data_3UG7 # _model_server_result.job_id gjg-UBxLAsxZlA5BVaPNrQ _model_server_result.datetime_utc '2024-11-27 16:09:19' _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 3ug7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":401}' # _entry.id 3UG7 # _exptl.entry_id 3UG7 _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 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 94.24 _cell.angle_gamma 90 _cell.entry_id 3UG7 _cell.length_a 71.947 _cell.length_b 149.636 _cell.length_c 72.888 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3UG7 _symmetry.cell_setting ? _symmetry.Int_Tables_number 3 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 2 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 PISA tetrameric 4 author_and_software_defined_assembly 1 PISA tetrameric 4 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,E,F,G,N,O,P 1 1,2 B,C,H,I,J,K,L,M 2 1,3 # 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' 2_455 -x-1,y,-z -1 0 0 0 1 0 0 0 -1 -71.947 0 0 3 'crystal symmetry operation' 2_554 -x,y,-z-1 -1 0 0 0 1 0 0 0 -1 5.388933 0 -72.688513 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 E N N ? 2 H N N ? 2 K N N ? 2 N 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 metalc ? metalc1 A OG1 THR 40 A THR 40 1_555 F MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? metalc ? metalc2 A SG CYS 283 A CYS 283 1_555 G ZN ZN . A ZN 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.553 ? metalc ? metalc3 A SG CYS 286 A CYS 286 1_555 G ZN ZN . A ZN 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.357 ? metalc ? metalc4 E O2B ADP . A ADP 401 1_555 F MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? metalc ? metalc5 B OG1 THR 40 B THR 40 1_555 I MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? metalc ? metalc6 B SG CYS 283 B CYS 283 1_555 J ZN ZN . B ZN 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.532 ? metalc ? metalc7 B SG CYS 286 B CYS 286 1_555 J ZN ZN . B ZN 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.383 ? metalc ? metalc8 H O2B ADP . B ADP 401 1_555 I MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.986 ? metalc ? metalc9 C OG1 THR 40 C THR 40 1_555 L MG MG . C MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? metalc ? metalc10 C SG CYS 283 C CYS 283 1_555 M ZN ZN . C ZN 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.546 ? metalc ? metalc11 C SG CYS 286 C CYS 286 1_555 M ZN ZN . C ZN 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.306 ? metalc ? metalc12 K O1B ADP . C ADP 401 1_555 L MG MG . C MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? metalc ? metalc13 D OG1 THR 40 D THR 40 1_555 O MG MG . D MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? metalc ? metalc14 D SG CYS 283 D CYS 283 1_555 P ZN ZN . D ZN 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.534 ? metalc ? metalc15 D SG CYS 286 D CYS 286 1_555 P ZN ZN . D ZN 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? metalc ? metalc16 N O1B ADP . D ADP 401 1_555 O MG MG . D MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? # _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 3UG7 _atom_sites.fract_transf_matrix[1][1] 0.013899 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001031 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006683 _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] 0.013757 _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 E 2 ADP A 1 401 401 ADP ADP . F 3 MG A 1 403 403 MG MG . G 4 ZN A 1 404 404 ZN ZN . H 2 ADP B 1 401 401 ADP ADP . I 3 MG B 1 403 403 MG MG . J 4 ZN B 1 404 404 ZN ZN . K 2 ADP C 1 401 401 ADP ADP . L 3 MG C 1 403 403 MG MG . M 4 ZN C 1 404 404 ZN ZN . N 2 ADP D 1 401 401 ADP ADP . O 3 MG D 1 403 403 MG MG . P 4 ZN D 1 404 404 ZN ZN . # 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 . . . H 2 -2.065 72.013 -33.442 1 36.43 ? PB ADP 401 B 1 HETATM 2 O O1B ADP . . . H 2 -3.135 71.929 -34.499 1 36.09 ? O1B ADP 401 B 1 HETATM 3 O O2B ADP . . . H 2 -2.495 71.554 -32.069 1 36.44 ? O2B ADP 401 B 1 HETATM 4 O O3B ADP . . . H 2 -0.704 71.527 -33.883 1 35.36 ? O3B ADP 401 B 1 HETATM 5 P PA ADP . . . H 2 -2.328 74.394 -31.98 1 37.25 ? PA ADP 401 B 1 HETATM 6 O O1A ADP . . . H 2 -3.839 74.411 -31.922 1 36.47 ? O1A ADP 401 B 1 HETATM 7 O O2A ADP . . . H 2 -1.528 73.875 -30.808 1 38.01 ? O2A ADP 401 B 1 HETATM 8 O O3A ADP . . . H 2 -1.86 73.597 -33.295 1 25.22 ? O3A ADP 401 B 1 HETATM 9 O O5' ADP . . . H 2 -1.779 75.852 -32.358 1 48.01 ? O5' ADP 401 B 1 HETATM 10 C C5' ADP . . . H 2 -0.375 76.077 -32.383 1 48.79 ? C5' ADP 401 B 1 HETATM 11 C C4' ADP . . . H 2 -0.077 77.454 -31.806 1 49.66 ? C4' ADP 401 B 1 HETATM 12 O O4' ADP . . . H 2 -0.721 78.482 -32.574 1 49.69 ? O4' ADP 401 B 1 HETATM 13 C C3' ADP . . . H 2 -0.614 77.544 -30.388 1 50.76 ? C3' ADP 401 B 1 HETATM 14 O O3' ADP . . . H 2 0.408 78.084 -29.556 1 52.17 ? O3' ADP 401 B 1 HETATM 15 C C2' ADP . . . H 2 -1.769 78.514 -30.46 1 50.63 ? C2' ADP 401 B 1 HETATM 16 O O2' ADP . . . H 2 -1.85 79.321 -29.285 1 50.46 ? O2' ADP 401 B 1 HETATM 17 C C1' ADP . . . H 2 -1.455 79.344 -31.695 1 50.54 ? C1' ADP 401 B 1 HETATM 18 N N9 ADP . . . H 2 -2.702 79.843 -32.326 1 51.6 ? N9 ADP 401 B 1 HETATM 19 C C8 ADP . . . H 2 -3.56 79.14 -33.088 1 51.69 ? C8 ADP 401 B 1 HETATM 20 N N7 ADP . . . H 2 -4.601 79.915 -33.493 1 51.45 ? N7 ADP 401 B 1 HETATM 21 C C5 ADP . . . H 2 -4.416 81.146 -32.982 1 51.56 ? C5 ADP 401 B 1 HETATM 22 C C6 ADP . . . H 2 -5.132 82.446 -33.016 1 51.67 ? C6 ADP 401 B 1 HETATM 23 N N6 ADP . . . H 2 -6.294 82.601 -33.697 1 51.65 ? N6 ADP 401 B 1 HETATM 24 N N1 ADP . . . H 2 -4.584 83.48 -32.34 1 51.81 ? N1 ADP 401 B 1 HETATM 25 C C2 ADP . . . H 2 -3.433 83.353 -31.656 1 51.57 ? C2 ADP 401 B 1 HETATM 26 N N3 ADP . . . H 2 -2.731 82.209 -31.582 1 51.25 ? N3 ADP 401 B 1 HETATM 27 C C4 ADP . . . H 2 -3.163 81.09 -32.212 1 51.36 ? C4 ADP 401 B 1 # _model_server_stats.io_time_ms 24 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #