data_3UDT # _model_server_result.job_id yUvyE1CgOAqgMBm9xt0SlQ _model_server_result.datetime_utc '2024-11-13 03:39:22' _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 3udt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":912}' # _entry.id 3UDT # _exptl.entry_id 3UDT _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 90.02 _cell.angle_beta 97.04 _cell.angle_gamma 116.81 _cell.entry_id 3UDT _cell.length_a 59.362 _cell.length_b 59.913 _cell.length_c 83.146 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3UDT _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 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 monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 ? dimeric 2 author_defined_assembly 3 # 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 A,B,C,D,E,F,G,H,I,J 3 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 H 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 ND1 HIS 354 A HIS 320 1_555 F ZN ZN . A ZN 914 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.211 ? metalc ? metalc2 A SG CYS 364 A CYS 330 1_555 F ZN ZN . A ZN 914 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? metalc ? metalc3 A SG CYS 367 A CYS 333 1_555 F ZN ZN . A ZN 914 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.474 ? metalc ? metalc4 A NE2 HIS 380 A HIS 346 1_555 F ZN ZN . A ZN 914 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? metalc ? metalc5 A OD2 ASP 441 A ASP 407 1_555 E MG MG . A MG 913 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.114 ? metalc ? metalc6 D O2A ADP . A ADP 912 1_555 E MG MG . A MG 913 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.569 ? metalc ? metalc7 B ND1 HIS 354 B HIS 320 1_555 J ZN ZN . B ZN 914 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? metalc ? metalc8 B SG CYS 364 B CYS 330 1_555 J ZN ZN . B ZN 914 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.216 ? metalc ? metalc9 B SG CYS 367 B CYS 333 1_555 J ZN ZN . B ZN 914 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.53 ? metalc ? metalc10 B NE2 HIS 380 B HIS 346 1_555 J ZN ZN . B ZN 914 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? metalc ? metalc11 H O1A ADP . B ADP 912 1_555 I MG MG . B MG 913 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.223 ? # _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 50 n n PB O2B ADP sing 51 n n PB O3B ADP sing 52 n n PB O3A ADP sing 53 n n O2B HOB2 ADP sing 54 n n O3B HOB3 ADP sing 55 n n PA O1A ADP doub 56 n n PA O2A ADP sing 57 n n PA O3A ADP sing 58 n n PA O5' ADP sing 59 n n O2A HOA2 ADP sing 60 n n O5' C5' ADP sing 61 n n C5' C4' ADP sing 62 n n C5' "H5'1" ADP sing 63 n n C5' "H5'2" ADP sing 64 n n C4' O4' ADP sing 65 n n C4' C3' ADP sing 66 n n C4' H4' ADP sing 67 n n O4' C1' ADP sing 68 n n C3' O3' ADP sing 69 n n C3' C2' ADP sing 70 n n C3' H3' ADP sing 71 n n O3' HO3' ADP sing 72 n n C2' O2' ADP sing 73 n n C2' C1' ADP sing 74 n n C2' H2' ADP sing 75 n n O2' HO2' ADP sing 76 n n C1' N9 ADP sing 77 n n C1' H1' ADP sing 78 n n N9 C8 ADP sing 79 n y N9 C4 ADP sing 80 n y C8 N7 ADP doub 81 n y C8 H8 ADP sing 82 n n N7 C5 ADP sing 83 n y C5 C6 ADP sing 84 n y C5 C4 ADP doub 85 n y C6 N6 ADP sing 86 n n C6 N1 ADP doub 87 n y N6 HN61 ADP sing 88 n n N6 HN62 ADP sing 89 n n N1 C2 ADP sing 90 n y C2 N3 ADP doub 91 n y C2 H2 ADP sing 92 n n N3 C4 ADP sing 93 n y # _atom_sites.entry_id 3UDT _atom_sites.fract_transf_matrix[1][1] 0.016846 _atom_sites.fract_transf_matrix[1][2] 0.008513 _atom_sites.fract_transf_matrix[1][3] 0.00262 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018701 _atom_sites.fract_transf_matrix[2][3] 0.001177 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.012142 _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 5MY A 1 911 500 5MY I5P . D 3 ADP A 1 912 600 ADP ADP . E 4 MG A 1 913 700 MG MG . F 5 ZN A 1 914 800 ZN ZN . G 2 5MY B 1 911 500 5MY I5P . H 3 ADP B 1 912 600 ADP ADP . I 4 MG B 1 913 700 MG MG . J 5 ZN B 1 914 800 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 . . . D 3 -39.537 1.025 -10.488 1 40.98 ? PB ADP 912 A 1 HETATM 2 O O1B ADP . . . D 3 -38.803 -0.29 -10.343 1 25.3 ? O1B ADP 912 A 1 HETATM 3 O O2B ADP . . . D 3 -38.841 2.152 -9.728 1 44.97 ? O2B ADP 912 A 1 HETATM 4 O O3B ADP . . . D 3 -41.05 0.949 -10.268 1 30.59 ? O3B ADP 912 A 1 HETATM 5 P PA ADP . . . D 3 -39.659 2.813 -12.776 1 43.48 ? PA ADP 912 A 1 HETATM 6 O O1A ADP . . . D 3 -41.113 2.947 -13.169 1 23.74 ? O1A ADP 912 A 1 HETATM 7 O O2A ADP . . . D 3 -38.967 3.907 -11.974 1 38.79 ? O2A ADP 912 A 1 HETATM 8 O O3A ADP . . . D 3 -39.366 1.37 -12.072 1 33.35 ? O3A ADP 912 A 1 HETATM 9 O O5' ADP . . . D 3 -38.852 2.686 -14.169 1 49.82 ? O5' ADP 912 A 1 HETATM 10 C C5' ADP . . . D 3 -37.645 1.94 -14.311 1 32.72 ? C5' ADP 912 A 1 HETATM 11 C C4' ADP . . . D 3 -36.815 2.728 -15.31 1 34.24 ? C4' ADP 912 A 1 HETATM 12 O O4' ADP . . . D 3 -37.33 2.493 -16.621 1 44.54 ? O4' ADP 912 A 1 HETATM 13 C C3' ADP . . . D 3 -36.941 4.236 -15.098 1 36.69 ? C3' ADP 912 A 1 HETATM 14 O O3' ADP . . . D 3 -35.939 4.767 -14.23 1 40.03 ? O3' ADP 912 A 1 HETATM 15 C C2' ADP . . . D 3 -36.898 4.846 -16.496 1 40.5 ? C2' ADP 912 A 1 HETATM 16 O O2' ADP . . . D 3 -35.6 5.238 -16.964 1 30.87 ? O2' ADP 912 A 1 HETATM 17 C C1' ADP . . . D 3 -37.393 3.717 -17.373 1 47.07 ? C1' ADP 912 A 1 HETATM 18 N N9 ADP . . . D 3 -38.791 4.098 -17.684 1 46.19 ? N9 ADP 912 A 1 HETATM 19 C C8 ADP . . . D 3 -39.919 3.739 -17.023 1 45.58 ? C8 ADP 912 A 1 HETATM 20 N N7 ADP . . . D 3 -41.02 4.296 -17.593 1 42.93 ? N7 ADP 912 A 1 HETATM 21 C C5 ADP . . . D 3 -40.582 5.036 -18.639 1 43.7 ? C5 ADP 912 A 1 HETATM 22 C C6 ADP . . . D 3 -41.196 5.9 -19.672 1 41.14 ? C6 ADP 912 A 1 HETATM 23 N N6 ADP . . . D 3 -42.537 6.082 -19.711 1 44.95 ? N6 ADP 912 A 1 HETATM 24 N N1 ADP . . . D 3 -40.378 6.498 -20.569 1 40.63 ? N1 ADP 912 A 1 HETATM 25 C C2 ADP . . . D 3 -39.039 6.324 -20.546 1 43.48 ? C2 ADP 912 A 1 HETATM 26 N N3 ADP . . . D 3 -38.403 5.56 -19.642 1 45.23 ? N3 ADP 912 A 1 HETATM 27 C C4 ADP . . . D 3 -39.115 4.907 -18.687 1 45.85 ? C4 ADP 912 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 200 _model_server_stats.encode_time_ms 17 _model_server_stats.element_count 27 #