data_3UBO # _model_server_result.job_id 3F91mybisqaTx_LTe0a21Q _model_server_result.datetime_utc '2024-11-28 15:12:35' _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 3ubo # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":354}' # _entry.id 3UBO # _exptl.entry_id 3UBO _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 3 _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 120 _cell.entry_id 3UBO _cell.length_a 156.307 _cell.length_b 156.307 _cell.length_c 89.081 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3UBO _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details PISA _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,E,F,G,H _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 ? 3 D N N ? 3 F N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order covale ? covale1 A C ALA 36 A ALA 34 1_555 A N MSE 37 A MSE 35 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.318 ? covale ? covale2 A C MSE 37 A MSE 35 1_555 A N ASN 38 A ASN 36 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale3 A C ARG 51 A ARG 49 1_555 A N MSE 52 A MSE 50 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale4 A C MSE 52 A MSE 50 1_555 A N GLY 53 A GLY 51 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale5 A C SER 117 A SER 115 1_555 A N MSE 118 A MSE 116 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale6 A C MSE 118 A MSE 116 1_555 A N ILE 119 A ILE 117 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale7 A C SER 128 A SER 126 1_555 A N MSE 129 A MSE 127 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale8 A C MSE 129 A MSE 127 1_555 A N ASN 130 A ASN 128 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale9 A C ALA 186 A ALA 184 1_555 A N MSE 187 A MSE 185 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale10 A C MSE 187 A MSE 185 1_555 A N THR 188 A THR 186 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale11 A C LEU 205 A LEU 203 1_555 A N MSE 206 A MSE 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale12 A C MSE 206 A MSE 204 1_555 A N ARG 207 A ARG 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale13 B C ALA 36 B ALA 34 1_555 B N MSE 37 B MSE 35 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale14 B C MSE 37 B MSE 35 1_555 B N ASN 38 B ASN 36 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale15 B C ARG 51 B ARG 49 1_555 B N MSE 52 B MSE 50 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale16 B C MSE 52 B MSE 50 1_555 B N GLY 53 B GLY 51 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale17 B C SER 117 B SER 115 1_555 B N MSE 118 B MSE 116 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale18 B C MSE 118 B MSE 116 1_555 B N ILE 119 B ILE 117 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale19 B C SER 128 B SER 126 1_555 B N MSE 129 B MSE 127 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.34 ? covale ? covale20 B C MSE 129 B MSE 127 1_555 B N ASN 130 B ASN 128 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.312 ? covale ? covale21 B C ALA 186 B ALA 184 1_555 B N MSE 187 B MSE 185 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale22 B C MSE 187 B MSE 185 1_555 B N THR 188 B THR 186 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.319 ? covale ? covale23 B C LEU 205 B LEU 203 1_555 B N MSE 206 B MSE 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale24 B C MSE 206 B MSE 204 1_555 B N ARG 207 B ARG 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? # _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 3UBO _atom_sites.fract_transf_matrix[1][1] 0.006398 _atom_sites.fract_transf_matrix[1][2] 0.003694 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007387 _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] 0.011226 _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 ADN A 1 353 1 ADN ADN . D 3 ADP A 1 354 1 ADP ADP . E 2 ADN B 1 353 2 ADN ADN . F 3 ADP B 1 354 2 ADP ADP . G 4 HOH A 1 355 6 HOH HOH . G 4 HOH A 2 356 8 HOH HOH . G 4 HOH A 3 357 9 HOH HOH . G 4 HOH A 4 358 10 HOH HOH . G 4 HOH A 5 359 16 HOH HOH . G 4 HOH A 6 360 31 HOH HOH . G 4 HOH A 7 361 41 HOH HOH . G 4 HOH A 8 362 43 HOH HOH . G 4 HOH A 9 363 45 HOH HOH . G 4 HOH A 10 364 46 HOH HOH . G 4 HOH A 11 365 51 HOH HOH . G 4 HOH A 12 366 53 HOH HOH . G 4 HOH A 13 367 55 HOH HOH . G 4 HOH A 14 368 56 HOH HOH . G 4 HOH A 15 369 57 HOH HOH . G 4 HOH A 16 370 59 HOH HOH . G 4 HOH A 17 371 60 HOH HOH . G 4 HOH A 18 372 62 HOH HOH . G 4 HOH A 19 373 66 HOH HOH . G 4 HOH A 20 374 68 HOH HOH . G 4 HOH A 21 375 74 HOH HOH . H 4 HOH B 1 355 3 HOH HOH . H 4 HOH B 2 356 12 HOH HOH . H 4 HOH B 3 357 15 HOH HOH . H 4 HOH B 4 358 17 HOH HOH . H 4 HOH B 5 359 19 HOH HOH . H 4 HOH B 6 360 20 HOH HOH . H 4 HOH B 7 361 21 HOH HOH . H 4 HOH B 8 362 23 HOH HOH . H 4 HOH B 9 363 25 HOH HOH . H 4 HOH B 10 364 30 HOH HOH . H 4 HOH B 11 365 34 HOH HOH . H 4 HOH B 12 366 35 HOH HOH . H 4 HOH B 13 367 36 HOH HOH . H 4 HOH B 14 368 39 HOH HOH . H 4 HOH B 15 369 42 HOH HOH . H 4 HOH B 16 370 44 HOH HOH . H 4 HOH B 17 371 47 HOH HOH . H 4 HOH B 18 372 48 HOH HOH . H 4 HOH B 19 373 49 HOH HOH . H 4 HOH B 20 374 50 HOH HOH . H 4 HOH B 21 375 52 HOH HOH . H 4 HOH B 22 376 58 HOH HOH . H 4 HOH B 23 377 61 HOH HOH . H 4 HOH B 24 378 72 HOH HOH . H 4 HOH B 25 379 75 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 . . . D 3 64.482 -7.926 -0.306 1 75.75 ? PB ADP 354 A 1 HETATM 2 O O1B ADP . . . D 3 63.662 -9.307 0.112 1 74.55 ? O1B ADP 354 A 1 HETATM 3 O O2B ADP . . . D 3 64.424 -6.654 0.786 1 71.97 ? O2B ADP 354 A 1 HETATM 4 O O3B ADP . . . D 3 65.911 -8.225 -0.588 1 70.07 ? O3B ADP 354 A 1 HETATM 5 P PA ADP . . . D 3 63.677 -6.764 -3.059 1 77.43 ? PA ADP 354 A 1 HETATM 6 O O1A ADP . . . D 3 63.027 -7.878 -4.084 1 70.75 ? O1A ADP 354 A 1 HETATM 7 O O2A ADP . . . D 3 62.815 -5.583 -3.008 1 74.24 ? O2A ADP 354 A 1 HETATM 8 O O3A ADP . . . D 3 63.53 -7.702 -1.663 1 78.44 ? O3A ADP 354 A 1 HETATM 9 O O5' ADP . . . D 3 65.22 -6.223 -3.445 1 70.89 ? O5' ADP 354 A 1 HETATM 10 C C5' ADP . . . D 3 65.83 -5.207 -2.658 1 68.75 ? C5' ADP 354 A 1 HETATM 11 C C4' ADP . . . D 3 66.666 -4.204 -3.519 1 70.41 ? C4' ADP 354 A 1 HETATM 12 O O4' ADP . . . D 3 67.932 -4.706 -4.162 1 70.35 ? O4' ADP 354 A 1 HETATM 13 C C3' ADP . . . D 3 65.936 -3.521 -4.794 1 71.08 ? C3' ADP 354 A 1 HETATM 14 O O3' ADP . . . D 3 64.92 -2.555 -4.596 1 70.9 ? O3' ADP 354 A 1 HETATM 15 C C2' ADP . . . D 3 67.037 -3.3 -5.824 1 70.77 ? C2' ADP 354 A 1 HETATM 16 O O2' ADP . . . D 3 67.744 -2.053 -5.894 1 70.59 ? O2' ADP 354 A 1 HETATM 17 C C1' ADP . . . D 3 67.833 -4.552 -5.588 1 69.14 ? C1' ADP 354 A 1 HETATM 18 N N9 ADP . . . D 3 67.319 -5.752 -6.318 1 71.7 ? N9 ADP 354 A 1 HETATM 19 C C8 ADP . . . D 3 66.574 -6.804 -5.832 1 70.31 ? C8 ADP 354 A 1 HETATM 20 N N7 ADP . . . D 3 66.304 -7.751 -6.907 1 69.22 ? N7 ADP 354 A 1 HETATM 21 C C5 ADP . . . D 3 66.895 -7.23 -8.094 1 69.89 ? C5 ADP 354 A 1 HETATM 22 C C6 ADP . . . D 3 66.974 -7.748 -9.474 1 71.02 ? C6 ADP 354 A 1 HETATM 23 N N6 ADP . . . D 3 66.382 -9.059 -9.803 1 68.88 ? N6 ADP 354 A 1 HETATM 24 N N1 ADP . . . D 3 67.649 -7.037 -10.417 1 68.47 ? N1 ADP 354 A 1 HETATM 25 C C2 ADP . . . D 3 68.279 -5.822 -10.096 1 67.57 ? C2 ADP 354 A 1 HETATM 26 N N3 ADP . . . D 3 68.199 -5.29 -8.757 1 68.71 ? N3 ADP 354 A 1 HETATM 27 C C4 ADP . . . D 3 67.527 -6.012 -7.774 1 71.29 ? C4 ADP 354 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 272 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 27 #