data_8X3Z # _model_server_result.job_id J0WKnJViybsUIWM9XYzSCA _model_server_result.datetime_utc '2024-11-21 09:49:09' _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 8x3z # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":601}' # _entry.id 8X3Z # _exptl.entry_id 8X3Z _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 2 _entity.src_method nat _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 8X3Z _cell.length_a 58.916 _cell.length_b 129.734 _cell.length_c 220.675 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8X3Z _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _symmetry.space_group_name_H-M 'P 21 21 21' # _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 ? 2 C N N ? 2 E 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 B OD1 ASP 430 B ASP 430 1_555 F MG MG . B MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.231 ? metalc ? metalc2 B OD2 ASP 430 B ASP 430 1_555 F MG MG . B MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.23 ? metalc ? metalc3 B OD1 ASN 457 B ASN 457 1_555 F MG MG . B MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.217 ? metalc ? metalc4 B O ARG 459 B ARG 459 1_555 F MG MG . B MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.267 ? metalc ? metalc5 D O1A TPP . B TPP 601 1_555 F MG MG . B MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.348 ? metalc ? metalc6 D O1B TPP . B TPP 601 1_555 F MG MG . B MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.516 ? metalc ? metalc7 D O3B TPP . B TPP 601 1_555 F MG MG . B MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? # _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 8X3Z _atom_sites.fract_transf_matrix[1][1] 0.016973 _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] 0.007708 _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] 0.004532 _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 1 601 601 ADP ADP . D 3 TPP B 1 601 601 TPP TPP . E 2 ADP B 1 602 701 ADP ADP . F 4 MG B 1 603 801 MG MG . G 5 HOH A 1 701 51 HOH HOH . G 5 HOH A 2 702 79 HOH HOH . G 5 HOH A 3 703 119 HOH HOH . G 5 HOH A 4 704 50 HOH HOH . G 5 HOH A 5 705 86 HOH HOH . G 5 HOH A 6 706 7 HOH HOH . G 5 HOH A 7 707 27 HOH HOH . G 5 HOH A 8 708 32 HOH HOH . G 5 HOH A 9 709 49 HOH HOH . G 5 HOH A 10 710 8 HOH HOH . G 5 HOH A 11 711 15 HOH HOH . G 5 HOH A 12 712 29 HOH HOH . G 5 HOH A 13 713 75 HOH HOH . G 5 HOH A 14 714 106 HOH HOH . G 5 HOH A 15 715 111 HOH HOH . G 5 HOH A 16 716 11 HOH HOH . G 5 HOH A 17 717 57 HOH HOH . G 5 HOH A 18 718 1 HOH HOH . G 5 HOH A 19 719 96 HOH HOH . G 5 HOH A 20 720 23 HOH HOH . G 5 HOH A 21 721 82 HOH HOH . G 5 HOH A 22 722 62 HOH HOH . G 5 HOH A 23 723 85 HOH HOH . G 5 HOH A 24 724 73 HOH HOH . G 5 HOH A 25 725 26 HOH HOH . G 5 HOH A 26 726 43 HOH HOH . G 5 HOH A 27 727 53 HOH HOH . G 5 HOH A 28 728 66 HOH HOH . G 5 HOH A 29 729 38 HOH HOH . G 5 HOH A 30 730 90 HOH HOH . G 5 HOH A 31 731 77 HOH HOH . G 5 HOH A 32 732 84 HOH HOH . G 5 HOH A 33 733 125 HOH HOH . G 5 HOH A 34 734 116 HOH HOH . G 5 HOH A 35 735 122 HOH HOH . H 5 HOH B 1 701 104 HOH HOH . H 5 HOH B 2 702 59 HOH HOH . H 5 HOH B 3 703 14 HOH HOH . H 5 HOH B 4 704 92 HOH HOH . H 5 HOH B 5 705 46 HOH HOH . H 5 HOH B 6 706 31 HOH HOH . H 5 HOH B 7 707 4 HOH HOH . H 5 HOH B 8 708 118 HOH HOH . H 5 HOH B 9 709 10 HOH HOH . H 5 HOH B 10 710 121 HOH HOH . H 5 HOH B 11 711 3 HOH HOH . H 5 HOH B 12 712 61 HOH HOH . H 5 HOH B 13 713 54 HOH HOH . H 5 HOH B 14 714 20 HOH HOH . H 5 HOH B 15 715 21 HOH HOH . H 5 HOH B 16 716 72 HOH HOH . H 5 HOH B 17 717 24 HOH HOH . H 5 HOH B 18 718 105 HOH HOH . H 5 HOH B 19 719 6 HOH HOH . H 5 HOH B 20 720 76 HOH HOH . H 5 HOH B 21 721 13 HOH HOH . H 5 HOH B 22 722 16 HOH HOH . H 5 HOH B 23 723 17 HOH HOH . H 5 HOH B 24 724 63 HOH HOH . H 5 HOH B 25 725 34 HOH HOH . H 5 HOH B 26 726 42 HOH HOH . H 5 HOH B 27 727 37 HOH HOH . H 5 HOH B 28 728 28 HOH HOH . H 5 HOH B 29 729 47 HOH HOH . H 5 HOH B 30 730 65 HOH HOH . H 5 HOH B 31 731 56 HOH HOH . H 5 HOH B 32 732 88 HOH HOH . H 5 HOH B 33 733 18 HOH HOH . H 5 HOH B 34 734 112 HOH HOH . H 5 HOH B 35 735 36 HOH HOH . H 5 HOH B 36 736 40 HOH HOH . H 5 HOH B 37 737 22 HOH HOH . H 5 HOH B 38 738 109 HOH HOH . H 5 HOH B 39 739 80 HOH HOH . H 5 HOH B 40 740 117 HOH HOH . H 5 HOH B 41 741 113 HOH HOH . H 5 HOH B 42 742 93 HOH HOH . H 5 HOH B 43 743 89 HOH HOH . H 5 HOH B 44 744 64 HOH HOH . H 5 HOH B 45 745 94 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 . . . C 2 -31.955 -45.06 42.128 1 31.44 ? PB ADP 601 A 1 HETATM 2 O O1B ADP . . . C 2 -32.741 -44.965 43.427 1 37.12 ? O1B ADP 601 A 1 HETATM 3 O O2B ADP . . . C 2 -31.754 -46.406 41.534 1 26.84 -1 O2B ADP 601 A 1 HETATM 4 O O3B ADP . . . C 2 -32.467 -44.089 41.094 1 42.89 ? O3B ADP 601 A 1 HETATM 5 P PA ADP . . . C 2 -29.976 -43.569 43.618 1 24.26 ? PA ADP 601 A 1 HETATM 6 O O1A ADP . . . C 2 -28.565 -43.161 43.324 1 25.28 -1 O1A ADP 601 A 1 HETATM 7 O O2A ADP . . . C 2 -31.019 -42.521 43.919 1 26.66 ? O2A ADP 601 A 1 HETATM 8 O O3A ADP . . . C 2 -30.44 -44.615 42.456 1 31.01 ? O3A ADP 601 A 1 HETATM 9 O O5' ADP . . . C 2 -29.986 -44.561 44.859 1 28.04 ? O5' ADP 601 A 1 HETATM 10 C C5' ADP . . . C 2 -28.855 -45.405 45.07 1 37.64 ? C5' ADP 601 A 1 HETATM 11 C C4' ADP . . . C 2 -28.716 -45.614 46.58 1 32.77 ? C4' ADP 601 A 1 HETATM 12 O O4' ADP . . . C 2 -28.009 -46.855 46.802 1 27.32 ? O4' ADP 601 A 1 HETATM 13 C C3' ADP . . . C 2 -27.977 -44.585 47.453 1 32.37 ? C3' ADP 601 A 1 HETATM 14 O O3' ADP . . . C 2 -28.898 -44.378 48.528 1 31.55 ? O3' ADP 601 A 1 HETATM 15 C C2' ADP . . . C 2 -26.662 -45.187 47.902 1 27.41 ? C2' ADP 601 A 1 HETATM 16 O O2' ADP . . . C 2 -26.404 -44.795 49.24 1 36.09 ? O2' ADP 601 A 1 HETATM 17 C C1' ADP . . . C 2 -26.945 -46.677 47.755 1 30.26 ? C1' ADP 601 A 1 HETATM 18 N N9 ADP . . . C 2 -25.804 -47.532 47.372 1 27.61 ? N9 ADP 601 A 1 HETATM 19 C C8 ADP . . . C 2 -24.99 -47.506 46.302 1 33.16 ? C8 ADP 601 A 1 HETATM 20 N N7 ADP . . . C 2 -24.065 -48.516 46.355 1 29.14 ? N7 ADP 601 A 1 HETATM 21 C C5 ADP . . . C 2 -24.325 -49.197 47.484 1 19.69 ? C5 ADP 601 A 1 HETATM 22 C C6 ADP . . . C 2 -23.745 -50.344 48.178 1 20.01 ? C6 ADP 601 A 1 HETATM 23 N N6 ADP . . . C 2 -22.695 -50.969 47.643 1 26.8 ? N6 ADP 601 A 1 HETATM 24 N N1 ADP . . . C 2 -24.273 -50.709 49.372 1 20.23 ? N1 ADP 601 A 1 HETATM 25 C C2 ADP . . . C 2 -25.316 -50.057 49.935 1 26.3 ? C2 ADP 601 A 1 HETATM 26 N N3 ADP . . . C 2 -25.919 -48.977 49.374 1 20.91 ? N3 ADP 601 A 1 HETATM 27 C C4 ADP . . . C 2 -25.448 -48.524 48.168 1 29.94 ? C4 ADP 601 A 1 HETATM 28 H "H5'1" ADP . . . C 2 -27.954 -44.94 44.665 1 45.17 ? "H5'1" ADP 601 A 1 HETATM 29 H "H5'2" ADP . . . C 2 -28.996 -46.362 44.564 1 45.17 ? "H5'2" ADP 601 A 1 HETATM 30 H H4' ADP . . . C 2 -29.766 -45.556 46.9 1 39.32 ? H4' ADP 601 A 1 HETATM 31 H H3' ADP . . . C 2 -27.718 -43.637 46.963 1 38.84 ? H3' ADP 601 A 1 HETATM 32 H HO3' ADP . . . C 2 -28.529 -43.736 49.15 1 37.86 ? HO3' ADP 601 A 1 HETATM 33 H H2' ADP . . . C 2 -25.768 -44.875 47.343 1 32.89 ? H2' ADP 601 A 1 HETATM 34 H HO2' ADP . . . C 2 -26.302 -43.834 49.281 1 43.31 ? HO2' ADP 601 A 1 HETATM 35 H H1' ADP . . . C 2 -27.211 -46.997 48.772 1 36.32 ? H1' ADP 601 A 1 HETATM 36 H H8 ADP . . . C 2 -25.056 -46.78 45.501 1 39.79 ? H8 ADP 601 A 1 HETATM 37 H HN61 ADP . . . C 2 -22.334 -50.652 46.759 1 32.16 ? HN61 ADP 601 A 1 HETATM 38 H HN62 ADP . . . C 2 -22.291 -51.769 48.097 1 32.16 ? HN62 ADP 601 A 1 HETATM 39 H H2 ADP . . . C 2 -25.691 -50.417 50.885 1 31.56 ? H2 ADP 601 A 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 230 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 39 #