data_6B5D # _model_server_result.job_id -FzoJ29sIQOoAgwr2DAmWQ _model_server_result.datetime_utc '2025-04-02 01:43:07' _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 6b5d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 6B5D # _exptl.entry_id 6B5D _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 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 120 _cell.entry_id 6B5D _cell.length_a 98.83 _cell.length_b 98.83 _cell.length_c 75.08 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6B5D _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 65' # _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 _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 2 _struct_asym.id B _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 covale ? covale1 A C THR 18 A THR 181 1_555 A N MSE 19 A MSE 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale2 A C MSE 19 A MSE 182 1_555 A N ALA 20 A ALA 183 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale3 A C THR 26 A THR 189 1_555 A N MSE 27 A MSE 190 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale4 A C MSE 27 A MSE 190 1_555 A N SER 28 A SER 191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale5 A C GLY 34 A GLY 197 1_555 A N MSE 35 A MSE 198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale6 A C MSE 35 A MSE 198 1_555 A N HIS 36 A HIS 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale7 A C ALA 65 A ALA 228 1_555 A N MSE 66 A MSE 229 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale8 A C MSE 66 A MSE 229 1_555 A N VAL 67 A VAL 230 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale9 A C GLN 157 A GLN 320 1_555 A N MSE 158 A MSE 321 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale10 A C MSE 158 A MSE 321 1_555 A N ASP 159 A ASP 322 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale11 A C SER 211 A SER 374 1_555 A N MSE 212 A MSE 375 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale12 A C MSE 212 A MSE 375 1_555 A N GLU 213 A GLU 376 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale13 A C ALA 266 A ALA 429 1_555 A N MSE 267 A MSE 430 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale14 A C MSE 267 A MSE 430 1_555 A N GLU 268 A GLU 431 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale15 A C THR 295 A THR 458 1_555 A N MSE 296 A MSE 459 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale16 A C MSE 296 A MSE 459 1_555 A N LEU 297 A LEU 460 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? # _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 6B5D _atom_sites.fract_transf_matrix[1][1] 0.010118 _atom_sites.fract_transf_matrix[1][2] 0.005842 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011684 _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] 0.013319 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # _pdbx_nonpoly_scheme.asym_id B _pdbx_nonpoly_scheme.entity_id 2 _pdbx_nonpoly_scheme.mon_id ADP _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 501 _pdbx_nonpoly_scheme.auth_seq_num 501 _pdbx_nonpoly_scheme.pdb_mon_id ADP _pdbx_nonpoly_scheme.auth_mon_id ADP _pdbx_nonpoly_scheme.pdb_ins_code . # 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 . . . B 2 81.381 29.744 3.052 1 84.23 ? PB ADP 501 A 1 HETATM 2 O O1B ADP . . . B 2 82.671 30.066 2.337 1 78.54 ? O1B ADP 501 A 1 HETATM 3 O O2B ADP . . . B 2 81.459 29.897 4.552 1 62.49 ? O2B ADP 501 A 1 HETATM 4 O O3B ADP . . . B 2 80.729 28.464 2.587 1 105.54 ? O3B ADP 501 A 1 HETATM 5 P PA ADP . . . B 2 79.925 31.123 1.04 1 87.27 ? PA ADP 501 A 1 HETATM 6 O O1A ADP . . . B 2 79.943 29.801 0.312 1 91.89 ? O1A ADP 501 A 1 HETATM 7 O O2A ADP . . . B 2 80.728 32.278 0.49 1 90.32 ? O2A ADP 501 A 1 HETATM 8 O O3A ADP . . . B 2 80.367 30.909 2.579 1 82.71 ? O3A ADP 501 A 1 HETATM 9 O O5' ADP . . . B 2 78.393 31.611 1.155 1 93.96 ? O5' ADP 501 A 1 HETATM 10 C C5' ADP . . . B 2 77.332 30.815 0.628 1 97.66 ? C5' ADP 501 A 1 HETATM 11 C C4' ADP . . . B 2 76.184 31.712 0.176 1 97.39 ? C4' ADP 501 A 1 HETATM 12 O O4' ADP . . . B 2 75.701 32.492 1.272 1 95.66 ? O4' ADP 501 A 1 HETATM 13 C C3' ADP . . . B 2 76.619 32.682 -0.911 1 98.72 ? C3' ADP 501 A 1 HETATM 14 O O3' ADP . . . B 2 76.069 32.306 -2.176 1 104.76 ? O3' ADP 501 A 1 HETATM 15 C C2' ADP . . . B 2 76.071 34.031 -0.5 1 95.88 ? C2' ADP 501 A 1 HETATM 16 O O2' ADP . . . B 2 75.08 34.456 -1.443 1 101.27 ? O2' ADP 501 A 1 HETATM 17 C C1' ADP . . . B 2 75.457 33.845 0.879 1 89.53 ? C1' ADP 501 A 1 HETATM 18 N N9 ADP . . . B 2 76.125 34.734 1.864 1 78.67 ? N9 ADP 501 A 1 HETATM 19 C C8 ADP . . . B 2 76.762 34.315 2.974 1 77.53 ? C8 ADP 501 A 1 HETATM 20 N N7 ADP . . . B 2 77.266 35.36 3.68 1 74.39 ? N7 ADP 501 A 1 HETATM 21 C C5 ADP . . . B 2 76.946 36.485 3.015 1 71.1 ? C5 ADP 501 A 1 HETATM 22 C C6 ADP . . . B 2 77.17 37.938 3.206 1 72.49 ? C6 ADP 501 A 1 HETATM 23 N N6 ADP . . . B 2 77.852 38.412 4.276 1 75.04 ? N6 ADP 501 A 1 HETATM 24 N N1 ADP . . . B 2 76.668 38.779 2.275 1 80.14 ? N1 ADP 501 A 1 HETATM 25 C C2 ADP . . . B 2 75.986 38.325 1.205 1 88.18 ? C2 ADP 501 A 1 HETATM 26 N N3 ADP . . . B 2 75.746 37.023 0.968 1 81.53 ? N3 ADP 501 A 1 HETATM 27 C C4 ADP . . . B 2 76.189 36.068 1.821 1 74.71 ? C4 ADP 501 A 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 383 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 27 #