data_3VTK # _model_server_result.job_id 1zdBWmR46YwEHd47BrQ_cQ _model_server_result.datetime_utc '2024-11-13 10:37:39' _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 3vtk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":400}' # _entry.id 3VTK # _exptl.entry_id 3VTK _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 1 _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 3VTK _cell.length_a 83.7 _cell.length_b 83.7 _cell.length_c 156.3 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VTK _symmetry.cell_setting ? _symmetry.Int_Tables_number 80 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 41' # _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 6_655 -x+1,-y,z -1 0 0 0 -1 0 0 0 1 83.7 0 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 35 n n PB O2B ADP sing 36 n n PB O3B ADP sing 37 n n PB O3A ADP sing 38 n n O2B HOB2 ADP sing 39 n n O3B HOB3 ADP sing 40 n n PA O1A ADP doub 41 n n PA O2A ADP sing 42 n n PA O3A ADP sing 43 n n PA O5' ADP sing 44 n n O2A HOA2 ADP sing 45 n n O5' C5' ADP sing 46 n n C5' C4' ADP sing 47 n n C5' "H5'1" ADP sing 48 n n C5' "H5'2" ADP sing 49 n n C4' O4' ADP sing 50 n n C4' C3' ADP sing 51 n n C4' H4' ADP sing 52 n n O4' C1' ADP sing 53 n n C3' O3' ADP sing 54 n n C3' C2' ADP sing 55 n n C3' H3' ADP sing 56 n n O3' HO3' ADP sing 57 n n C2' O2' ADP sing 58 n n C2' C1' ADP sing 59 n n C2' H2' ADP sing 60 n n O2' HO2' ADP sing 61 n n C1' N9 ADP sing 62 n n C1' H1' ADP sing 63 n n N9 C8 ADP sing 64 n y N9 C4 ADP sing 65 n y C8 N7 ADP doub 66 n y C8 H8 ADP sing 67 n n N7 C5 ADP sing 68 n y C5 C6 ADP sing 69 n y C5 C4 ADP doub 70 n y C6 N6 ADP sing 71 n n C6 N1 ADP doub 72 n y N6 HN61 ADP sing 73 n n N6 HN62 ADP sing 74 n n N1 C2 ADP sing 75 n y C2 N3 ADP doub 76 n y C2 H2 ADP sing 77 n n N3 C4 ADP sing 78 n y # _atom_sites.entry_id 3VTK _atom_sites.fract_transf_matrix[1][1] 0.011947 _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] 0.011947 _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] 0.006398 _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 B 2 ADP A 1 400 400 ADP ADP . C 3 5IU A 1 500 500 5IU 5IU . D 4 HOH A 1 601 601 HOH HOH . D 4 HOH A 2 602 602 HOH HOH . D 4 HOH A 3 603 603 HOH HOH . D 4 HOH A 4 604 604 HOH HOH . D 4 HOH A 5 605 605 HOH HOH . D 4 HOH A 6 606 606 HOH HOH . # 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 . . . B 2 38.566 25.069 35.141 1 44.25 ? PB ADP 400 A 1 HETATM 2 O O1B ADP . . . B 2 37.392 25.525 35.91 1 34.63 ? O1B ADP 400 A 1 HETATM 3 O O2B ADP . . . B 2 39.605 24.517 36.032 1 36.12 ? O2B ADP 400 A 1 HETATM 4 O O3B ADP . . . B 2 38.142 24.06 34.16 1 36.39 ? O3B ADP 400 A 1 HETATM 5 P PA ADP . . . B 2 39.554 27.607 34.499 1 56.58 ? PA ADP 400 A 1 HETATM 6 O O1A ADP . . . B 2 39.97 27.969 35.88 1 57.82 ? O1A ADP 400 A 1 HETATM 7 O O2A ADP . . . B 2 40.552 28.033 33.479 1 58.12 ? O2A ADP 400 A 1 HETATM 8 O O3A ADP . . . B 2 39.11 26.192 34.331 1 49.48 ? O3A ADP 400 A 1 HETATM 9 O O5' ADP . . . B 2 38.245 28.504 34.184 1 50.67 ? O5' ADP 400 A 1 HETATM 10 C C5' ADP . . . B 2 37.422 28.282 33.011 1 57.78 ? C5' ADP 400 A 1 HETATM 11 C C4' ADP . . . B 2 37.532 29.461 32.018 1 60.02 ? C4' ADP 400 A 1 HETATM 12 O O4' ADP . . . B 2 36.656 30.57 32.448 1 60.98 ? O4' ADP 400 A 1 HETATM 13 C C3' ADP . . . B 2 38.928 30.042 32.036 1 63.31 ? C3' ADP 400 A 1 HETATM 14 O O3' ADP . . . B 2 39.175 30.607 30.744 1 63.14 ? O3' ADP 400 A 1 HETATM 15 C C2' ADP . . . B 2 38.883 31.131 33.071 1 66.28 ? C2' ADP 400 A 1 HETATM 16 O O2' ADP . . . B 2 39.816 32.169 32.791 1 73.19 ? O2' ADP 400 A 1 HETATM 17 C C1' ADP . . . B 2 37.446 31.645 33.072 1 65.61 ? C1' ADP 400 A 1 HETATM 18 N N9 ADP . . . B 2 36.963 31.975 34.437 1 66 ? N9 ADP 400 A 1 HETATM 19 C C8 ADP . . . B 2 37.134 31.263 35.609 1 67.55 ? C8 ADP 400 A 1 HETATM 20 N N7 ADP . . . B 2 36.593 31.842 36.644 1 69.82 ? N7 ADP 400 A 1 HETATM 21 C C5 ADP . . . B 2 36.003 33.006 36.209 1 66.08 ? C5 ADP 400 A 1 HETATM 22 C C6 ADP . . . B 2 35.266 34.026 36.844 1 65.04 ? C6 ADP 400 A 1 HETATM 23 N N6 ADP . . . B 2 34.997 34.013 38.166 1 63.23 ? N6 ADP 400 A 1 HETATM 24 N N1 ADP . . . B 2 34.836 35.054 36.072 1 63.35 ? N1 ADP 400 A 1 HETATM 25 C C2 ADP . . . B 2 35.101 35.047 34.766 1 64.27 ? C2 ADP 400 A 1 HETATM 26 N N3 ADP . . . B 2 35.77 34.147 34.044 1 66.16 ? N3 ADP 400 A 1 HETATM 27 C C4 ADP . . . B 2 36.219 33.106 34.809 1 65.74 ? C4 ADP 400 A 1 # _model_server_stats.io_time_ms 57 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 316 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #