data_4TYP # _model_server_result.job_id RSZ8KE0KtQczKukQLf6Fgw _model_server_result.datetime_utc '2025-02-28 05:04:54' _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 4typ # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":302}' # _entry.id 4TYP # _exptl.entry_id 4TYP _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 916.367 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "BIS(ADENOSINE)-5'-PENTAPHOSPHATE" _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 98.28 _cell.angle_gamma 90 _cell.entry_id 4TYP _cell.length_a 43.641 _cell.length_b 123.338 _cell.length_c 86.693 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4TYP _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 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 PISA monomeric 1 author_and_software_defined_assembly 3 PISA monomeric 1 author_and_software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,E,K 1 1 B,F,G,L 2 1 C,H,I,M 3 1 D,J 4 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 E N N ? 2 G N N ? 2 I N N ? 2 J 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 SG CYS 130 B CYS 130 1_555 F ZN ZN . B ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.968 ? metalc ? metalc2 B SG CYS 133 B CYS 133 1_555 F ZN ZN . B ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? metalc ? metalc3 B SG CYS 150 B CYS 150 1_555 F ZN ZN . B ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.219 ? metalc ? metalc4 B OD2 ASP 153 B ASP 153 1_555 F ZN ZN . B ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.822 ? metalc ? metalc5 C SG CYS 130 A CYS 130 1_555 H ZN ZN . A ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.912 ? metalc ? metalc6 C SG CYS 133 A CYS 133 1_555 H ZN ZN . A ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.869 ? metalc ? metalc7 C OD1 ASP 153 A ASP 153 1_555 H ZN ZN . A ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.691 ? metalc ? metalc8 C OD2 ASP 153 A ASP 153 1_555 H ZN ZN . A ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? # _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 4TYP _atom_sites.fract_transf_matrix[1][1] 0.022914 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003336 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008108 _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] 0.011657 _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 E 2 AP5 C 1 301 220 AP5 AP5 . F 3 ZN B 1 301 218 ZN ZN . G 2 AP5 B 1 302 224 AP5 AP5 . H 3 ZN A 1 301 218 ZN ZN . I 2 AP5 A 1 302 220 AP5 AP5 . J 2 AP5 D 1 301 220 AP5 AP5 . K 4 HOH C 1 401 6 HOH HOH . K 4 HOH C 2 402 3 HOH HOH . K 4 HOH C 3 403 37 HOH HOH . K 4 HOH C 4 404 12 HOH HOH . K 4 HOH C 5 405 33 HOH HOH . K 4 HOH C 6 406 36 HOH HOH . K 4 HOH C 7 407 72 HOH HOH . L 4 HOH B 1 401 11 HOH HOH . L 4 HOH B 2 402 24 HOH HOH . L 4 HOH B 3 403 77 HOH HOH . L 4 HOH B 4 404 102 HOH HOH . M 4 HOH A 1 401 9 HOH HOH . M 4 HOH A 2 402 1 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 . . . I 2 -12.079 -20.478 103.068 1 79.43 ? PA AP5 302 A 1 HETATM 2 O O1A AP5 . . . I 2 -11.39 -21.212 104.154 1 79.15 ? O1A AP5 302 A 1 HETATM 3 O O2A AP5 . . . I 2 -12.559 -21.199 101.87 1 79.05 ? O2A AP5 302 A 1 HETATM 4 O O3A AP5 . . . I 2 -13.27 -19.639 103.676 1 84.92 ? O3A AP5 302 A 1 HETATM 5 P PB AP5 . . . I 2 -13.711 -19.994 105.154 1 83.71 ? PB AP5 302 A 1 HETATM 6 O O1B AP5 . . . I 2 -12.523 -19.882 106.037 1 83.44 ? O1B AP5 302 A 1 HETATM 7 O O2B AP5 . . . I 2 -14.484 -21.275 105.131 1 83.97 ? O2B AP5 302 A 1 HETATM 8 O O3B AP5 . . . I 2 -14.665 -18.782 105.451 1 81.89 ? O3B AP5 302 A 1 HETATM 9 P PG AP5 . . . I 2 -16.104 -18.74 104.775 1 83.65 ? PG AP5 302 A 1 HETATM 10 O O1G AP5 . . . I 2 -15.981 -17.779 103.664 1 83.21 ? O1G AP5 302 A 1 HETATM 11 O O2G AP5 . . . I 2 -16.611 -20.101 104.419 1 79.8 ? O2G AP5 302 A 1 HETATM 12 O O3G AP5 . . . I 2 -16.925 -17.954 105.907 1 84.11 ? O3G AP5 302 A 1 HETATM 13 P PD AP5 . . . I 2 -18.271 -18.26 106.709 1 80.59 ? PD AP5 302 A 1 HETATM 14 O O1D AP5 . . . I 2 -17.974 -19.21 107.815 1 78.44 ? O1D AP5 302 A 1 HETATM 15 O O2D AP5 . . . I 2 -18.813 -16.942 107.088 1 78.87 ? O2D AP5 302 A 1 HETATM 16 O O3D AP5 . . . I 2 -19.348 -18.77 105.664 1 83.06 ? O3D AP5 302 A 1 HETATM 17 P PE AP5 . . . I 2 -19.909 -20.253 105.67 1 83.18 ? PE AP5 302 A 1 HETATM 18 O O1E AP5 . . . I 2 -19.827 -20.804 104.278 1 81.01 ? O1E AP5 302 A 1 HETATM 19 O O2E AP5 . . . I 2 -19.405 -21.043 106.834 1 83.74 ? O2E AP5 302 A 1 HETATM 20 O O5F AP5 . . . I 2 -11.077 -19.364 102.621 1 85.79 ? O5F AP5 302 A 1 HETATM 21 C C5F AP5 . . . I 2 -11.46 -18.028 102.477 1 91.15 ? C5F AP5 302 A 1 HETATM 22 C C4F AP5 . . . I 2 -10.354 -17.353 101.71 1 95.67 ? C4F AP5 302 A 1 HETATM 23 O O4F AP5 . . . I 2 -9.175 -17.352 102.505 1 96.14 ? O4F AP5 302 A 1 HETATM 24 C C3F AP5 . . . I 2 -10.027 -18.141 100.464 1 99.14 ? C3F AP5 302 A 1 HETATM 25 O O3F AP5 . . . I 2 -10.004 -17.32 99.299 1 101.28 ? O3F AP5 302 A 1 HETATM 26 C C2F AP5 . . . I 2 -8.62 -18.585 100.648 1 98.09 ? C2F AP5 302 A 1 HETATM 27 O O2F AP5 . . . I 2 -8.01 -18.294 99.418 1 102.55 ? O2F AP5 302 A 1 HETATM 28 C C1F AP5 . . . I 2 -8.05 -17.709 101.722 1 96.18 ? C1F AP5 302 A 1 HETATM 29 N N9A AP5 . . . I 2 -7.139 -18.516 102.518 1 94.99 ? N9A AP5 302 A 1 HETATM 30 C C8A AP5 . . . I 2 -7.434 -19.717 102.991 1 97.63 ? C8A AP5 302 A 1 HETATM 31 N N7A AP5 . . . I 2 -6.422 -20.231 103.7 1 99.84 ? N7A AP5 302 A 1 HETATM 32 C C5A AP5 . . . I 2 -5.451 -19.336 103.68 1 98.12 ? C5A AP5 302 A 1 HETATM 33 C C6A AP5 . . . I 2 -4.109 -19.267 104.231 1 100.17 ? C6A AP5 302 A 1 HETATM 34 N N6A AP5 . . . I 2 -3.597 -20.272 104.962 1 102.43 ? N6A AP5 302 A 1 HETATM 35 N N1A AP5 . . . I 2 -3.411 -18.166 103.977 1 99.38 ? N1A AP5 302 A 1 HETATM 36 C C2A AP5 . . . I 2 -3.921 -17.166 103.254 1 97.34 ? C2A AP5 302 A 1 HETATM 37 N N3A AP5 . . . I 2 -5.143 -17.173 102.726 1 93.82 ? N3A AP5 302 A 1 HETATM 38 C C4A AP5 . . . I 2 -5.933 -18.214 102.899 1 94.16 ? C4A AP5 302 A 1 HETATM 39 O O5J AP5 . . . I 2 -21.427 -19.952 105.899 1 84.53 ? O5J AP5 302 A 1 HETATM 40 C C5J AP5 . . . I 2 -22.02 -18.836 105.278 1 85.05 ? C5J AP5 302 A 1 HETATM 41 C C4J AP5 . . . I 2 -23.314 -18.525 105.998 1 83.92 ? C4J AP5 302 A 1 HETATM 42 O O4J AP5 . . . I 2 -23.878 -19.688 106.582 1 82.68 ? O4J AP5 302 A 1 HETATM 43 C C3J AP5 . . . I 2 -23.095 -17.575 107.134 1 81.58 ? C3J AP5 302 A 1 HETATM 44 O O3J AP5 . . . I 2 -23.499 -16.303 106.69 1 78.96 ? O3J AP5 302 A 1 HETATM 45 C C2J AP5 . . . I 2 -24.078 -18.011 108.161 1 80.68 ? C2J AP5 302 A 1 HETATM 46 O O2J AP5 . . . I 2 -25.151 -17.125 107.976 1 81.32 ? O2J AP5 302 A 1 HETATM 47 C C1J AP5 . . . I 2 -24.578 -19.369 107.768 1 79.8 ? C1J AP5 302 A 1 HETATM 48 N N9B AP5 . . . I 2 -24.233 -20.328 108.82 1 76.83 ? N9B AP5 302 A 1 HETATM 49 C C8B AP5 . . . I 2 -23.458 -21.386 108.652 1 75.33 ? C8B AP5 302 A 1 HETATM 50 N N7B AP5 . . . I 2 -23.301 -22.07 109.79 1 73.95 ? N7B AP5 302 A 1 HETATM 51 C C5B AP5 . . . I 2 -23.991 -21.444 110.712 1 75.9 ? C5B AP5 302 A 1 HETATM 52 C C6B AP5 . . . I 2 -24.242 -21.643 112.128 1 76.6 ? C6B AP5 302 A 1 HETATM 53 N N6B AP5 . . . I 2 -23.717 -22.675 112.789 1 76.01 ? N6B AP5 302 A 1 HETATM 54 N N1B AP5 . . . I 2 -25.019 -20.771 112.749 1 78.68 ? N1B AP5 302 A 1 HETATM 55 C C2B AP5 . . . I 2 -25.546 -19.734 112.108 1 78.71 ? C2B AP5 302 A 1 HETATM 56 N N3B AP5 . . . I 2 -25.35 -19.503 110.817 1 78.77 ? N3B AP5 302 A 1 HETATM 57 C C4B AP5 . . . I 2 -24.602 -20.304 110.072 1 76.74 ? C4B AP5 302 A 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 250 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 57 #