data_1NY6 # _model_server_result.job_id gNwsPg-zeucL2jm1tIYBCA _model_server_result.datetime_utc '2024-11-07 21:51:38' _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 1ny6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"S","auth_seq_id":3}' # _entry.id 1NY6 # _exptl.entry_id 1NY6 _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 14 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 70.25 _cell.angle_beta 85.9 _cell.angle_gamma 73.27 _cell.entry_id 1NY6 _cell.length_a 106.788 _cell.length_b 108.265 _cell.length_c 110.02 _cell.Z_PDB 14 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1NY6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 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 ? heptameric 7 author_defined_assembly 1 ? heptameric 7 author_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,G,O,P,Q,R,S,T,U 1 1 H,I,J,K,L,M,N,V,W,X,Y,Z,AA,BA 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 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 ? 2 Y N N ? 2 Z N N ? 2 AA N N ? 2 BA 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 1NY6 _atom_sites.fract_transf_matrix[1][1] 0.009364 _atom_sites.fract_transf_matrix[1][2] -0.002814 _atom_sites.fract_transf_matrix[1][3] 0.00028 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009645 _atom_sites.fract_transf_matrix[2][3] -0.003396 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.009661 _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 O 2 ADP A 1 6 6 ADP ADP . P 2 ADP B 1 7 7 ADP ADP . Q 2 ADP C 1 1 1 ADP ADP . R 2 ADP D 1 2 2 ADP ADP . S 2 ADP E 1 3 3 ADP ADP . T 2 ADP F 1 4 4 ADP ADP . U 2 ADP G 1 5 5 ADP ADP . V 2 ADP H 1 14 14 ADP ADP . W 2 ADP I 1 8 8 ADP ADP . X 2 ADP J 1 9 9 ADP ADP . Y 2 ADP K 1 10 10 ADP ADP . Z 2 ADP L 1 11 11 ADP ADP . AA 2 ADP M 1 12 12 ADP ADP . BA 2 ADP N 1 13 13 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 . . . S 2 46.462 83.003 52.423 1 63.31 ? PB ADP 3 E 1 HETATM 2 O O1B ADP . . . S 2 47.706 82.373 52.872 1 69.86 ? O1B ADP 3 E 1 HETATM 3 O O2B ADP . . . S 2 46.03 84.163 53.45 1 55.17 ? O2B ADP 3 E 1 HETATM 4 O O3B ADP . . . S 2 46.592 83.539 51.04 1 69.56 ? O3B ADP 3 E 1 HETATM 5 P PA ADP . . . S 2 43.947 82.147 53.276 1 64.07 ? PA ADP 3 E 1 HETATM 6 O O1A ADP . . . S 2 44.202 82.259 54.703 1 68.35 ? O1A ADP 3 E 1 HETATM 7 O O2A ADP . . . S 2 43.269 83.34 52.823 1 79.96 ? O2A ADP 3 E 1 HETATM 8 O O3A ADP . . . S 2 45.284 81.999 52.501 1 51.01 ? O3A ADP 3 E 1 HETATM 9 O O5' ADP . . . S 2 43.005 80.951 52.912 1 54.74 ? O5' ADP 3 E 1 HETATM 10 C C5' ADP . . . S 2 43.28 79.904 52.004 1 57.13 ? C5' ADP 3 E 1 HETATM 11 C C4' ADP . . . S 2 42.036 78.97 52 1 62.01 ? C4' ADP 3 E 1 HETATM 12 O O4' ADP . . . S 2 42.396 77.924 52.875 1 69.55 ? O4' ADP 3 E 1 HETATM 13 C C3' ADP . . . S 2 40.706 79.528 52.578 1 64.84 ? C3' ADP 3 E 1 HETATM 14 O O3' ADP . . . S 2 39.583 79.001 51.854 1 63.58 ? O3' ADP 3 E 1 HETATM 15 C C2' ADP . . . S 2 40.652 79.086 54.015 1 66.81 ? C2' ADP 3 E 1 HETATM 16 O O2' ADP . . . S 2 39.292 79.01 54.49 1 63.54 ? O2' ADP 3 E 1 HETATM 17 C C1' ADP . . . S 2 41.437 77.772 53.942 1 70.34 ? C1' ADP 3 E 1 HETATM 18 N N9 ADP . . . S 2 42.233 77.445 55.166 1 69.84 ? N9 ADP 3 E 1 HETATM 19 C C8 ADP . . . S 2 43.442 77.978 55.471 1 69.82 ? C8 ADP 3 E 1 HETATM 20 N N7 ADP . . . S 2 43.869 77.487 56.609 1 74.31 ? N7 ADP 3 E 1 HETATM 21 C C5 ADP . . . S 2 42.976 76.651 57.051 1 68.85 ? C5 ADP 3 E 1 HETATM 22 C C6 ADP . . . S 2 42.862 75.849 58.173 1 64.48 ? C6 ADP 3 E 1 HETATM 23 N N6 ADP . . . S 2 43.838 75.858 59.068 1 66.93 ? N6 ADP 3 E 1 HETATM 24 N N1 ADP . . . S 2 41.743 75.043 58.358 1 62.86 ? N1 ADP 3 E 1 HETATM 25 C C2 ADP . . . S 2 40.717 75.008 57.46 1 63.3 ? C2 ADP 3 E 1 HETATM 26 N N3 ADP . . . S 2 40.817 75.797 56.352 1 69.06 ? N3 ADP 3 E 1 HETATM 27 C C4 ADP . . . S 2 41.904 76.617 56.122 1 68.68 ? C4 ADP 3 E 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 327 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #