data_5DYI # _model_server_result.job_id hgQrpRFeH_CJRPN8c-rIOw _model_server_result.datetime_utc '2024-11-16 12:32:29' _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":"T","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 . . . T 2 -59.823 -25.332 87.29 1 71.02 ? PB ADP 800 H 1 HETATM 2 O O1B ADP . . . T 2 -60.851 -25.92 86.441 1 71.15 ? O1B ADP 800 H 1 HETATM 3 O O2B ADP . . . T 2 -60.196 -23.925 87.083 1 71.81 ? O2B ADP 800 H 1 HETATM 4 O O3B ADP . . . T 2 -58.373 -25.658 87.228 1 69.85 ? O3B ADP 800 H 1 HETATM 5 P PA ADP . . . T 2 -60.979 -26.164 89.817 1 74.03 ? PA ADP 800 H 1 HETATM 6 O O1A ADP . . . T 2 -61.997 -25.139 89.556 1 73.04 ? O1A ADP 800 H 1 HETATM 7 O O2A ADP . . . T 2 -61.283 -27.593 90.05 1 74.8 ? O2A ADP 800 H 1 HETATM 8 O O3A ADP . . . T 2 -59.867 -25.926 88.739 1 72.51 ? O3A ADP 800 H 1 HETATM 9 O O5' ADP . . . T 2 -60.092 -25.853 91.103 1 74.52 ? O5' ADP 800 H 1 HETATM 10 C C5' ADP . . . T 2 -60.72 -25.195 92.183 1 75.77 ? C5' ADP 800 H 1 HETATM 11 C C4' ADP . . . T 2 -60.104 -25.53 93.536 1 77.11 ? C4' ADP 800 H 1 HETATM 12 O O4' ADP . . . T 2 -60.229 -24.405 94.442 1 76.35 ? O4' ADP 800 H 1 HETATM 13 C C3' ADP . . . T 2 -60.815 -26.71 94.173 1 77.67 ? C3' ADP 800 H 1 HETATM 14 O O3' ADP . . . T 2 -59.818 -27.673 94.53 1 80.39 ? O3' ADP 800 H 1 HETATM 15 C C2' ADP . . . T 2 -61.599 -26.132 95.35 1 76.48 ? C2' ADP 800 H 1 HETATM 16 O O2' ADP . . . T 2 -61.218 -26.686 96.61 1 76.63 ? O2' ADP 800 H 1 HETATM 17 C C1' ADP . . . T 2 -61.329 -24.633 95.332 1 75.18 ? C1' ADP 800 H 1 HETATM 18 N N9 ADP . . . T 2 -62.526 -23.823 94.92 1 72.96 ? N9 ADP 800 H 1 HETATM 19 C C8 ADP . . . T 2 -62.592 -22.995 93.855 1 72.05 ? C8 ADP 800 H 1 HETATM 20 N N7 ADP . . . T 2 -63.791 -22.38 93.754 1 70.93 ? N7 ADP 800 H 1 HETATM 21 C C5 ADP . . . T 2 -64.538 -22.806 94.772 1 71.37 ? C5 ADP 800 H 1 HETATM 22 C C6 ADP . . . T 2 -65.915 -22.538 95.248 1 72.57 ? C6 ADP 800 H 1 HETATM 23 N N6 ADP . . . T 2 -66.704 -21.679 94.578 1 73.64 ? N6 ADP 800 H 1 HETATM 24 N N1 ADP . . . T 2 -66.351 -23.179 96.349 1 73.71 ? N1 ADP 800 H 1 HETATM 25 C C2 ADP . . . T 2 -65.533 -24.03 97.005 1 74.13 ? C2 ADP 800 H 1 HETATM 26 N N3 ADP . . . T 2 -64.272 -24.317 96.625 1 73.46 ? N3 ADP 800 H 1 HETATM 27 C C4 ADP . . . T 2 -63.707 -23.746 95.538 1 72.26 ? C4 ADP 800 H 1 # _model_server_stats.io_time_ms 89 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 54 _model_server_stats.query_time_ms 279 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #