data_2NO9 # _model_server_result.job_id s9RNUj6VBhciEfFvci4VIQ _model_server_result.datetime_utc '2024-12-24 03:33:30' _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 2no9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":301}' # _entry.id 2NO9 # _exptl.entry_id 2NO9 _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 2 _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 2NO9 _cell.length_a 52.85 _cell.length_b 134.46 _cell.length_c 155.34 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2NO9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 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 dimeric 2 author_and_software_defined_assembly 1 PISA tetrameric 4 software_defined_assembly 2 PISA tetrameric 4 software_defined_assembly 3 # 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,H 1 1 A,C,D,G 2 1,2 B,E,F,H 2 3,4 A,B,C,D,E,F,G,H 3 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' 4_566 x,-y+1,-z+1 1 0 0 0 -1 0 0 0 -1 0 134.46 155.34 3 'crystal symmetry operation' 5_545 x+1/2,y-1/2,z 1 0 0 0 1 0 0 0 1 26.425 -67.23 0 4 'crystal symmetry operation' 8_566 x+1/2,-y+3/2,-z+1 1 0 0 0 -1 0 0 0 -1 26.425 201.69 155.34 # 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 E 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 2NO9 _atom_sites.fract_transf_matrix[1][1] 0.018921 _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] 0.007437 _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] 0.006437 _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 1 301 301 ADP ADP . D 3 LTT A 1 302 1 LTT TRO . E 2 ADP B 1 301 301 ADP ADP . F 3 LTT B 1 302 2 LTT TRO . G 4 HOH A 1 303 1 HOH HOH . G 4 HOH A 2 304 2 HOH HOH . G 4 HOH A 3 305 3 HOH HOH . G 4 HOH A 4 306 4 HOH HOH . G 4 HOH A 5 307 5 HOH HOH . G 4 HOH A 6 308 7 HOH HOH . G 4 HOH A 7 309 8 HOH HOH . G 4 HOH A 8 310 9 HOH HOH . G 4 HOH A 9 311 10 HOH HOH . G 4 HOH A 10 312 11 HOH HOH . G 4 HOH A 11 313 12 HOH HOH . G 4 HOH A 12 314 16 HOH HOH . G 4 HOH A 13 315 17 HOH HOH . G 4 HOH A 14 316 18 HOH HOH . G 4 HOH A 15 317 20 HOH HOH . G 4 HOH A 16 318 24 HOH HOH . G 4 HOH A 17 319 26 HOH HOH . G 4 HOH A 18 320 28 HOH HOH . G 4 HOH A 19 321 29 HOH HOH . G 4 HOH A 20 322 31 HOH HOH . G 4 HOH A 21 323 32 HOH HOH . G 4 HOH A 22 324 33 HOH HOH . G 4 HOH A 23 325 35 HOH HOH . G 4 HOH A 24 326 36 HOH HOH . G 4 HOH A 25 327 40 HOH HOH . G 4 HOH A 26 328 41 HOH HOH . G 4 HOH A 27 329 42 HOH HOH . G 4 HOH A 28 330 46 HOH HOH . G 4 HOH A 29 331 48 HOH HOH . G 4 HOH A 30 332 49 HOH HOH . G 4 HOH A 31 333 50 HOH HOH . G 4 HOH A 32 334 51 HOH HOH . G 4 HOH A 33 335 55 HOH HOH . G 4 HOH A 34 336 56 HOH HOH . G 4 HOH A 35 337 57 HOH HOH . G 4 HOH A 36 338 58 HOH HOH . G 4 HOH A 37 339 62 HOH HOH . G 4 HOH A 38 340 63 HOH HOH . G 4 HOH A 39 341 66 HOH HOH . G 4 HOH A 40 342 68 HOH HOH . G 4 HOH A 41 343 69 HOH HOH . G 4 HOH A 42 344 70 HOH HOH . G 4 HOH A 43 345 71 HOH HOH . G 4 HOH A 44 346 72 HOH HOH . G 4 HOH A 45 347 73 HOH HOH . G 4 HOH A 46 348 74 HOH HOH . G 4 HOH A 47 349 78 HOH HOH . G 4 HOH A 48 350 81 HOH HOH . G 4 HOH A 49 351 82 HOH HOH . H 4 HOH B 1 303 6 HOH HOH . H 4 HOH B 2 304 13 HOH HOH . H 4 HOH B 3 305 14 HOH HOH . H 4 HOH B 4 306 15 HOH HOH . H 4 HOH B 5 307 19 HOH HOH . H 4 HOH B 6 308 21 HOH HOH . H 4 HOH B 7 309 22 HOH HOH . H 4 HOH B 8 310 23 HOH HOH . H 4 HOH B 9 311 25 HOH HOH . H 4 HOH B 10 312 27 HOH HOH . H 4 HOH B 11 313 30 HOH HOH . H 4 HOH B 12 314 34 HOH HOH . H 4 HOH B 13 315 37 HOH HOH . H 4 HOH B 14 316 38 HOH HOH . H 4 HOH B 15 317 39 HOH HOH . H 4 HOH B 16 318 43 HOH HOH . H 4 HOH B 17 319 44 HOH HOH . H 4 HOH B 18 320 45 HOH HOH . H 4 HOH B 19 321 47 HOH HOH . H 4 HOH B 20 322 52 HOH HOH . H 4 HOH B 21 323 53 HOH HOH . H 4 HOH B 22 324 54 HOH HOH . H 4 HOH B 23 325 59 HOH HOH . H 4 HOH B 24 326 61 HOH HOH . H 4 HOH B 25 327 64 HOH HOH . H 4 HOH B 26 328 67 HOH HOH . H 4 HOH B 27 329 75 HOH HOH . H 4 HOH B 28 330 77 HOH HOH . H 4 HOH B 29 331 79 HOH HOH . H 4 HOH B 30 332 80 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 . . . E 2 29.972 102.388 94.004 1 24.66 ? PB ADP 301 B 1 HETATM 2 O O1B ADP . . . E 2 31.382 101.933 94.242 1 24.65 ? O1B ADP 301 B 1 HETATM 3 O O2B ADP . . . E 2 28.872 101.864 94.806 1 22.93 ? O2B ADP 301 B 1 HETATM 4 O O3B ADP . . . E 2 29.665 102.323 92.511 1 21.87 ? O3B ADP 301 B 1 HETATM 5 P PA ADP . . . E 2 29.223 104.696 95.523 1 27.35 ? PA ADP 301 B 1 HETATM 6 O O1A ADP . . . E 2 27.728 104.534 95.456 1 23.75 ? O1A ADP 301 B 1 HETATM 7 O O2A ADP . . . E 2 29.916 104.383 96.799 1 25.6 ? O2A ADP 301 B 1 HETATM 8 O O3A ADP . . . E 2 29.978 103.974 94.315 1 23.78 ? O3A ADP 301 B 1 HETATM 9 O O5' ADP . . . E 2 29.577 106.214 95.12 1 26.36 ? O5' ADP 301 B 1 HETATM 10 C C5' ADP . . . E 2 30.954 106.625 95.144 1 25.93 ? C5' ADP 301 B 1 HETATM 11 C C4' ADP . . . E 2 31.074 108.028 95.742 1 28.51 ? C4' ADP 301 B 1 HETATM 12 O O4' ADP . . . E 2 30.549 108.958 94.799 1 27.46 ? O4' ADP 301 B 1 HETATM 13 C C3' ADP . . . E 2 30.304 108.307 97.038 1 28.31 ? C3' ADP 301 B 1 HETATM 14 O O3' ADP . . . E 2 31.006 109.366 97.677 1 28.45 ? O3' ADP 301 B 1 HETATM 15 C C2' ADP . . . E 2 28.995 108.885 96.588 1 29.75 ? C2' ADP 301 B 1 HETATM 16 O O2' ADP . . . E 2 28.394 109.787 97.51 1 30.37 ? O2' ADP 301 B 1 HETATM 17 C C1' ADP . . . E 2 29.391 109.624 95.323 1 28.88 ? C1' ADP 301 B 1 HETATM 18 N N9 ADP . . . E 2 28.367 109.614 94.253 1 29.36 ? N9 ADP 301 B 1 HETATM 19 C C8 ADP . . . E 2 27.617 108.599 93.757 1 28.99 ? C8 ADP 301 B 1 HETATM 20 N N7 ADP . . . E 2 26.796 109.053 92.764 1 28.26 ? N7 ADP 301 B 1 HETATM 21 C C5 ADP . . . E 2 27.033 110.354 92.621 1 28.72 ? C5 ADP 301 B 1 HETATM 22 C C6 ADP . . . E 2 26.508 111.402 91.737 1 30.8 ? C6 ADP 301 B 1 HETATM 23 N N6 ADP . . . E 2 25.631 111.131 90.861 1 32.34 ? N6 ADP 301 B 1 HETATM 24 N N1 ADP . . . E 2 26.97 112.636 91.898 1 28.68 ? N1 ADP 301 B 1 HETATM 25 C C2 ADP . . . E 2 27.986 113.017 92.881 1 30.16 ? C2 ADP 301 B 1 HETATM 26 N N3 ADP . . . E 2 28.475 111.931 93.719 1 30.47 ? N3 ADP 301 B 1 HETATM 27 C C4 ADP . . . E 2 27.986 110.67 93.551 1 30.23 ? C4 ADP 301 B 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 325 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 27 #