data_5X6J # _model_server_result.job_id -tYZH7DA_PGGMCZTWin5Ow _model_server_result.datetime_utc '2024-11-15 09:36:01' _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 5x6j # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":302}' # _entry.id 5X6J # _exptl.entry_id 5X6J _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 916.367 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "BIS(ADENOSINE)-5'-PENTAPHOSPHATE" _entity.pdbx_number_of_molecules 1 _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 120 _cell.entry_id 5X6J _cell.length_a 65.106 _cell.length_b 65.106 _cell.length_c 94.565 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5X6J _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 SG CYS 130 A CYS 130 1_555 B ZN ZN . A ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? metalc ? metalc2 A SG CYS 133 A CYS 133 1_555 B ZN ZN . A ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? metalc ? metalc3 A SG CYS 150 A CYS 150 1_555 B ZN ZN . A ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.393 ? metalc ? metalc4 A OD2 ASP 153 A ASP 153 1_555 B ZN ZN . A ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? # _chem_comp.formula 'C20 H29 N10 O22 P5' _chem_comp.formula_weight 916.367 _chem_comp.id AP5 _chem_comp.mon_nstd_flag . _chem_comp.name "BIS(ADENOSINE)-5'-PENTAPHOSPHATE" _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 AP5 doub 13 n n PA O2A AP5 sing 14 n n PA O3A AP5 sing 15 n n PA O5F AP5 sing 16 n n O2A HOA2 AP5 sing 17 n n O3A PB AP5 sing 18 n n PB O1B AP5 doub 19 n n PB O2B AP5 sing 20 n n PB O3B AP5 sing 21 n n O2B HOB2 AP5 sing 22 n n O3B PG AP5 sing 23 n n PG O1G AP5 doub 24 n n PG O2G AP5 sing 25 n n PG O3G AP5 sing 26 n n O2G HOG2 AP5 sing 27 n n O3G PD AP5 sing 28 n n PD O1D AP5 doub 29 n n PD O2D AP5 sing 30 n n PD O3D AP5 sing 31 n n O2D HOD2 AP5 sing 32 n n O3D PE AP5 sing 33 n n PE O1E AP5 doub 34 n n PE O2E AP5 sing 35 n n PE O5J AP5 sing 36 n n O2E HOE2 AP5 sing 37 n n O5F C5F AP5 sing 38 n n C5F C4F AP5 sing 39 n n C5F H51A AP5 sing 40 n n C5F H52A AP5 sing 41 n n C4F O4F AP5 sing 42 n n C4F C3F AP5 sing 43 n n C4F H4F AP5 sing 44 n n O4F C1F AP5 sing 45 n n C3F O3F AP5 sing 46 n n C3F C2F AP5 sing 47 n n C3F H3F AP5 sing 48 n n O3F HO3A AP5 sing 49 n n C2F O2F AP5 sing 50 n n C2F C1F AP5 sing 51 n n C2F H2F AP5 sing 52 n n O2F HO2A AP5 sing 53 n n C1F N9A AP5 sing 54 n n C1F H1F AP5 sing 55 n n N9A C8A AP5 sing 56 n y N9A C4A AP5 sing 57 n y C8A N7A AP5 doub 58 n y C8A H8A AP5 sing 59 n n N7A C5A AP5 sing 60 n y C5A C6A AP5 sing 61 n y C5A C4A AP5 doub 62 n y C6A N6A AP5 sing 63 n n C6A N1A AP5 doub 64 n y N6A H61A AP5 sing 65 n n N6A H62A AP5 sing 66 n n N1A C2A AP5 sing 67 n y C2A N3A AP5 doub 68 n y C2A H2A AP5 sing 69 n n N3A C4A AP5 sing 70 n y O5J C5J AP5 sing 71 n n C5J C4J AP5 sing 72 n n C5J H51B AP5 sing 73 n n C5J H52B AP5 sing 74 n n C4J O4J AP5 sing 75 n n C4J C3J AP5 sing 76 n n C4J H4J AP5 sing 77 n n O4J C1J AP5 sing 78 n n C3J O3J AP5 sing 79 n n C3J C2J AP5 sing 80 n n C3J H3J AP5 sing 81 n n O3J HO3B AP5 sing 82 n n C2J O2J AP5 sing 83 n n C2J C1J AP5 sing 84 n n C2J H2J AP5 sing 85 n n O2J HO2B AP5 sing 86 n n C1J N9B AP5 sing 87 n n C1J H1J AP5 sing 88 n n N9B C8B AP5 sing 89 n y N9B C4B AP5 sing 90 n y C8B N7B AP5 doub 91 n y C8B H8B AP5 sing 92 n n N7B C5B AP5 sing 93 n y C5B C6B AP5 sing 94 n y C5B C4B AP5 doub 95 n y C6B N6B AP5 sing 96 n n C6B N1B AP5 doub 97 n y N6B H61B AP5 sing 98 n n N6B H62B AP5 sing 99 n n N1B C2B AP5 sing 100 n y C2B N3B AP5 doub 101 n y C2B H2B AP5 sing 102 n n N3B C4B AP5 sing 103 n y # _atom_sites.entry_id 5X6J _atom_sites.fract_transf_matrix[1][1] 0.01536 _atom_sites.fract_transf_matrix[1][2] 0.008868 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017736 _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] 0.010575 _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 B 2 ZN A 1 301 219 ZN ZN . C 3 AP5 A 1 302 218 AP5 AP5 . D 4 HOH A 1 401 169 HOH HOH . D 4 HOH A 2 402 28 HOH HOH . D 4 HOH A 3 403 178 HOH HOH . D 4 HOH A 4 404 17 HOH HOH . D 4 HOH A 5 405 83 HOH HOH . D 4 HOH A 6 406 30 HOH HOH . D 4 HOH A 7 407 66 HOH HOH . D 4 HOH A 8 408 49 HOH HOH . D 4 HOH A 9 409 65 HOH HOH . D 4 HOH A 10 410 50 HOH HOH . D 4 HOH A 11 411 42 HOH HOH . D 4 HOH A 12 412 160 HOH HOH . D 4 HOH A 13 413 7 HOH HOH . D 4 HOH A 14 414 46 HOH HOH . D 4 HOH A 15 415 67 HOH HOH . D 4 HOH A 16 416 48 HOH HOH . D 4 HOH A 17 417 174 HOH HOH . D 4 HOH A 18 418 10 HOH HOH . D 4 HOH A 19 419 123 HOH HOH . D 4 HOH A 20 420 168 HOH HOH . D 4 HOH A 21 421 39 HOH HOH . D 4 HOH A 22 422 35 HOH HOH . D 4 HOH A 23 423 37 HOH HOH . D 4 HOH A 24 424 186 HOH HOH . D 4 HOH A 25 425 44 HOH HOH . D 4 HOH A 26 426 16 HOH HOH . D 4 HOH A 27 427 64 HOH HOH . D 4 HOH A 28 428 33 HOH HOH . D 4 HOH A 29 429 51 HOH HOH . D 4 HOH A 30 430 72 HOH HOH . D 4 HOH A 31 431 25 HOH HOH . D 4 HOH A 32 432 59 HOH HOH . D 4 HOH A 33 433 14 HOH HOH . D 4 HOH A 34 434 43 HOH HOH . D 4 HOH A 35 435 8 HOH HOH . D 4 HOH A 36 436 88 HOH HOH . D 4 HOH A 37 437 27 HOH HOH . D 4 HOH A 38 438 91 HOH HOH . D 4 HOH A 39 439 5 HOH HOH . D 4 HOH A 40 440 21 HOH HOH . D 4 HOH A 41 441 53 HOH HOH . D 4 HOH A 42 442 9 HOH HOH . D 4 HOH A 43 443 24 HOH HOH . D 4 HOH A 44 444 12 HOH HOH . D 4 HOH A 45 445 6 HOH HOH . D 4 HOH A 46 446 23 HOH HOH . D 4 HOH A 47 447 38 HOH HOH . D 4 HOH A 48 448 165 HOH HOH . D 4 HOH A 49 449 29 HOH HOH . D 4 HOH A 50 450 58 HOH HOH . D 4 HOH A 51 451 77 HOH HOH . D 4 HOH A 52 452 177 HOH HOH . D 4 HOH A 53 453 184 HOH HOH . D 4 HOH A 54 454 36 HOH HOH . D 4 HOH A 55 455 1 HOH HOH . D 4 HOH A 56 456 60 HOH HOH . D 4 HOH A 57 457 2 HOH HOH . D 4 HOH A 58 458 86 HOH HOH . D 4 HOH A 59 459 40 HOH HOH . D 4 HOH A 60 460 20 HOH HOH . D 4 HOH A 61 461 173 HOH HOH . D 4 HOH A 62 462 32 HOH HOH . D 4 HOH A 63 463 55 HOH HOH . D 4 HOH A 64 464 22 HOH HOH . D 4 HOH A 65 465 18 HOH HOH . D 4 HOH A 66 466 180 HOH HOH . D 4 HOH A 67 467 157 HOH HOH . D 4 HOH A 68 468 129 HOH HOH . D 4 HOH A 69 469 200 HOH HOH . D 4 HOH A 70 470 161 HOH HOH . D 4 HOH A 71 471 156 HOH HOH . D 4 HOH A 72 472 104 HOH HOH . D 4 HOH A 73 473 97 HOH HOH . D 4 HOH A 74 474 192 HOH HOH . D 4 HOH A 75 475 153 HOH HOH . D 4 HOH A 76 476 68 HOH HOH . D 4 HOH A 77 477 70 HOH HOH . D 4 HOH A 78 478 182 HOH HOH . D 4 HOH A 79 479 111 HOH HOH . D 4 HOH A 80 480 63 HOH HOH . D 4 HOH A 81 481 79 HOH HOH . D 4 HOH A 82 482 76 HOH HOH . D 4 HOH A 83 483 124 HOH HOH . D 4 HOH A 84 484 162 HOH HOH . D 4 HOH A 85 485 52 HOH HOH . D 4 HOH A 86 486 98 HOH HOH . D 4 HOH A 87 487 87 HOH HOH . D 4 HOH A 88 488 130 HOH HOH . D 4 HOH A 89 489 149 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 PA AP5 . . . C 3 -21.726 19.44 -0.513 1 29.94 ? PA AP5 302 A 1 HETATM 2 O O1A AP5 . . . C 3 -22.343 20.714 -0.99 1 25.21 ? O1A AP5 302 A 1 HETATM 3 O O2A AP5 . . . C 3 -20.438 19.046 0.194 1 31.9 ? O2A AP5 302 A 1 HETATM 4 O O3A AP5 . . . C 3 -22.047 18.342 -1.752 1 31.88 ? O3A AP5 302 A 1 HETATM 5 P PB AP5 . . . C 3 -21.07 17.639 -2.838 1 30.55 ? PB AP5 302 A 1 HETATM 6 O O1B AP5 . . . C 3 -20.949 16.219 -2.311 1 33.2 ? O1B AP5 302 A 1 HETATM 7 O O2B AP5 . . . C 3 -19.797 18.482 -2.887 1 33.73 ? O2B AP5 302 A 1 HETATM 8 O O3B AP5 . . . C 3 -22.075 17.899 -4.054 1 36.11 ? O3B AP5 302 A 1 HETATM 9 P PG AP5 . . . C 3 -21.555 18.416 -5.497 1 40.33 ? PG AP5 302 A 1 HETATM 10 O O1G AP5 . . . C 3 -20.099 18.027 -5.752 1 35.84 ? O1G AP5 302 A 1 HETATM 11 O O2G AP5 . . . C 3 -22.019 19.855 -5.759 1 40.38 ? O2G AP5 302 A 1 HETATM 12 O O3G AP5 . . . C 3 -22.556 17.507 -6.415 1 38.5 ? O3G AP5 302 A 1 HETATM 13 P PD AP5 . . . C 3 -22.534 17.633 -8.098 1 43.08 ? PD AP5 302 A 1 HETATM 14 O O1D AP5 . . . C 3 -22.304 16.26 -8.718 1 48.46 ? O1D AP5 302 A 1 HETATM 15 O O2D AP5 . . . C 3 -23.536 18.636 -8.556 1 52.86 ? O2D AP5 302 A 1 HETATM 16 O O3D AP5 . . . C 3 -21.193 18.461 -8.256 1 48.55 ? O3D AP5 302 A 1 HETATM 17 P PE AP5 . . . C 3 -20.682 19.631 -9.196 1 42.11 ? PE AP5 302 A 1 HETATM 18 O O1E AP5 . . . C 3 -19.333 19.062 -8.868 1 43.41 ? O1E AP5 302 A 1 HETATM 19 O O2E AP5 . . . C 3 -21.293 20.963 -8.745 1 38.83 ? O2E AP5 302 A 1 HETATM 20 O O5F AP5 . . . C 3 -22.864 18.869 0.536 1 32.07 ? O5F AP5 302 A 1 HETATM 21 C C5F AP5 . . . C 3 -24.239 18.878 0.115 1 30.46 ? C5F AP5 302 A 1 HETATM 22 C C4F AP5 . . . C 3 -25.16 19.477 1.167 1 33.35 ? C4F AP5 302 A 1 HETATM 23 O O4F AP5 . . . C 3 -25.071 18.69 2.35 1 32.82 ? O4F AP5 302 A 1 HETATM 24 C C3F AP5 . . . C 3 -24.757 20.898 1.555 1 31.64 ? C3F AP5 302 A 1 HETATM 25 O O3F AP5 . . . C 3 -25.984 21.658 1.683 1 29.14 ? O3F AP5 302 A 1 HETATM 26 C C2F AP5 . . . C 3 -23.964 20.734 2.857 1 32.3 ? C2F AP5 302 A 1 HETATM 27 O O2F AP5 . . . C 3 -24.136 21.886 3.718 1 39.18 ? O2F AP5 302 A 1 HETATM 28 C C1F AP5 . . . C 3 -24.619 19.495 3.474 1 32.9 ? C1F AP5 302 A 1 HETATM 29 N N9A AP5 . . . C 3 -23.783 18.519 4.202 1 29.38 ? N9A AP5 302 A 1 HETATM 30 C C8A AP5 . . . C 3 -22.531 18.243 3.94 1 26.59 ? C8A AP5 302 A 1 HETATM 31 N N7A AP5 . . . C 3 -22.09 17.247 4.735 1 33.02 ? N7A AP5 302 A 1 HETATM 32 C C5A AP5 . . . C 3 -23.114 16.886 5.527 1 31.24 ? C5A AP5 302 A 1 HETATM 33 C C6A AP5 . . . C 3 -23.274 15.886 6.598 1 37.17 ? C6A AP5 302 A 1 HETATM 34 N N6A AP5 . . . C 3 -22.261 15.062 6.978 1 36.69 ? N6A AP5 302 A 1 HETATM 35 N N1A AP5 . . . C 3 -24.489 15.817 7.111 1 36.05 ? N1A AP5 302 A 1 HETATM 36 C C2A AP5 . . . C 3 -25.504 16.653 6.771 1 37.75 ? C2A AP5 302 A 1 HETATM 37 N N3A AP5 . . . C 3 -25.42 17.6 5.825 1 33.43 ? N3A AP5 302 A 1 HETATM 38 C C4A AP5 . . . C 3 -24.224 17.74 5.192 1 30.55 ? C4A AP5 302 A 1 HETATM 39 O O5J AP5 . . . C 3 -21.097 19.353 -10.767 1 31.24 ? O5J AP5 302 A 1 HETATM 40 C C5J AP5 . . . C 3 -22.191 19.968 -11.386 1 29.55 ? C5J AP5 302 A 1 HETATM 41 C C4J AP5 . . . C 3 -22.296 19.425 -12.809 1 31.35 ? C4J AP5 302 A 1 HETATM 42 O O4J AP5 . . . C 3 -21.043 19.566 -13.51 1 29.52 ? O4J AP5 302 A 1 HETATM 43 C C3J AP5 . . . C 3 -22.691 17.963 -12.929 1 30.47 ? C3J AP5 302 A 1 HETATM 44 O O3J AP5 . . . C 3 -24.117 17.82 -12.693 1 34.17 ? O3J AP5 302 A 1 HETATM 45 C C2J AP5 . . . C 3 -22.184 17.662 -14.321 1 28.99 ? C2J AP5 302 A 1 HETATM 46 O O2J AP5 . . . C 3 -23.053 18.281 -15.254 1 26.84 ? O2J AP5 302 A 1 HETATM 47 C C1J AP5 . . . C 3 -20.885 18.491 -14.443 1 28.16 ? C1J AP5 302 A 1 HETATM 48 N N9B AP5 . . . C 3 -19.704 17.705 -14.047 1 32.41 ? N9B AP5 302 A 1 HETATM 49 C C8B AP5 . . . C 3 -18.972 17.926 -12.941 1 31.52 ? C8B AP5 302 A 1 HETATM 50 N N7B AP5 . . . C 3 -17.936 17.1 -12.882 1 29.57 ? N7B AP5 302 A 1 HETATM 51 C C5B AP5 . . . C 3 -18.028 16.24 -13.963 1 29.53 ? C5B AP5 302 A 1 HETATM 52 C C6B AP5 . . . C 3 -17.236 15.072 -14.483 1 32.05 ? C6B AP5 302 A 1 HETATM 53 N N6B AP5 . . . C 3 -16.143 14.589 -13.822 1 32.51 ? N6B AP5 302 A 1 HETATM 54 N N1B AP5 . . . C 3 -17.659 14.498 -15.66 1 33.61 ? N1B AP5 302 A 1 HETATM 55 C C2B AP5 . . . C 3 -18.754 15.001 -16.336 1 32.65 ? C2B AP5 302 A 1 HETATM 56 N N3B AP5 . . . C 3 -19.484 16.043 -15.907 1 30.13 ? N3B AP5 302 A 1 HETATM 57 C C4B AP5 . . . C 3 -19.181 16.667 -14.741 1 30.8 ? C4B AP5 302 A 1 # _model_server_stats.io_time_ms 63 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 409 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 57 #