data_5YZX # _model_server_result.job_id NI-lmCVyDnxoDGK5TKZkCA _model_server_result.datetime_utc '2025-03-13 17:42:32' _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 5yzx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":601}' # _entry.id 5YZX # _exptl.entry_id 5YZX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 836.387 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "BIS(ADENOSINE)-5'-TETRAPHOSPHATE" _entity.pdbx_number_of_molecules 3 _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 5YZX _cell.length_a 144.544 _cell.length_b 249.855 _cell.length_c 179.652 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YZX _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 dimeric 2 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,C,D,E,F,G,L,M,N,O 1 1 B,H,I,J,K 2 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 0 249.855 179.652 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 D N N ? 2 H N N ? 2 L 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 OE2 GLU 285 A GLU 264 1_555 E CA CA . A CA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.354 ? metalc ? metalc2 A OE2 GLU 435 A GLU 414 1_555 F CA CA . A CA 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.337 ? metalc ? metalc3 A OE1 GLU 435 A GLU 414 1_555 G CA CA . A CA 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.192 ? metalc ? metalc4 A OE1 GLU 442 A GLU 421 1_555 F CA CA . A CA 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.967 ? metalc ? metalc5 A OE2 GLU 442 A GLU 421 1_555 F CA CA . A CA 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.46 ? metalc ? metalc6 D O2A B4P . A B4P 601 1_555 E CA CA . A CA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.971 ? metalc ? metalc7 D O1B B4P . A B4P 601 1_555 E CA CA . A CA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.634 ? metalc ? metalc8 D O1G B4P . A B4P 601 1_555 E CA CA . A CA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? metalc ? metalc9 D O2G B4P . A B4P 601 1_555 F CA CA . A CA 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.353 ? metalc ? metalc10 D O1D B4P . A B4P 601 1_555 F CA CA . A CA 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.517 ? metalc ? metalc11 D O1A B4P . A B4P 601 1_555 G CA CA . A CA 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.776 ? metalc ? metalc12 B OE2 GLU 285 B GLU 264 1_555 I CA CA . B CA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.465 ? metalc ? metalc13 B OD2 ASP 397 B ASP 376 1_555 K CA CA . B CA 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.934 ? metalc ? metalc14 B OE2 GLU 435 B GLU 414 1_555 J CA CA . B CA 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.279 ? metalc ? metalc15 B OE1 GLU 442 B GLU 421 1_555 J CA CA . B CA 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.477 ? metalc ? metalc16 B OE2 GLU 442 B GLU 421 1_555 J CA CA . B CA 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.776 ? metalc ? metalc17 H O2A B4P . B B4P 601 1_555 I CA CA . B CA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.082 ? metalc ? metalc18 H O1B B4P . B B4P 601 1_555 I CA CA . B CA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.731 ? metalc ? metalc19 H O1G B4P . B B4P 601 1_555 I CA CA . B CA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.285 ? metalc ? metalc20 H O2G B4P . B B4P 601 1_555 J CA CA . B CA 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.445 ? metalc ? metalc21 H O1D B4P . B B4P 601 1_555 J CA CA . B CA 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.306 ? metalc ? metalc22 H O1A B4P . B B4P 601 1_555 K CA CA . B CA 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.358 ? metalc ? metalc23 C OE2 GLU 285 C GLU 264 1_555 N CA CA . C CA 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.804 ? metalc ? metalc24 C OE2 GLU 435 C GLU 414 1_555 O CA CA . C CA 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.227 ? metalc ? metalc25 C OE1 GLU 442 C GLU 421 1_555 O CA CA . C CA 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.598 ? metalc ? metalc26 C OE2 GLU 442 C GLU 421 1_555 O CA CA . C CA 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.575 ? metalc ? metalc27 L O1A B4P . C B4P 601 1_555 M CA CA . C CA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.665 ? metalc ? metalc28 L O1G B4P . C B4P 601 1_555 N CA CA . C CA 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.32 ? metalc ? metalc29 L O2G B4P . C B4P 601 1_555 O CA CA . C CA 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.494 ? metalc ? metalc30 L O1D B4P . C B4P 601 1_555 O CA CA . C CA 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.242 ? # _chem_comp.formula 'C20 H28 N10 O19 P4' _chem_comp.formula_weight 836.387 _chem_comp.id B4P _chem_comp.mon_nstd_flag . _chem_comp.name "BIS(ADENOSINE)-5'-TETRAPHOSPHATE" _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 PA O1A B4P doub 70 n n PA O2A B4P sing 71 n n PA O3A B4P sing 72 n n PA O5E B4P sing 73 n n O2A HOA2 B4P sing 74 n n O3A PB B4P sing 75 n n PB O1B B4P doub 76 n n PB O2B B4P sing 77 n n PB O3B B4P sing 78 n n O2B HOB2 B4P sing 79 n n O3B PG B4P sing 80 n n PG O1G B4P doub 81 n n PG O2G B4P sing 82 n n PG O3G B4P sing 83 n n O2G HOG2 B4P sing 84 n n O3G PD B4P sing 85 n n PD O1D B4P doub 86 n n PD O2D B4P sing 87 n n PD O5F B4P sing 88 n n O2D HOD2 B4P sing 89 n n O5E C5E B4P sing 90 n n C5E C4E B4P sing 91 n n C5E H51A B4P sing 92 n n C5E H52A B4P sing 93 n n C4E O4E B4P sing 94 n n C4E C3E B4P sing 95 n n C4E H4E B4P sing 96 n n O4E C1E B4P sing 97 n n C3E O3E B4P sing 98 n n C3E C2E B4P sing 99 n n C3E H3E B4P sing 100 n n O3E HO3A B4P sing 101 n n C2E O2E B4P sing 102 n n C2E C1E B4P sing 103 n n C2E H2E B4P sing 104 n n O2E HO2A B4P sing 105 n n C1E N9A B4P sing 106 n n C1E H1E B4P sing 107 n n N9A C8A B4P sing 108 n y N9A C4A B4P sing 109 n y C8A N7A B4P doub 110 n y C8A H8A B4P sing 111 n n N7A C5A B4P sing 112 n y C5A C6A B4P sing 113 n y C5A C4A B4P doub 114 n y C6A N6A B4P sing 115 n n C6A N1A B4P doub 116 n y N6A H61A B4P sing 117 n n N6A H62A B4P sing 118 n n N1A C2A B4P sing 119 n y C2A N3A B4P doub 120 n y C2A H2A B4P sing 121 n n N3A C4A B4P sing 122 n y O5F C5F B4P sing 123 n n C5F C4F B4P sing 124 n n C5F H51B B4P sing 125 n n C5F H52B B4P sing 126 n n C4F O4F B4P sing 127 n n C4F C3F B4P sing 128 n n C4F H4F B4P sing 129 n n O4F C1F B4P sing 130 n n C3F O3F B4P sing 131 n n C3F C2F B4P sing 132 n n C3F H3F B4P sing 133 n n O3F HO3B B4P sing 134 n n C2F O2F B4P sing 135 n n C2F C1F B4P sing 136 n n C2F H2F B4P sing 137 n n O2F HO2B B4P sing 138 n n C1F N9B B4P sing 139 n n C1F H1F B4P sing 140 n n N9B C8B B4P sing 141 n y N9B C4B B4P sing 142 n y C8B N7B B4P doub 143 n y C8B H8B B4P sing 144 n n N7B C5B B4P sing 145 n y C5B C6B B4P sing 146 n y C5B C4B B4P doub 147 n y C6B N6B B4P sing 148 n n C6B N1B B4P doub 149 n y N6B H61B B4P sing 150 n n N6B H62B B4P sing 151 n n N1B C2B B4P sing 152 n y C2B N3B B4P doub 153 n y C2B H2B B4P sing 154 n n N3B C4B B4P sing 155 n y # _atom_sites.entry_id 5YZX _atom_sites.fract_transf_matrix[1][1] 0.006918 _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] 0.004002 _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] 0.005566 _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 D 2 B4P A 1 601 1 B4P B4P . E 3 CA A 1 602 1 CA CA . F 3 CA A 1 603 2 CA CA . G 3 CA A 1 604 3 CA CA . H 2 B4P B 1 601 3 B4P B4P . I 3 CA B 1 602 7 CA CA . J 3 CA B 1 603 8 CA CA . K 3 CA B 1 604 9 CA CA . L 2 B4P C 1 601 2 B4P B4P . M 3 CA C 1 602 4 CA CA . N 3 CA C 1 603 5 CA CA . O 3 CA C 1 604 6 CA CA . # 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 PA B4P . . . D 2 95.837 71.867 45.021 1 82.86 ? PA B4P 601 A 1 HETATM 2 O O1A B4P . . . D 2 94.398 72.234 44.658 1 80.4 ? O1A B4P 601 A 1 HETATM 3 O O2A B4P . . . D 2 96.781 72.28 43.85 1 73.55 ? O2A B4P 601 A 1 HETATM 4 O O3A B4P . . . D 2 95.928 70.194 45.334 1 74.48 ? O3A B4P 601 A 1 HETATM 5 P PB B4P . . . D 2 96.767 69.093 44.454 1 62.94 ? PB B4P 601 A 1 HETATM 6 O O1B B4P . . . D 2 98.022 69.719 43.953 1 81.77 ? O1B B4P 601 A 1 HETATM 7 O O2B B4P . . . D 2 97.092 67.922 45.32 1 54.25 ? O2B B4P 601 A 1 HETATM 8 O O3B B4P . . . D 2 95.83 68.547 43.138 1 44.99 ? O3B B4P 601 A 1 HETATM 9 P PG B4P . . . D 2 95.746 69.322 41.64 1 57.4 ? PG B4P 601 A 1 HETATM 10 O O1G B4P . . . D 2 96.649 70.52 41.622 1 62.94 ? O1G B4P 601 A 1 HETATM 11 O O2G B4P . . . D 2 94.349 69.779 41.419 1 75.88 ? O2G B4P 601 A 1 HETATM 12 O O3G B4P . . . D 2 96.192 68.271 40.443 1 36.94 ? O3G B4P 601 A 1 HETATM 13 P PD B4P . . . D 2 95.157 67.751 39.244 1 38.46 ? PD B4P 601 A 1 HETATM 14 O O1D B4P . . . D 2 93.763 67.521 39.83 1 45.75 ? O1D B4P 601 A 1 HETATM 15 O O2D B4P . . . D 2 95.094 68.781 38.122 1 28.54 ? O2D B4P 601 A 1 HETATM 16 O O5E B4P . . . D 2 96.28 72.674 46.437 1 102.46 ? O5E B4P 601 A 1 HETATM 17 C C5E B4P . . . D 2 95.573 72.428 47.583 1 106.41 ? C5E B4P 601 A 1 HETATM 18 C C4E B4P . . . D 2 96.48 71.809 48.664 1 97.84 ? C4E B4P 601 A 1 HETATM 19 O O4E B4P . . . D 2 97.324 70.949 48.122 1 96.69 ? O4E B4P 601 A 1 HETATM 20 C C3E B4P . . . D 2 97.349 72.886 49.309 1 93.08 ? C3E B4P 601 A 1 HETATM 21 O O3E B4P . . . D 2 96.749 73.367 50.425 1 90.1 ? O3E B4P 601 A 1 HETATM 22 C C2E B4P . . . D 2 98.676 72.141 49.673 1 103.11 ? C2E B4P 601 A 1 HETATM 23 O O2E B4P . . . D 2 98.615 71.652 51.075 1 106.58 ? O2E B4P 601 A 1 HETATM 24 C C1E B4P . . . D 2 98.766 71.136 48.852 1 102.52 ? C1E B4P 601 A 1 HETATM 25 N N9A B4P . . . D 2 99.813 71.356 47.847 1 106.01 ? N9A B4P 601 A 1 HETATM 26 C C8A B4P . . . D 2 99.612 71.615 46.539 1 101.84 ? C8A B4P 601 A 1 HETATM 27 N N7A B4P . . . D 2 100.805 71.748 45.947 1 92.84 ? N7A B4P 601 A 1 HETATM 28 C C5A B4P . . . D 2 101.75 71.568 46.886 1 93.93 ? C5A B4P 601 A 1 HETATM 29 C C6A B4P . . . D 2 103.12 71.595 46.824 1 81.16 ? C6A B4P 601 A 1 HETATM 30 N N6A B4P . . . D 2 104.011 71.833 45.698 1 70.5 ? N6A B4P 601 A 1 HETATM 31 N N1A B4P . . . D 2 103.843 71.382 47.917 1 80.97 ? N1A B4P 601 A 1 HETATM 32 C C2A B4P . . . D 2 103.229 71.139 49.093 1 85.04 ? C2A B4P 601 A 1 HETATM 33 N N3A B4P . . . D 2 101.874 71.11 49.161 1 89.6 ? N3A B4P 601 A 1 HETATM 34 C C4A B4P . . . D 2 101.139 71.325 48.057 1 97.29 ? C4A B4P 601 A 1 HETATM 35 O O5F B4P . . . D 2 95.708 66.303 38.651 1 50.25 ? O5F B4P 601 A 1 HETATM 36 C C5F B4P . . . D 2 94.942 65.169 38.951 1 62.97 ? C5F B4P 601 A 1 HETATM 37 C C4F B4P . . . D 2 95.709 64.258 39.971 1 52.43 ? C4F B4P 601 A 1 HETATM 38 O O4F B4P . . . D 2 96.99 64.303 39.738 1 54.48 ? O4F B4P 601 A 1 HETATM 39 C C3F B4P . . . D 2 95.577 64.796 41.392 1 32.82 ? C3F B4P 601 A 1 HETATM 40 O O3F B4P . . . D 2 94.49 64.277 41.971 1 40.67 ? O3F B4P 601 A 1 HETATM 41 C C2F B4P . . . D 2 96.863 64.265 42.099 1 41.22 ? C2F B4P 601 A 1 HETATM 42 O O2F B4P . . . D 2 96.555 62.987 42.82 1 40.38 ? O2F B4P 601 A 1 HETATM 43 C C1F B4P . . . D 2 97.725 64.034 41.167 1 50.34 ? C1F B4P 601 A 1 HETATM 44 N N9B B4P . . . D 2 98.857 64.923 41.297 1 48.74 ? N9B B4P 601 A 1 HETATM 45 C C8B B4P . . . D 2 98.842 66.234 41.013 1 59 ? C8B B4P 601 A 1 HETATM 46 N N7B B4P . . . D 2 100.067 66.73 41.252 1 48.21 ? N7B B4P 601 A 1 HETATM 47 C C5B B4P . . . D 2 100.833 65.727 41.678 1 30.94 ? C5B B4P 601 A 1 HETATM 48 C C6B B4P . . . D 2 102.162 65.676 42.059 1 28.89 ? C6B B4P 601 A 1 HETATM 49 N N6B B4P . . . D 2 103.297 66.666 42.171 1 31.64 ? N6B B4P 601 A 1 HETATM 50 N N1B B4P . . . D 2 102.701 64.519 42.454 1 37.75 ? N1B B4P 601 A 1 HETATM 51 C C2B B4P . . . D 2 101.935 63.388 42.483 1 46.16 ? C2B B4P 601 A 1 HETATM 52 N N3B B4P . . . D 2 100.625 63.436 42.103 1 43.86 ? N3B B4P 601 A 1 HETATM 53 C C4B B4P . . . D 2 100.084 64.607 41.706 1 35.59 ? C4B B4P 601 A 1 # _model_server_stats.io_time_ms 29 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 313 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 53 #