data_3X2S # _model_server_result.job_id rrfy609nyCyci2zULez4nA _model_server_result.datetime_utc '2024-12-22 05:51:19' _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 3x2s # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":303}' # _entry.id 3X2S # _exptl.entry_id 3X2S _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 2 _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 3X2S _cell.length_a 60.114 _cell.length_b 58.992 _cell.length_c 118.308 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3X2S _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 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 monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 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,K 1 1 B,G,H,I,J,L 2 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 ? 3 E N N ? 3 I 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 covale ? covale1 A SG CYS 55 A CYS 55 1_555 C C1 JPY . A JPY 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.79 ? covale ? covale2 A SG CYS 169 A CYS 169 1_555 D C1 JPY . A JPY 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.771 ? covale ? covale3 B SG CYS 55 B CYS 55 1_555 G C1 JPY . B JPY 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.785 ? covale ? covale4 B SG CYS 169 B CYS 169 1_555 H C1 JPY . B JPY 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.769 ? metalc ? metalc1 E O1D AP5 . A AP5 303 1_555 F MG MG . A MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.96 ? metalc ? metalc2 E O2G AP5 . A AP5 303 1_555 F MG MG . A MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.61 ? metalc ? metalc3 E O3D AP5 . A AP5 303 1_555 F MG MG . A MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.955 ? metalc ? metalc4 F MG MG . A MG 304 1_555 K O HOH . A HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? metalc ? metalc5 F MG MG . A MG 304 1_555 K O HOH . A HOH 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? metalc ? metalc6 F MG MG . A MG 304 1_555 K O HOH . A HOH 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? metalc ? metalc7 F MG MG . A MG 304 1_555 K O HOH . A HOH 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.996 ? metalc ? metalc8 I O1D AP5 . B AP5 303 1_555 J MG MG . B MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.936 ? metalc ? metalc9 I O2G AP5 . B AP5 303 1_555 J MG MG . B MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? metalc ? metalc10 J MG MG . B MG 304 1_555 L O HOH . B HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.304 ? metalc ? metalc11 J MG MG . B MG 304 1_555 L O HOH . B HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.361 ? metalc ? metalc12 J MG MG . B MG 304 1_555 L O HOH . B HOH 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.884 ? metalc ? metalc13 J MG MG . B MG 304 1_555 L O HOH . B HOH 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.925 ? # _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 3X2S _atom_sites.fract_transf_matrix[1][1] 0.016635 _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] 0.016951 _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] 0.008453 _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 C 2 JPY A 1 301 55 JPY CPY . D 2 JPY A 1 302 169 JPY CPY . E 3 AP5 A 1 303 1 AP5 AP5 . F 4 MG A 1 304 1 MG MG2 . G 2 JPY B 1 301 55 JPY CPY . H 2 JPY B 1 302 169 JPY CPY . I 3 AP5 B 1 303 2 AP5 AP5 . J 4 MG B 1 304 2 MG MG2 . K 5 HOH A 1 401 1 HOH HOH . K 5 HOH A 2 402 6 HOH HOH . K 5 HOH A 3 403 8 HOH HOH . K 5 HOH A 4 404 9 HOH HOH . K 5 HOH A 5 405 10 HOH HOH . K 5 HOH A 6 406 11 HOH HOH . K 5 HOH A 7 407 12 HOH HOH . K 5 HOH A 8 408 13 HOH HOH . K 5 HOH A 9 409 14 HOH HOH . K 5 HOH A 10 410 15 HOH HOH . K 5 HOH A 11 411 26 HOH HOH . K 5 HOH A 12 412 27 HOH HOH . L 5 HOH B 1 401 2 HOH HOH . L 5 HOH B 2 402 3 HOH HOH . L 5 HOH B 3 403 4 HOH HOH . L 5 HOH B 4 404 5 HOH HOH . L 5 HOH B 5 405 7 HOH HOH . L 5 HOH B 6 406 16 HOH HOH . L 5 HOH B 7 407 17 HOH HOH . L 5 HOH B 8 408 18 HOH HOH . L 5 HOH B 9 409 19 HOH HOH . L 5 HOH B 10 410 20 HOH HOH . L 5 HOH B 11 411 21 HOH HOH . L 5 HOH B 12 412 22 HOH HOH . L 5 HOH B 13 413 23 HOH HOH . L 5 HOH B 14 414 24 HOH HOH . L 5 HOH B 15 415 25 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 3 38.519 27.365 2.973 1 47.94 ? PA AP5 303 B 1 HETATM 2 O O1A AP5 . . . I 3 38.897 26.677 1.725 1 47.68 ? O1A AP5 303 B 1 HETATM 3 O O2A AP5 . . . I 3 37.282 28.341 2.659 1 49.26 ? O2A AP5 303 B 1 HETATM 4 O O3A AP5 . . . I 3 38.123 26.249 4.08 1 47.62 ? O3A AP5 303 B 1 HETATM 5 P PB AP5 . . . I 3 37.078 26.818 5.197 1 48.09 ? PB AP5 303 B 1 HETATM 6 O O1B AP5 . . . I 3 37.497 26.278 6.514 1 48.6 ? O1B AP5 303 B 1 HETATM 7 O O2B AP5 . . . I 3 37.092 28.421 5.282 1 47.7 ? O2B AP5 303 B 1 HETATM 8 O O3B AP5 . . . I 3 35.545 26.339 4.861 1 43.94 ? O3B AP5 303 B 1 HETATM 9 P PG AP5 . . . I 3 35.561 24.816 4.339 1 38.89 ? PG AP5 303 B 1 HETATM 10 O O1G AP5 . . . I 3 36.499 24.032 5.181 1 37.88 ? O1G AP5 303 B 1 HETATM 11 O O2G AP5 . . . I 3 36.057 24.793 2.81 1 38.14 ? O2G AP5 303 B 1 HETATM 12 O O3G AP5 . . . I 3 34.094 24.109 4.475 1 41.78 ? O3G AP5 303 B 1 HETATM 13 P PD AP5 . . . I 3 32.906 24.826 3.6 1 40.62 ? PD AP5 303 B 1 HETATM 14 O O1D AP5 . . . I 3 33.381 25.235 2.267 1 41.92 ? O1D AP5 303 B 1 HETATM 15 O O2D AP5 . . . I 3 32.368 26.118 4.375 1 42.33 ? O2D AP5 303 B 1 HETATM 16 O O3D AP5 . . . I 3 31.652 23.785 3.478 1 42.29 ? O3D AP5 303 B 1 HETATM 17 P PE AP5 . . . I 3 32.064 22.425 2.675 1 39.51 ? PE AP5 303 B 1 HETATM 18 O O1E AP5 . . . I 3 30.84 21.817 2.136 1 36.5 ? O1E AP5 303 B 1 HETATM 19 O O2E AP5 . . . I 3 33.032 22.774 1.452 1 43.7 ? O2E AP5 303 B 1 HETATM 20 O O5F AP5 . . . I 3 39.764 28.219 3.505 1 48.32 ? O5F AP5 303 B 1 HETATM 21 C C5F AP5 . . . I 3 40.869 27.312 3.597 1 50.23 ? C5F AP5 303 B 1 HETATM 22 C C4F AP5 . . . I 3 42.12 28.067 4.002 1 48.53 ? C4F AP5 303 B 1 HETATM 23 O O4F AP5 . . . I 3 42.364 29.164 3.089 1 47.38 ? O4F AP5 303 B 1 HETATM 24 C C3F AP5 . . . I 3 41.933 28.624 5.411 1 48.91 ? C3F AP5 303 B 1 HETATM 25 O O3F AP5 . . . I 3 42.78 27.926 6.337 1 52.07 ? O3F AP5 303 B 1 HETATM 26 C C2F AP5 . . . I 3 42.246 30.126 5.299 1 47.4 ? C2F AP5 303 B 1 HETATM 27 O O2F AP5 . . . I 3 43.334 30.501 6.145 1 50.45 ? O2F AP5 303 B 1 HETATM 28 C C1F AP5 . . . I 3 42.583 30.399 3.814 1 45.7 ? C1F AP5 303 B 1 HETATM 29 N N9A AP5 . . . I 3 41.694 31.467 3.301 1 43.02 ? N9A AP5 303 B 1 HETATM 30 C C8A AP5 . . . I 3 40.705 31.334 2.345 1 43.22 ? C8A AP5 303 B 1 HETATM 31 N N7A AP5 . . . I 3 40.108 32.474 2.146 1 40.58 ? N7A AP5 303 B 1 HETATM 32 C C5A AP5 . . . I 3 40.662 33.412 2.944 1 38.17 ? C5A AP5 303 B 1 HETATM 33 C C6A AP5 . . . I 3 40.429 34.789 3.169 1 36.68 ? C6A AP5 303 B 1 HETATM 34 N N6A AP5 . . . I 3 39.432 35.452 2.471 1 35.85 ? N6A AP5 303 B 1 HETATM 35 N N1A AP5 . . . I 3 41.193 35.439 4.07 1 34.94 ? N1A AP5 303 B 1 HETATM 36 C C2A AP5 . . . I 3 42.156 34.809 4.752 1 36.6 ? C2A AP5 303 B 1 HETATM 37 N N3A AP5 . . . I 3 42.403 33.512 4.575 1 36.78 ? N3A AP5 303 B 1 HETATM 38 C C4A AP5 . . . I 3 41.69 32.785 3.698 1 39.4 ? C4A AP5 303 B 1 HETATM 39 O O5J AP5 . . . I 3 32.839 21.383 3.638 1 39.85 ? O5J AP5 303 B 1 HETATM 40 C C5J AP5 . . . I 3 31.956 20.981 4.694 1 40.11 ? C5J AP5 303 B 1 HETATM 41 C C4J AP5 . . . I 3 31.812 19.429 4.803 1 40.61 ? C4J AP5 303 B 1 HETATM 42 O O4J AP5 . . . I 3 30.485 19.218 5.263 1 42.55 ? O4J AP5 303 B 1 HETATM 43 C C3J AP5 . . . I 3 31.95 18.758 3.423 1 40.78 ? C3J AP5 303 B 1 HETATM 44 O O3J AP5 . . . I 3 32.866 17.661 3.522 1 38.14 ? O3J AP5 303 B 1 HETATM 45 C C2J AP5 . . . I 3 30.549 18.209 3.073 1 39.89 ? C2J AP5 303 B 1 HETATM 46 O O2J AP5 . . . I 3 30.603 16.869 2.601 1 40.54 ? O2J AP5 303 B 1 HETATM 47 C C1J AP5 . . . I 3 29.744 18.327 4.384 1 41.34 ? C1J AP5 303 B 1 HETATM 48 N N9B AP5 . . . I 3 28.424 18.942 4.205 1 41.45 ? N9B AP5 303 B 1 HETATM 49 C C8B AP5 . . . I 3 28.128 20.057 3.456 1 40.64 ? C8B AP5 303 B 1 HETATM 50 N N7B AP5 . . . I 3 26.864 20.329 3.548 1 42.82 ? N7B AP5 303 B 1 HETATM 51 C C5B AP5 . . . I 3 26.259 19.416 4.358 1 41.74 ? C5B AP5 303 B 1 HETATM 52 C C6B AP5 . . . I 3 24.93 19.205 4.834 1 40.12 ? C6B AP5 303 B 1 HETATM 53 N N6B AP5 . . . I 3 23.907 20.057 4.466 1 39.93 ? N6B AP5 303 B 1 HETATM 54 N N1B AP5 . . . I 3 24.693 18.163 5.648 1 40.8 ? N1B AP5 303 B 1 HETATM 55 C C2B AP5 . . . I 3 25.673 17.327 6.022 1 41.07 ? C2B AP5 303 B 1 HETATM 56 N N3B AP5 . . . I 3 26.93 17.49 5.608 1 40.51 ? N3B AP5 303 B 1 HETATM 57 C C4B AP5 . . . I 3 27.262 18.509 4.788 1 40.97 ? C4B AP5 303 B 1 # _model_server_stats.io_time_ms 51 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 57 #