 0.025509 _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] 0.010985 _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] 0.009191 _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 MG A 1 1417 1417 MG MG . C 3 CL A 1 1418 1418 CL CL . D 4 LA8 A 1 1419 1419 LA8 LA8 . E 5 ALF A 1 1420 1420 ALF ALF . F 6 3PG A 1 1421 1421 3PG 3PG . G 7 HOH A 1 2001 2001 HOH HOH . G 7 HOH A 2 2002 2002 HOH HOH . G 7 HOH A 3 2003 2003 HOH HOH . G 7 HOH A 4 2004 2004 HOH HOH . G 7 HOH A 5 2005 2005 HOH HOH . G 7 HOH A 6 2006 2006 HOH HOH . G 7 HOH A 7 2007 2007 HOH HOH . G 7 HOH A 8 2008 2008 HOH HOH . G 7 HOH A 9 2009 2009 HOH HOH . G 7 HOH A 10 2010 2010 HOH HOH . G 7 HOH A 11 2011 2011 HOH HOH . G 7 HOH A 12 2012 2012 HOH HOH . G 7 HOH A 13 2013 2013 HOH HOH . G 7 HOH A 14 2014 2014 HOH HOH . G 7 HOH A 15 2015 2015 HOH HOH . G 7 HOH A 16 2016 2016 HOH HOH . G 7 HOH A 17 2017 2017 HOH HOH . G 7 HOH A 18 2018 2018 HOH HOH . G 7 HOH A 19 2019 2019 HOH HOH . G 7 HOH A 20 2020 2020 HOH HOH . G 7 HOH A 21 2021 2021 HOH HOH . G 7 HOH A 22 2022 2022 HOH HOH . G 7 HOH A 23 2023 2023 HOH HOH . G 7 HOH A 24 2024 2024 HOH HOH . G 7 HOH A 25 2025 2025 HOH HOH . G 7 HOH A 26 2026 2026 HOH HOH . G 7 HOH A 27 2027 2027 HOH HOH . G 7 HOH A 28 2028 2028 HOH HOH . G 7 HOH A 29 2029 2029 HOH HOH . G 7 HOH A 30 2030 2030 HOH HOH . G 7 HOH A 31 2031 2031 HOH HOH . G 7 HOH A 32 2032 2032 HOH HOH . G 7 HOH A 33 2033 2033 HOH HOH . G 7 HOH A 34 2034 2034 HOH HOH . G 7 HOH A 35 2035 2035 HOH HOH . G 7 HOH A 36 2036 2036 HOH HOH . G 7 HOH A 37 2037 2037 HOH HOH . G 7 HOH A 38 2038 2038 HOH HOH . G 7 HOH A 39 2039 2039 HOH HOH . G 7 HOH A 40 2040 2040 HOH HOH . G 7 HOH A 41 2041 2041 HOH HOH . G 7 HOH A 42 2042 2042 HOH HOH . G 7 HOH A 43 2043 2043 HOH HOH . G 7 HOH A 44 2044 2044 HOH HOH . G 7 HOH A 45 2045 2045 HOH HOH . G 7 HOH A 46 2046 2046 HOH HOH . G 7 HOH A 47 2047 2047 HOH HOH . G 7 HOH A 48 2048 2048 HOH HOH . G 7 HOH A 49 2049 2049 HOH HOH . G 7 HOH A 50 2050 2050 HOH HOH . G 7 HOH A 51 2051 2051 HOH HOH . G 7 HOH A 52 2052 2052 HOH HOH . G 7 HOH A 53 2053 2053 HOH HOH . G 7 HOH A 54 2054 2054 HOH HOH . G 7 HOH A 55 2055 2055 HOH HOH . G 7 HOH A 56 2056 2056 HOH HOH . G 7 HOH A 57 2057 2057 HOH HOH . G 7 HOH A 58 2058 2058 HOH HOH . G 7 HOH A 59 2059 2059 HOH HOH . G 7 HOH A 60 2060 2060 HOH HOH . G 7 HOH A 61 2061 2061 HOH HOH . G 7 HOH A 62 2062 2062 HOH HOH . G 7 HOH A 63 2063 2063 HOH HOH . G 7 HOH A 64 2064 2064 HOH HOH . G 7 HOH A 65 2065 2065 HOH HOH . G 7 HOH A 66 2066 2066 HOH HOH . G 7 HOH A 67 2067 2067 HOH HOH . G 7 HOH A 68 2068 2068 HOH HOH . G 7 HOH A 69 2069 2069 HOH HOH . G 7 HOH A 70 2070 2070 HOH HOH . G 7 HOH A 71 2071 2071 HOH HOH . G 7 HOH A 72 2072 2072 HOH HOH . G 7 HOH A 73 2073 2073 HOH HOH . G 7 HOH A 74 2074 2074 HOH HOH . G 7 HOH A 75 2075 2075 HOH HOH . G 7 HOH A 76 2076 2076 HOH HOH . G 7 HOH A 77 2077 2077 HOH HOH . G 7 HOH A 78 2078 2078 HOH HOH . G 7 HOH A 79 2079 2079 HOH HOH . G 7 HOH A 80 2080 2080 HOH HOH . G 7 HOH A 81 2081 2081 HOH HOH . G 7 HOH A 82 2082 2082 HOH HOH . G 7 HOH A 83 2083 2083 HOH HOH . G 7 HOH A 84 2084 2084 HOH HOH . G 7 HOH A 85 2085 2085 HOH HOH . G 7 HOH A 86 2086 2086 HOH HOH . G 7 HOH A 87 2087 2087 HOH HOH . G 7 HOH A 88 2088 2088 HOH HOH . G 7 HOH A 89 2089 2089 HOH HOH . G 7 HOH A 90 2090 2090 HOH HOH . G 7 HOH A 91 2091 2091 HOH HOH . G 7 HOH A 92 2092 2092 HOH HOH . G 7 HOH A 93 2093 2093 HOH HOH . G 7 HOH A 94 2094 2094 HOH HOH . G 7 HOH A 95 2095 2095 HOH HOH . G 7 HOH A 96 2096 2096 HOH HOH . G 7 HOH A 97 2097 2097 HOH HOH . G 7 HOH A 98 2098 2098 HOH HOH . G 7 HOH A 99 2099 2099 HOH HOH . G 7 HOH A 100 2100 2100 HOH HOH . G 7 HOH A 101 2101 2101 HOH HOH . G 7 HOH A 102 2102 2102 HOH HOH . G 7 HOH A 103 2103 2103 HOH HOH . G 7 HOH A 104 2104 2104 HOH HOH . G 7 HOH A 105 2105 2105 HOH HOH . G 7 HOH A 106 2106 2106 HOH HOH . G 7 HOH A 107 2107 2107 HOH HOH . G 7 HOH A 108 2108 2108 HOH HOH . G 7 HOH A 109 2109 2109 HOH HOH . G 7 HOH A 110 2110 2110 HOH HOH . G 7 HOH A 111 2111 2111 HOH HOH . G 7 HOH A 112 2112 2112 HOH HOH . G 7 HOH A 113 2113 2113 HOH HOH . G 7 HOH A 114 2114 2114 HOH HOH . G 7 HOH A 115 2115 2115 HOH HOH . G 7 HOH A 116 2116 2116 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 N N1 LA8 . . . D 4 -11.081 -18.25 23.234 1 31.36 ? N1 LA8 1419 A 1 HETATM 2 C C2 LA8 . . . D 4 -10.981 -17.229 22.389 1 37.32 ? C2 LA8 1419 A 1 HETATM 3 N N3 LA8 . . . D 4 -10.94 -15.948 22.778 1 32.91 ? N3 LA8 1419 A 1 HETATM 4 C C4 LA8 . . . D 4 -11.042 -15.648 24.07 1 33.34 ? C4 LA8 1419 A 1 HETATM 5 C C5 LA8 . . . D 4 -11.147 -16.682 24.996 1 32.17 ? C5 LA8 1419 A 1 HETATM 6 C C6 LA8 . . . D 4 -11.155 -17.989 24.548 1 38.2 ? C6 LA8 1419 A 1 HETATM 7 N N6 LA8 . . . D 4 -11.207 -18.962 25.454 1 35.12 ? N6 LA8 1419 A 1 HETATM 8 N N7 LA8 . . . D 4 -11.155 -16.145 26.213 1 36.22 ? N7 LA8 1419 A 1 HETATM 9 C C8 LA8 . . . D 4 -11.118 -14.766 26.046 1 34.82 ? C8 LA8 1419 A 1 HETATM 10 N N9 LA8 . . . D 4 -11.045 -14.465 24.728 1 34.62 ? N9 LA8 1419 A 1 HETATM 11 P PA LA8 . . . D 4 -5.704 -11.372 22.137 1 25.02 ? PA LA8 1419 A 1 HETATM 12 P PB LA8 . . . D 4 -5.096 -8.774 21.992 1 25.34 ? PB LA8 1419 A 1 HETATM 13 C C1' LA8 . . . D 4 -10.981 -13.075 24.049 1 30.66 ? C1' LA8 1419 A 1 HETATM 14 O O1A LA8 . . . D 4 -5.616 -11.454 20.423 1 22.17 ? O1A LA8 1419 A 1 HETATM 15 O O1B LA8 . . . D 4 -3.467 -8.532 21.844 1 26.37 ? O1B LA8 1419 A 1 HETATM 16 C C2' LA8 . . . D 4 -10.704 -12.848 21.611 1 32.08 ? C2' LA8 1419 A 1 HETATM 17 O O2' LA8 . . . D 4 -11.25 -11.923 20.661 1 27.46 ? O2' LA8 1419 A 1 HETATM 18 O O2A LA8 . . . D 4 -5.188 -12.583 22.798 1 29.42 ? O2A LA8 1419 A 1 HETATM 19 O O2B LA8 . . . D 4 -5.449 -7.562 22.937 1 29.61 ? O2B LA8 1419 A 1 HETATM 20 C C3' LA8 . . . D 4 -11.757 -13.05 22.719 1 30.58 ? C3' LA8 1419 A 1 HETATM 21 O O3' LA8 . . . D 4 -12.561 -11.846 22.731 1 29.45 ? O3' LA8 1419 A 1 HETATM 22 O O3A LA8 . . . D 4 -5.11 -10.113 22.778 1 27.12 ? O3A LA8 1419 A 1 HETATM 23 O O3B LA8 . . . D 4 -5.819 -8.707 20.659 1 27.63 ? O3B LA8 1419 A 1 HETATM 24 C C4' LA8 . . . D 4 -9.66 -12.075 22.374 1 31.4 ? C4' LA8 1419 A 1 HETATM 25 O O4' LA8 . . . D 4 -9.635 -12.767 23.68 1 31.67 ? O4' LA8 1419 A 1 HETATM 26 C C5' LA8 . . . D 4 -8.272 -12.205 21.781 1 30.64 ? C5' LA8 1419 A 1 HETATM 27 O O5' LA8 . . . D 4 -7.345 -11.282 22.473 1 28.28 ? O5' LA8 1419 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 293 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 27 #