data_3VKH # _model_server_result.job_id tAIsV_XnmhblK9_IuYc5Eg _model_server_result.datetime_utc '2024-12-20 01:27:43' _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 3vkh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":9004}' # _entry.id 3VKH # _exptl.entry_id 3VKH _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 8 _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 3VKH _cell.length_a 195.726 _cell.length_b 228.955 _cell.length_c 201.168 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VKH _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 ? monomeric 1 author_defined_assembly 1 ? monomeric 1 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,C,D,E,F 1 1 B,G,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 C N N ? 2 D N N ? 2 E N N ? 2 F N N ? 2 G N N ? 2 H N N ? 2 I N N ? 2 J 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 3VKH _atom_sites.fract_transf_matrix[1][1] 0.005109 _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] 0.004368 _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] 0.004971 _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 C 2 ADP A 1 9001 9001 ADP ADP . D 2 ADP A 1 9002 9002 ADP ADP . E 2 ADP A 1 9003 9003 ADP ADP . F 2 ADP A 1 9004 9004 ADP ADP . G 2 ADP B 1 9007 9007 ADP ADP . H 2 ADP B 1 9008 9008 ADP ADP . I 2 ADP B 1 9009 9009 ADP ADP . J 2 ADP B 1 9010 9010 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 . . . F 2 63.421 87.258 109.31 1 129.3 ? PB ADP 9004 A 1 HETATM 2 O O1B ADP . . . F 2 64.282 87.881 108.238 1 129.3 ? O1B ADP 9004 A 1 HETATM 3 O O2B ADP . . . F 2 64.169 86.334 110.236 1 129.3 ? O2B ADP 9004 A 1 HETATM 4 O O3B ADP . . . F 2 62.501 88.231 110.007 1 129.3 ? O3B ADP 9004 A 1 HETATM 5 P PA ADP . . . F 2 61.566 85.107 109.187 1 129.3 ? PA ADP 9004 A 1 HETATM 6 O O1A ADP . . . F 2 60.128 85.254 108.754 1 129.3 ? O1A ADP 9004 A 1 HETATM 7 O O2A ADP . . . F 2 61.887 85.058 110.666 1 129.3 ? O2A ADP 9004 A 1 HETATM 8 O O3A ADP . . . F 2 62.413 86.297 108.485 1 129.3 ? O3A ADP 9004 A 1 HETATM 9 O O5' ADP . . . F 2 62.148 83.782 108.466 1 129.3 ? O5' ADP 9004 A 1 HETATM 10 C C5' ADP . . . F 2 63.273 83.056 108.976 1 129.3 ? C5' ADP 9004 A 1 HETATM 11 C C4' ADP . . . F 2 63.246 81.625 108.432 1 129.3 ? C4' ADP 9004 A 1 HETATM 12 O O4' ADP . . . F 2 64.374 80.877 108.918 1 129.3 ? O4' ADP 9004 A 1 HETATM 13 C C3' ADP . . . F 2 61.986 80.876 108.855 1 129.3 ? C3' ADP 9004 A 1 HETATM 14 O O3' ADP . . . F 2 61.183 80.546 107.713 1 129.3 ? O3' ADP 9004 A 1 HETATM 15 C C2' ADP . . . F 2 62.454 79.64 109.616 1 129.3 ? C2' ADP 9004 A 1 HETATM 16 O O2' ADP . . . F 2 61.977 78.426 109.014 1 129.3 ? O2' ADP 9004 A 1 HETATM 17 C C1' ADP . . . F 2 63.971 79.692 109.62 1 129.3 ? C1' ADP 9004 A 1 HETATM 18 N N9 ADP . . . F 2 64.502 79.686 111.023 1 129.3 ? N9 ADP 9004 A 1 HETATM 19 C C8 ADP . . . F 2 64.641 80.76 111.839 1 129.3 ? C8 ADP 9004 A 1 HETATM 20 N N7 ADP . . . F 2 65.155 80.392 113.044 1 129.3 ? N7 ADP 9004 A 1 HETATM 21 C C5 ADP . . . F 2 65.355 79.065 113.015 1 129.3 ? C5 ADP 9004 A 1 HETATM 22 C C6 ADP . . . F 2 65.876 78.021 113.951 1 129.3 ? C6 ADP 9004 A 1 HETATM 23 N N6 ADP . . . F 2 66.296 78.346 115.196 1 129.3 ? N6 ADP 9004 A 1 HETATM 24 N N1 ADP . . . F 2 65.915 76.722 113.511 1 129.3 ? N1 ADP 9004 A 1 HETATM 25 C C2 ADP . . . F 2 65.502 76.355 112.266 1 129.3 ? C2 ADP 9004 A 1 HETATM 26 N N3 ADP . . . F 2 65.019 77.26 111.373 1 129.3 ? N3 ADP 9004 A 1 HETATM 27 C C4 ADP . . . F 2 64.922 78.598 111.677 1 129.3 ? C4 ADP 9004 A 1 # _model_server_stats.io_time_ms 77 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 38 _model_server_stats.query_time_ms 282 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 27 #