data_5DYI # _model_server_result.job_id Pd2h3bpoPvBaVMpRiLMZAQ _model_server_result.datetime_utc '2024-11-16 12:37:25' _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 5dyi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":800}' # _entry.id 5DYI # _exptl.entry_id 5DYI _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 12 _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 5DYI _cell.length_a 146.44 _cell.length_b 176.21 _cell.length_c 256.87 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5DYI _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # 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 hexameric 6 author_and_software_defined_assembly 1 PISA hexameric 6 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,C,D,E,F,M,N,O,P,Q,R 1 1 G,H,I,J,K,L,S,T,U,V,W,X 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 M N N ? 2 N N N ? 2 O N N ? 2 P N N ? 2 Q N N ? 2 R N N ? 2 S N N ? 2 T N N ? 2 U N N ? 2 V N N ? 2 W N N ? 2 X 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 5DYI _atom_sites.fract_transf_matrix[1][1] 0.006829 _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] 0.005675 _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] 0.003893 _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 M 2 ADP A 1 800 800 ADP ADP . N 2 ADP B 1 800 800 ADP ADP . O 2 ADP C 1 800 800 ADP ADP . P 2 ADP D 1 800 800 ADP ADP . Q 2 ADP E 1 800 800 ADP ADP . R 2 ADP F 1 800 800 ADP ADP . S 2 ADP G 1 800 800 ADP ADP . T 2 ADP H 1 800 800 ADP ADP . U 2 ADP I 1 800 800 ADP ADP . V 2 ADP J 1 800 800 ADP ADP . W 2 ADP K 1 800 800 ADP ADP . X 2 ADP L 1 800 800 ADP ADP . # 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 . . . M 2 -15.279 -69.095 55.776 1 81.24 ? PB ADP 800 A 1 HETATM 2 O O1B ADP . . . M 2 -16.074 -68.178 54.894 1 80.52 ? O1B ADP 800 A 1 HETATM 3 O O2B ADP . . . M 2 -15.231 -70.518 55.264 1 79.23 ? O2B ADP 800 A 1 HETATM 4 O O3B ADP . . . M 2 -15.285 -68.78 57.266 1 82.9 ? O3B ADP 800 A 1 HETATM 5 P PA ADP . . . M 2 -12.698 -67.994 55.01 1 72.56 ? PA ADP 800 A 1 HETATM 6 O O1A ADP . . . M 2 -12.42 -68.445 53.665 1 75.4 ? O1A ADP 800 A 1 HETATM 7 O O2A ADP . . . M 2 -13.028 -66.613 55.132 1 73.28 ? O2A ADP 800 A 1 HETATM 8 O O3A ADP . . . M 2 -13.733 -68.994 55.568 1 76 ? O3A ADP 800 A 1 HETATM 9 O O5' ADP . . . M 2 -11.47 -68.044 55.963 1 70.45 ? O5' ADP 800 A 1 HETATM 10 C C5' ADP . . . M 2 -10.375 -68.782 55.552 1 69.95 ? C5' ADP 800 A 1 HETATM 11 C C4' ADP . . . M 2 -9.172 -68.128 56.172 1 70.94 ? C4' ADP 800 A 1 HETATM 12 O O4' ADP . . . M 2 -8.207 -69.174 56.432 1 70.88 ? O4' ADP 800 A 1 HETATM 13 C C3' ADP . . . M 2 -8.556 -67.086 55.237 1 70.98 ? C3' ADP 800 A 1 HETATM 14 O O3' ADP . . . M 2 -8.496 -65.796 55.868 1 73.67 ? O3' ADP 800 A 1 HETATM 15 C C2' ADP . . . M 2 -7.207 -67.708 54.811 1 70.02 ? C2' ADP 800 A 1 HETATM 16 O O2' ADP . . . M 2 -6.016 -66.946 55.162 1 67.45 ? O2' ADP 800 A 1 HETATM 17 C C1' ADP . . . M 2 -7.185 -69.136 55.412 1 70.04 ? C1' ADP 800 A 1 HETATM 18 N N9 ADP . . . M 2 -7.404 -70.3 54.43 1 69.48 ? N9 ADP 800 A 1 HETATM 19 C C8 ADP . . . M 2 -8.434 -71.215 54.427 1 68.49 ? C8 ADP 800 A 1 HETATM 20 N N7 ADP . . . M 2 -8.369 -72.143 53.428 1 67.01 ? N7 ADP 800 A 1 HETATM 21 C C5 ADP . . . M 2 -7.243 -71.825 52.755 1 68.64 ? C5 ADP 800 A 1 HETATM 22 C C6 ADP . . . M 2 -6.531 -72.374 51.567 1 70.63 ? C6 ADP 800 A 1 HETATM 23 N N6 ADP . . . M 2 -7.038 -73.451 50.963 1 70.8 ? N6 ADP 800 A 1 HETATM 24 N N1 ADP . . . M 2 -5.389 -71.784 51.103 1 73.35 ? N1 ADP 800 A 1 HETATM 25 C C2 ADP . . . M 2 -4.89 -70.688 51.749 1 73.21 ? C2 ADP 800 A 1 HETATM 26 N N3 ADP . . . M 2 -5.476 -70.14 52.837 1 71.61 ? N3 ADP 800 A 1 HETATM 27 C C4 ADP . . . M 2 -6.618 -70.641 53.397 1 69.69 ? C4 ADP 800 A 1 # _model_server_stats.io_time_ms 84 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 69 _model_server_stats.query_time_ms 283 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #