data_5YZX # _model_server_result.job_id ZcEN7mRQfIZDyoO2QQemUw _model_server_result.datetime_utc '2025-03-13 17:52:26' _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":"L","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 . . . L 2 122.347 56.151 13.985 1 88.78 ? PA B4P 601 C 1 HETATM 2 O O1A B4P . . . L 2 123.327 54.987 14.14 1 86.92 ? O1A B4P 601 C 1 HETATM 3 O O2A B4P . . . L 2 122.441 57.088 15.23 1 75.93 ? O2A B4P 601 C 1 HETATM 4 O O3A B4P . . . L 2 120.775 55.53 13.836 1 81.83 ? O3A B4P 601 C 1 HETATM 5 P PB B4P . . . L 2 119.573 55.856 14.893 1 64.6 ? PB B4P 601 C 1 HETATM 6 O O1B B4P . . . L 2 119.64 57.293 15.274 1 71.41 ? O1B B4P 601 C 1 HETATM 7 O O2B B4P . . . L 2 118.269 55.551 14.237 1 63.21 ? O2B B4P 601 C 1 HETATM 8 O O3B B4P . . . L 2 119.758 54.871 16.272 1 53.1 ? O3B B4P 601 C 1 HETATM 9 P PG B4P . . . L 2 120.471 55.343 17.729 1 68.84 ? PG B4P 601 C 1 HETATM 10 O O1G B4P . . . L 2 120.585 56.836 17.775 1 75.5 ? O1G B4P 601 C 1 HETATM 11 O O2G B4P . . . L 2 121.835 54.759 17.826 1 83.21 ? O2G B4P 601 C 1 HETATM 12 O O3G B4P . . . L 2 119.526 54.802 18.982 1 54.64 ? O3G B4P 601 C 1 HETATM 13 P PD B4P . . . L 2 119.983 53.687 20.141 1 47.1 ? PD B4P 601 C 1 HETATM 14 O O1D B4P . . . L 2 120.967 52.663 19.576 1 69.82 ? O1D B4P 601 C 1 HETATM 15 O O2D B4P . . . L 2 120.622 54.413 21.318 1 56.23 ? O2D B4P 601 C 1 HETATM 16 O O5E B4P . . . L 2 122.694 57.012 12.569 1 114.82 ? O5E B4P 601 C 1 HETATM 17 C C5E B4P . . . L 2 122.831 56.338 11.384 1 106.45 ? C5E B4P 601 C 1 HETATM 18 C C4E B4P . . . L 2 122.171 57.114 10.225 1 100.56 ? C4E B4P 601 C 1 HETATM 19 O O4E B4P . . . L 2 120.94 57.477 10.54 1 100.44 ? O4E B4P 601 C 1 HETATM 20 C C3E B4P . . . L 2 122.912 58.422 9.949 1 99.11 ? C3E B4P 601 C 1 HETATM 21 O O3E B4P . . . L 2 123.899 58.229 9.042 1 95.24 ? O3E B4P 601 C 1 HETATM 22 C C2E B4P . . . L 2 121.8 59.356 9.365 1 108.06 ? C2E B4P 601 C 1 HETATM 23 O O2E B4P . . . L 2 121.741 59.224 7.884 1 103.34 ? O2E B4P 601 C 1 HETATM 24 C C1E B4P . . . L 2 120.685 58.953 9.902 1 106.58 ? C1E B4P 601 C 1 HETATM 25 N N9A B4P . . . L 2 120.253 59.876 10.955 1 101.82 ? N9A B4P 601 C 1 HETATM 26 C C8A B4P . . . L 2 120.491 59.732 12.272 1 90.99 ? C8A B4P 601 C 1 HETATM 27 N N7A B4P . . . L 2 119.943 60.771 12.909 1 89.82 ? N7A B4P 601 C 1 HETATM 28 C C5A B4P . . . L 2 119.357 61.559 11.992 1 90.29 ? C5A B4P 601 C 1 HETATM 29 C C6A B4P . . . L 2 118.66 62.736 12.108 1 71.32 ? C6A B4P 601 C 1 HETATM 30 N N6A B4P . . . L 2 118.32 63.522 13.289 1 47.94 ? N6A B4P 601 C 1 HETATM 31 N N1A B4P . . . L 2 118.178 63.328 11.022 1 75.03 ? N1A B4P 601 C 1 HETATM 32 C C2A B4P . . . L 2 118.37 62.773 9.806 1 78.52 ? C2A B4P 601 C 1 HETATM 33 N N3A B4P . . . L 2 119.059 61.609 9.688 1 85.62 ? N3A B4P 601 C 1 HETATM 34 C C4A B4P . . . L 2 119.55 61.007 10.784 1 95.57 ? C4A B4P 601 C 1 HETATM 35 O O5F B4P . . . L 2 118.647 52.859 20.668 1 40.32 ? O5F B4P 601 C 1 HETATM 36 C C5F B4P . . . L 2 117.43 53.541 20.681 1 51.91 ? C5F B4P 601 C 1 HETATM 37 C C4F B4P . . . L 2 116.404 52.75 19.8 1 50.45 ? C4F B4P 601 C 1 HETATM 38 O O4F B4P . . . L 2 115.233 53.339 19.832 1 45.12 ? O4F B4P 601 C 1 HETATM 39 C C3F B4P . . . L 2 116.884 52.755 18.348 1 39.22 ? C3F B4P 601 C 1 HETATM 40 O O3F B4P . . . L 2 117.259 51.519 17.997 1 51.53 ? O3F B4P 601 C 1 HETATM 41 C C2F B4P . . . L 2 115.653 53.222 17.51 1 30.8 ? C2F B4P 601 C 1 HETATM 42 O O2F B4P . . . L 2 114.934 52.026 16.969 1 30.58 ? O2F B4P 601 C 1 HETATM 43 C C1F B4P . . . L 2 114.869 53.835 18.324 1 37.63 ? C1F B4P 601 C 1 HETATM 44 N N9B B4P . . . L 2 115.003 55.272 18.216 1 39.6 ? N9B B4P 601 C 1 HETATM 45 C C8B B4P . . . L 2 116.09 55.989 18.53 1 37.28 ? C8B B4P 601 C 1 HETATM 46 N N7B B4P . . . L 2 115.823 57.282 18.296 1 33.65 ? N7B B4P 601 C 1 HETATM 47 C C5B B4P . . . L 2 114.574 57.363 17.845 1 31.14 ? C5B B4P 601 C 1 HETATM 48 C C6B B4P . . . L 2 113.802 58.44 17.454 1 31.2 ? C6B B4P 601 C 1 HETATM 49 N N6B B4P . . . L 2 113.99 59.933 17.359 1 31.45 ? N6B B4P 601 C 1 HETATM 50 N N1B B4P . . . L 2 112.554 58.245 17.028 1 35.09 ? N1B B4P 601 C 1 HETATM 51 C C2B B4P . . . L 2 112.041 56.979 16.979 1 47.35 ? C2B B4P 601 C 1 HETATM 52 N N3B B4P . . . L 2 112.798 55.914 17.365 1 41.03 ? N3B B4P 601 C 1 HETATM 53 C C4B B4P . . . L 2 114.064 56.118 17.793 1 42.12 ? C4B B4P 601 C 1 # _model_server_stats.io_time_ms 28 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 284 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 53 #