data_6OBY # _model_server_result.job_id UwIsEqY57fQyL4aokk2toQ _model_server_result.datetime_utc '2024-11-22 04:56:20' _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 6oby # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":301}' # _entry.id 6OBY # _exptl.entry_id 6OBY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 2 _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 90.09 _cell.angle_gamma 90 _cell.entry_id 6OBY _cell.length_a 51.44 _cell.length_b 67.682 _cell.length_c 79.403 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6OBY _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 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 _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 covale ? covale1 A C VAL 23 A VAL 23 1_555 A N MSE 24 A MSE 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.345 ? covale ? covale2 A C MSE 24 A MSE 24 1_555 A N SER 25 A SER 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? covale ? covale3 A C VAL 92 A VAL 92 1_555 A N MSE 93 A MSE 93 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale4 A C MSE 93 A MSE 93 1_555 A N SER 94 A SER 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale5 A C GLY 115 A GLY 115 1_555 A N MSE 116 A MSE 116 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? covale ? covale6 A C MSE 116 A MSE 116 1_555 A N ILE 117 A ILE 117 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale7 A C VAL 147 A VAL 147 1_555 A N MSE 148 A MSE 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale8 A C MSE 148 A MSE 148 1_555 A N GLN 149 A GLN 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.342 ? covale ? covale9 A C THR 175 A THR 175 1_555 A N MSE 176 A MSE 176 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.346 ? covale ? covale10 A C MSE 176 A MSE 176 1_555 A N ALA 177 A ALA 177 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.34 ? covale ? covale11 A C ASN 190 A ASN 190 1_555 A N MSE 191 A MSE 191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale12 A C MSE 191 A MSE 191 1_555 A N ALA 192 A ALA 192 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale13 B C VAL 23 B VAL 23 1_555 B N MSE 24 B MSE 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.346 ? covale ? covale14 B C MSE 24 B MSE 24 1_555 B N SER 25 B SER 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? covale ? covale15 B C VAL 92 B VAL 92 1_555 B N MSE 93 B MSE 93 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale16 B C MSE 93 B MSE 93 1_555 B N SER 94 B SER 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale17 B C GLY 115 B GLY 115 1_555 B N MSE 116 B MSE 116 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.34 ? covale ? covale18 B C MSE 116 B MSE 116 1_555 B N ILE 117 B ILE 117 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale19 B C VAL 147 B VAL 147 1_555 B N MSE 148 B MSE 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale20 B C MSE 148 B MSE 148 1_555 B N GLN 149 B GLN 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.341 ? covale ? covale21 B C THR 175 B THR 175 1_555 B N MSE 176 B MSE 176 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.342 ? covale ? covale22 B C MSE 176 B MSE 176 1_555 B N ALA 177 B ALA 177 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? covale ? covale23 B C ASN 190 B ASN 190 1_555 B N MSE 191 B MSE 191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale24 B C MSE 191 B MSE 191 1_555 B N ALA 192 B ALA 192 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? # _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 6OBY _atom_sites.fract_transf_matrix[1][1] 0.01944 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000031 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014775 _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] 0.012594 _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 ADP A 1 301 301 ADP ADP . D 3 CO A 1 302 1 CO CO . E 2 ADP B 1 301 301 ADP ADP . F 4 HOH A 1 401 275 HOH HOH . F 4 HOH A 2 402 277 HOH HOH . F 4 HOH A 3 403 271 HOH HOH . F 4 HOH A 4 404 274 HOH HOH . G 4 HOH B 1 401 270 HOH HOH . G 4 HOH B 2 402 271 HOH HOH . G 4 HOH B 3 403 275 HOH HOH . G 4 HOH B 4 404 274 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 2 -9.719 -20.283 23.64 1 43.4 ? PB ADP 301 B 1 HETATM 2 O O1B ADP . . . E 2 -10.633 -20.169 22.467 1 44.28 ? O1B ADP 301 B 1 HETATM 3 O O2B ADP . . . E 2 -9.787 -19.103 24.588 1 45.38 ? O2B ADP 301 B 1 HETATM 4 O O3B ADP . . . E 2 -9.841 -21.604 24.346 1 47.16 ? O3B ADP 301 B 1 HETATM 5 P PA ADP . . . E 2 -7.636 -21.39 22.116 1 45.03 ? PA ADP 301 B 1 HETATM 6 O O1A ADP . . . E 2 -8.554 -21.636 20.967 1 44.07 ? O1A ADP 301 B 1 HETATM 7 O O2A ADP . . . E 2 -7.324 -22.542 23.014 1 47.46 ? O2A ADP 301 B 1 HETATM 8 O O3A ADP . . . E 2 -8.267 -20.241 23.012 1 43.23 ? O3A ADP 301 B 1 HETATM 9 O O5' ADP . . . E 2 -6.268 -20.692 21.632 1 42.48 ? O5' ADP 301 B 1 HETATM 10 C C5' ADP . . . E 2 -6.316 -19.57 20.72 1 41.34 ? C5' ADP 301 B 1 HETATM 11 C C4' ADP . . . E 2 -5.31 -19.77 19.613 1 41.85 ? C4' ADP 301 B 1 HETATM 12 O O4' ADP . . . E 2 -3.982 -19.468 20.109 1 40.56 ? O4' ADP 301 B 1 HETATM 13 C C3' ADP . . . E 2 -5.178 -21.184 19.036 1 44.25 ? C3' ADP 301 B 1 HETATM 14 O O3' ADP . . . E 2 -4.676 -21.101 17.713 1 43.6 ? O3' ADP 301 B 1 HETATM 15 C C2' ADP . . . E 2 -4.107 -21.793 19.942 1 47.41 ? C2' ADP 301 B 1 HETATM 16 O O2' ADP . . . E 2 -3.517 -22.982 19.449 1 51.25 ? O2' ADP 301 B 1 HETATM 17 C C1' ADP . . . E 2 -3.158 -20.603 20 1 41.3 ? C1' ADP 301 B 1 HETATM 18 N N9 ADP . . . E 2 -2.295 -20.596 21.163 1 38.71 ? N9 ADP 301 B 1 HETATM 19 C C8 ADP . . . E 2 -2.699 -20.677 22.469 1 35.84 ? C8 ADP 301 B 1 HETATM 20 N N7 ADP . . . E 2 -1.702 -20.613 23.312 1 36.28 ? N7 ADP 301 B 1 HETATM 21 C C5 ADP . . . E 2 -0.575 -20.477 22.512 1 35.76 ? C5 ADP 301 B 1 HETATM 22 C C6 ADP . . . E 2 0.793 -20.346 22.813 1 34.91 ? C6 ADP 301 B 1 HETATM 23 N N6 ADP . . . E 2 1.276 -20.304 24.051 1 33.69 ? N6 ADP 301 B 1 HETATM 24 N N1 ADP . . . E 2 1.648 -20.215 21.771 1 35.44 ? N1 ADP 301 B 1 HETATM 25 C C2 ADP . . . E 2 1.153 -20.227 20.527 1 34.15 ? C2 ADP 301 B 1 HETATM 26 N N3 ADP . . . E 2 -0.108 -20.343 20.126 1 33.95 ? N3 ADP 301 B 1 HETATM 27 C C4 ADP . . . E 2 -0.932 -20.462 21.178 1 36.28 ? C4 ADP 301 B 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 268 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #