data_3H86 # _model_server_result.job_id xCYyWbpGf_gfaaDRC3CHEQ _model_server_result.datetime_utc '2024-11-15 05:29:41' _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 3h86 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":193}' # _entry.id 3H86 # _exptl.entry_id 3H86 _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 90 _cell.angle_gamma 120 _cell.entry_id 3H86 _cell.length_a 102.84 _cell.length_b 102.84 _cell.length_c 228.72 _cell.Z_PDB 36 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3H86 _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3' # 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 trimeric 3 author_and_software_defined_assembly 1 PISA trimeric 3 author_and_software_defined_assembly 2 PISA dodecameric 12 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,E,F,G,I,J,K 1 1 D,H,L 2 1,2,3 D,H,L 3 4,5,6 A,B,C,E,F,G,I,J,K 3 1,7,8 # 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' 2_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 0 4 'crystal symmetry operation' 4_555 x+2/3,y+1/3,z+1/3 1 0 0 0 1 0 0 0 1 51.42 29.687351 76.24 5 'crystal symmetry operation' 5_555 -y+2/3,x-y+1/3,z+1/3 -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 51.42 29.687351 76.24 6 'crystal symmetry operation' 6_555 -x+y+2/3,-x+1/3,z+1/3 -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 51.42 29.687351 76.24 7 'crystal symmetry operation' 2_655 -y+1,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 102.84 0 0 8 'crystal symmetry operation' 3_665 -x+y+1,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 51.42 89.062053 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 F N N ? 2 G N N ? 2 H N N # _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 3H86 _atom_sites.fract_transf_matrix[1][1] 0.009724 _atom_sites.fract_transf_matrix[1][2] 0.005614 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011228 _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] 0.004372 _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 B 1 193 1 AP5 AP5 . F 2 AP5 A 1 193 1 AP5 AP5 . G 2 AP5 C 1 193 1 AP5 AP5 . H 2 AP5 G 1 193 1 AP5 AP5 . I 3 HOH B 1 194 6 HOH HOH . I 3 HOH B 2 195 8 HOH HOH . I 3 HOH B 3 196 16 HOH HOH . I 3 HOH B 4 197 18 HOH HOH . I 3 HOH B 5 198 19 HOH HOH . I 3 HOH B 6 199 32 HOH HOH . I 3 HOH B 7 200 33 HOH HOH . I 3 HOH B 8 201 34 HOH HOH . J 3 HOH A 1 194 1 HOH HOH . J 3 HOH A 2 195 2 HOH HOH . J 3 HOH A 3 196 3 HOH HOH . J 3 HOH A 4 197 4 HOH HOH . J 3 HOH A 5 198 26 HOH HOH . J 3 HOH A 6 199 28 HOH HOH . J 3 HOH A 7 200 29 HOH HOH . J 3 HOH A 8 201 35 HOH HOH . J 3 HOH A 9 202 36 HOH HOH . J 3 HOH A 10 203 39 HOH HOH . J 3 HOH A 11 204 42 HOH HOH . J 3 HOH A 12 205 43 HOH HOH . K 3 HOH C 1 194 5 HOH HOH . K 3 HOH C 2 195 11 HOH HOH . K 3 HOH C 3 196 12 HOH HOH . K 3 HOH C 4 197 14 HOH HOH . K 3 HOH C 5 198 15 HOH HOH . K 3 HOH C 6 199 20 HOH HOH . K 3 HOH C 7 200 22 HOH HOH . K 3 HOH C 8 201 25 HOH HOH . K 3 HOH C 9 202 27 HOH HOH . K 3 HOH C 10 203 30 HOH HOH . K 3 HOH C 11 204 31 HOH HOH . K 3 HOH C 12 205 37 HOH HOH . K 3 HOH C 13 206 38 HOH HOH . K 3 HOH C 14 207 40 HOH HOH . K 3 HOH C 15 208 41 HOH HOH . L 3 HOH G 1 194 7 HOH HOH . L 3 HOH G 2 195 9 HOH HOH . L 3 HOH G 3 196 10 HOH HOH . L 3 HOH G 4 197 13 HOH HOH . L 3 HOH G 5 198 17 HOH HOH . L 3 HOH G 6 199 21 HOH HOH . L 3 HOH G 7 200 23 HOH HOH . L 3 HOH G 8 201 24 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 . . . E 2 50.923 -8.21 14.827 1 60.82 ? PA AP5 193 B 1 HETATM 2 O O1A AP5 . . . E 2 50.981 -8.333 16.353 1 60.68 ? O1A AP5 193 B 1 HETATM 3 O O2A AP5 . . . E 2 49.513 -8.513 14.363 1 61.96 ? O2A AP5 193 B 1 HETATM 4 O O3A AP5 . . . E 2 51.396 -6.824 14.255 1 53.01 ? O3A AP5 193 B 1 HETATM 5 P PB AP5 . . . E 2 52.692 -6.126 14.833 1 51.37 ? PB AP5 193 B 1 HETATM 6 O O1B AP5 . . . E 2 53.354 -5.27 13.801 1 55.05 ? O1B AP5 193 B 1 HETATM 7 O O2B AP5 . . . E 2 53.789 -7.018 15.281 1 55.26 ? O2B AP5 193 B 1 HETATM 8 O O3B AP5 . . . E 2 52.059 -5.2 16.013 1 53.2 ? O3B AP5 193 B 1 HETATM 9 P PG AP5 . . . E 2 52.902 -4.763 17.301 1 51.68 ? PG AP5 193 B 1 HETATM 10 O O1G AP5 . . . E 2 54.308 -4.519 16.937 1 45.16 ? O1G AP5 193 B 1 HETATM 11 O O2G AP5 . . . E 2 52.976 -5.914 18.282 1 54.46 ? O2G AP5 193 B 1 HETATM 12 O O3G AP5 . . . E 2 52.195 -3.438 17.789 1 46.89 ? O3G AP5 193 B 1 HETATM 13 P PD AP5 . . . E 2 51.143 -3.475 18.984 1 50.26 ? PD AP5 193 B 1 HETATM 14 O O1D AP5 . . . E 2 49.983 -4.38 18.708 1 44.09 ? O1D AP5 193 B 1 HETATM 15 O O2D AP5 . . . E 2 50.616 -2.06 19.206 1 45.67 ? O2D AP5 193 B 1 HETATM 16 O O3D AP5 . . . E 2 52.109 -4.087 20.135 1 45.85 ? O3D AP5 193 B 1 HETATM 17 P PE AP5 . . . E 2 51.973 -3.653 21.65 1 51.39 ? PE AP5 193 B 1 HETATM 18 O O1E AP5 . . . E 2 53.033 -4.428 22.318 1 48.35 ? O1E AP5 193 B 1 HETATM 19 O O2E AP5 . . . E 2 50.568 -3.942 22.142 1 52.15 ? O2E AP5 193 B 1 HETATM 20 O O5F AP5 . . . E 2 51.947 -9.235 14.212 1 57.36 ? O5F AP5 193 B 1 HETATM 21 C C5F AP5 . . . E 2 52.84 -8.828 13.196 1 63.76 ? C5F AP5 193 B 1 HETATM 22 C C4F AP5 . . . E 2 52.576 -9.553 11.872 1 63.89 ? C4F AP5 193 B 1 HETATM 23 O O4F AP5 . . . E 2 51.264 -10.121 11.845 1 62.27 ? O4F AP5 193 B 1 HETATM 24 C C3F AP5 . . . E 2 52.748 -8.586 10.71 1 63.79 ? C3F AP5 193 B 1 HETATM 25 O O3F AP5 . . . E 2 53.728 -9.101 9.816 1 67.14 ? O3F AP5 193 B 1 HETATM 26 C C2F AP5 . . . E 2 51.432 -8.622 10.003 1 62.7 ? C2F AP5 193 B 1 HETATM 27 O O2F AP5 . . . E 2 51.66 -8.884 8.634 1 60.84 ? O2F AP5 193 B 1 HETATM 28 C C1F AP5 . . . E 2 50.738 -9.856 10.575 1 62.08 ? C1F AP5 193 B 1 HETATM 29 N N9A AP5 . . . E 2 49.257 -9.715 10.586 1 60.08 ? N9A AP5 193 B 1 HETATM 30 C C8A AP5 . . . E 2 48.399 -9.512 11.651 1 59.59 ? C8A AP5 193 B 1 HETATM 31 N N7A AP5 . . . E 2 47.12 -9.454 11.186 1 55.23 ? N7A AP5 193 B 1 HETATM 32 C C5A AP5 . . . E 2 47.186 -9.608 9.856 1 50.15 ? C5A AP5 193 B 1 HETATM 33 C C6A AP5 . . . E 2 46.21 -9.65 8.912 1 44.81 ? C6A AP5 193 B 1 HETATM 34 N N6A AP5 . . . E 2 45.084 -9.061 9.182 1 41.38 ? N6A AP5 193 B 1 HETATM 35 N N1A AP5 . . . E 2 46.554 -9.839 7.606 1 44.56 ? N1A AP5 193 B 1 HETATM 36 C C2A AP5 . . . E 2 47.854 -9.991 7.196 1 47.29 ? C2A AP5 193 B 1 HETATM 37 N N3A AP5 . . . E 2 48.85 -9.96 8.164 1 52.71 ? N3A AP5 193 B 1 HETATM 38 C C4A AP5 . . . E 2 48.501 -9.76 9.461 1 52.76 ? C4A AP5 193 B 1 HETATM 39 O O5J AP5 . . . E 2 52.329 -2.049 21.785 1 43.74 ? O5J AP5 193 B 1 HETATM 40 C C5J AP5 . . . E 2 53.632 -1.608 21.519 1 46.14 ? C5J AP5 193 B 1 HETATM 41 C C4J AP5 . . . E 2 54.482 -1.266 22.763 1 47.53 ? C4J AP5 193 B 1 HETATM 42 O O4J AP5 . . . E 2 54.241 0.031 23.29 1 45.52 ? O4J AP5 193 B 1 HETATM 43 C C3J AP5 . . . E 2 54.184 -2.194 23.899 1 48.63 ? C3J AP5 193 B 1 HETATM 44 O O3J AP5 . . . E 2 55.423 -2.484 24.465 1 52.77 ? O3J AP5 193 B 1 HETATM 45 C C2J AP5 . . . E 2 53.374 -1.364 24.865 1 45.85 ? C2J AP5 193 B 1 HETATM 46 O O2J AP5 . . . E 2 53.588 -1.915 26.112 1 40.83 ? O2J AP5 193 B 1 HETATM 47 C C1J AP5 . . . E 2 54.044 -0.039 24.694 1 45.9 ? C1J AP5 193 B 1 HETATM 48 N N9B AP5 . . . E 2 53.292 1.139 25.255 1 44.22 ? N9B AP5 193 B 1 HETATM 49 C C8B AP5 . . . E 2 53.856 2.246 25.88 1 41.59 ? C8B AP5 193 B 1 HETATM 50 N N7B AP5 . . . E 2 52.875 3.125 26.245 1 35.12 ? N7B AP5 193 B 1 HETATM 51 C C5B AP5 . . . E 2 51.748 2.575 25.882 1 34.86 ? C5B AP5 193 B 1 HETATM 52 C C6B AP5 . . . E 2 50.492 3.086 26.016 1 39.95 ? C6B AP5 193 B 1 HETATM 53 N N6B AP5 . . . E 2 50.418 4.388 26.283 1 35.33 ? N6B AP5 193 B 1 HETATM 54 N N1B AP5 . . . E 2 49.443 2.332 25.501 1 40.87 ? N1B AP5 193 B 1 HETATM 55 C C2B AP5 . . . E 2 49.7 1.101 24.914 1 40.14 ? C2B AP5 193 B 1 HETATM 56 N N3B AP5 . . . E 2 50.984 0.607 24.79 1 38.14 ? N3B AP5 193 B 1 HETATM 57 C C4B AP5 . . . E 2 51.962 1.354 25.265 1 35.84 ? C4B AP5 193 B 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 36 _model_server_stats.create_model_time_ms 36 _model_server_stats.query_time_ms 301 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 57 #