data_4BIY # _model_server_result.job_id ul2VMVR6r0qnv9-q-3iFBQ _model_server_result.datetime_utc '2024-11-14 17:36:41' _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 4biy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":501}' # _entry.id 4BIY # _exptl.entry_id 4BIY _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 99.19 _cell.angle_gamma 90 _cell.entry_id 4BIY _cell.length_a 91.753 _cell.length_b 139.109 _cell.length_c 114.077 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4BIY _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 1 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,G 1 1 C,D,H,I,J 2 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 E N N ? 2 H 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 4BIY _atom_sites.fract_transf_matrix[1][1] 0.010899 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001763 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007189 _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] 0.00888 _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 E 2 ADP A 1 501 501 ADP ADP . F 3 SO4 A 1 1457 1457 SO4 SO4 . G 3 SO4 B 1 1457 1457 SO4 SO4 . H 2 ADP C 1 501 501 ADP ADP . I 3 SO4 C 1 1457 1457 SO4 SO4 . J 3 SO4 D 1 1457 1457 SO4 SO4 . # 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 . . . H 2 79.214 -24.302 8.449 1 98.82 ? PB ADP 501 C 1 HETATM 2 O O1B ADP . . . H 2 78.652 -25.681 8.157 1 100.85 ? O1B ADP 501 C 1 HETATM 3 O O2B ADP . . . H 2 78.072 -23.289 8.845 1 94.84 ? O2B ADP 501 C 1 HETATM 4 O O3B ADP . . . H 2 79.98 -23.811 7.194 1 99.9 ? O3B ADP 501 C 1 HETATM 5 P PA ADP . . . H 2 80.2 -25.379 10.958 1 92.75 ? PA ADP 501 C 1 HETATM 6 O O1A ADP . . . H 2 80.394 -24.56 12.18 1 91.62 ? O1A ADP 501 C 1 HETATM 7 O O2A ADP . . . H 2 78.845 -26.111 11.012 1 94.05 ? O2A ADP 501 C 1 HETATM 8 O O3A ADP . . . H 2 80.229 -24.409 9.683 1 95.44 ? O3A ADP 501 C 1 HETATM 9 O O5' ADP . . . H 2 81.39 -26.414 10.827 1 90.01 ? O5' ADP 501 C 1 HETATM 10 C C5' ADP . . . H 2 82.757 -25.959 10.826 1 86.1 ? C5' ADP 501 C 1 HETATM 11 C C4' ADP . . . H 2 83.546 -26.63 9.733 1 86.27 ? C4' ADP 501 C 1 HETATM 12 O O4' ADP . . . H 2 83.72 -28.018 10.08 1 89.43 ? O4' ADP 501 C 1 HETATM 13 C C3' ADP . . . H 2 82.927 -26.661 8.34 1 87.33 ? C3' ADP 501 C 1 HETATM 14 O O3' ADP . . . H 2 83.107 -25.468 7.587 1 86.27 ? O3' ADP 501 C 1 HETATM 15 C C2' ADP . . . H 2 83.637 -27.856 7.707 1 90.15 ? C2' ADP 501 C 1 HETATM 16 O O2' ADP . . . H 2 84.902 -27.508 7.157 1 88.34 ? O2' ADP 501 C 1 HETATM 17 C C1' ADP . . . H 2 83.756 -28.815 8.905 1 91.72 ? C1' ADP 501 C 1 HETATM 18 N N9 ADP . . . H 2 82.721 -29.859 8.98 1 92.34 ? N9 ADP 501 C 1 HETATM 19 C C8 ADP . . . H 2 81.479 -29.771 9.567 1 89.76 ? C8 ADP 501 C 1 HETATM 20 N N7 ADP . . . H 2 80.745 -30.842 9.416 1 89.78 ? N7 ADP 501 C 1 HETATM 21 C C5 ADP . . . H 2 81.55 -31.706 8.682 1 93.68 ? C5 ADP 501 C 1 HETATM 22 C C6 ADP . . . H 2 81.347 -33.001 8.183 1 98.74 ? C6 ADP 501 C 1 HETATM 23 N N6 ADP . . . H 2 80.198 -33.665 8.303 1 101.25 ? N6 ADP 501 C 1 HETATM 24 N N1 ADP . . . H 2 82.366 -33.584 7.502 1 100.78 ? N1 ADP 501 C 1 HETATM 25 C C2 ADP . . . H 2 83.498 -32.894 7.323 1 99.91 ? C2 ADP 501 C 1 HETATM 26 N N3 ADP . . . H 2 83.797 -31.658 7.736 1 97.11 ? N3 ADP 501 C 1 HETATM 27 C C4 ADP . . . H 2 82.774 -31.106 8.42 1 94.38 ? C4 ADP 501 C 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 219 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 27 #