data_1MRN # _model_server_result.job_id mTdf2wBqRap3pbwF6_DDMA _model_server_result.datetime_utc '2024-10-26 18:20:49' _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 1mrn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":301}' # _entry.id 1MRN # _exptl.entry_id 1MRN _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 891.354 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "P1-(5'-ADENOSYL)P5-(5'-THYMIDYL)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 1MRN _cell.length_a 75.46 _cell.length_b 75.46 _cell.length_c 133.34 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1MRN _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65 2 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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' 8_555 x-y,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id E _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 OD1 ASP 9 A ASP 9 1_555 D MG MG . A MG 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.972 ? metalc ? metalc2 A OE2 GLU 166 A GLU 166 1_555 D MG MG . A MG 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.322 ? metalc ? metalc3 D MG MG . A MG 300 1_555 E O1B T5A . A T5A 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.65 ? metalc ? metalc4 D MG MG . A MG 300 1_555 E O2A T5A . A T5A 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.932 ? metalc ? metalc5 D MG MG . A MG 300 1_555 E O3A T5A . A T5A 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.363 ? # _chem_comp.formula 'C20 H30 N7 O23 P5' _chem_comp.formula_weight 891.354 _chem_comp.id T5A _chem_comp.mon_nstd_flag . _chem_comp.name "P1-(5'-ADENOSYL)P5-(5'-THYMIDYL)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 N1B C6B T5A sing 294 n n N1B C2B T5A sing 295 n n N1B C1E T5A sing 296 n n C6B C5B T5A doub 297 n n C6B HB6 T5A sing 298 n n C2B O2B T5A doub 299 n n C2B N3B T5A sing 300 n n N3B C4B T5A sing 301 n n N3B HN3 T5A sing 302 n n C4B O4B T5A doub 303 n n C4B C5B T5A sing 304 n n C5B C7B T5A sing 305 n n C7B HB71 T5A sing 306 n n C7B HB72 T5A sing 307 n n C7B HB73 T5A sing 308 n n C5E C4E T5A sing 309 n n C5E O5E T5A sing 310 n n C5E HB51 T5A sing 311 n n C5E HB52 T5A sing 312 n n C4E O4E T5A sing 313 n n C4E C3E T5A sing 314 n n C4E HB4 T5A sing 315 n n O4E C1E T5A sing 316 n n C1E C2E T5A sing 317 n n C1E HB1 T5A sing 318 n n C2E C3E T5A sing 319 n n C2E HB21 T5A sing 320 n n C2E HB22 T5A sing 321 n n C3E O3E T5A sing 322 n n C3E HB3 T5A sing 323 n n O3E "HB'3" T5A sing 324 n n PA O1A T5A sing 325 n n PA O2A T5A doub 326 n n PA O5E T5A sing 327 n n PA O3A T5A sing 328 n n O1A HO1A T5A sing 329 n n O3A PB T5A sing 330 n n PB O1B T5A doub 331 n n PB O2X T5A sing 332 n n PB O3B T5A sing 333 n n O2X HO2B T5A sing 334 n n O3B PC T5A sing 335 n n PC O1C T5A doub 336 n n PC O2C T5A sing 337 n n PC O3C T5A sing 338 n n O2C HO2C T5A sing 339 n n O3C PD T5A sing 340 n n PD O1D T5A sing 341 n n PD O2D T5A doub 342 n n PD O3D T5A sing 343 n n O1D HO1D T5A sing 344 n n O3D PE T5A sing 345 n n PE O1E T5A sing 346 n n PE O2E T5A doub 347 n n PE O5F T5A sing 348 n n O1E HO1E T5A sing 349 n n O5F C5F T5A sing 350 n n C5F C4F T5A sing 351 n n C5F HA51 T5A sing 352 n n C5F HA52 T5A sing 353 n n C4F O4F T5A sing 354 n n C4F C3F T5A sing 355 n n C4F HA4 T5A sing 356 n n O4F C1F T5A sing 357 n n C1F C2F T5A sing 358 n n C1F N9A T5A sing 359 n n C1F HA1 T5A sing 360 n n C2F O2F T5A sing 361 n n C2F C3F T5A sing 362 n n C2F HC2 T5A sing 363 n n O2F HO2 T5A sing 364 n n C3F O3F T5A sing 365 n n C3F HC3 T5A sing 366 n n O3F HA3 T5A sing 367 n n N9A C4A T5A sing 368 n y N9A C8A T5A sing 369 n y C4A N3A T5A sing 370 n y C4A C5A T5A doub 371 n y N3A C2A T5A doub 372 n y C2A N1A T5A sing 373 n y C2A HA2 T5A sing 374 n n N1A C6A T5A doub 375 n y C6A N6A T5A sing 376 n n C6A C5A T5A sing 377 n y N6A HA61 T5A sing 378 n n N6A HA62 T5A sing 379 n n C5A N7A T5A sing 380 n y N7A C8A T5A doub 381 n y C8A HA8 T5A sing 382 n n # _atom_sites.entry_id 1MRN _atom_sites.fract_transf_matrix[1][1] 0.013252 _atom_sites.fract_transf_matrix[1][2] 0.007651 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015302 _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] 0.0075 _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 SO4 A 1 219 219 SO4 SO4 . C 2 SO4 A 1 220 220 SO4 SO4 . D 3 MG A 1 300 300 MG MG . E 4 T5A A 1 301 214 T5A T5A . F 5 HOH A 1 302 1 HOH HOH . F 5 HOH A 2 303 2 HOH HOH . F 5 HOH A 3 304 3 HOH HOH . F 5 HOH A 4 305 4 HOH HOH . F 5 HOH A 5 306 5 HOH HOH . F 5 HOH A 6 307 6 HOH HOH . F 5 HOH A 7 308 7 HOH HOH . F 5 HOH A 8 309 8 HOH HOH . F 5 HOH A 9 310 9 HOH HOH . F 5 HOH A 10 311 10 HOH HOH . F 5 HOH A 11 312 11 HOH HOH . F 5 HOH A 12 313 12 HOH HOH . F 5 HOH A 13 314 13 HOH HOH . F 5 HOH A 14 315 14 HOH HOH . F 5 HOH A 15 316 15 HOH HOH . F 5 HOH A 16 317 16 HOH HOH . F 5 HOH A 17 318 17 HOH HOH . F 5 HOH A 18 319 18 HOH HOH . F 5 HOH A 19 320 19 HOH HOH . F 5 HOH A 20 321 20 HOH HOH . F 5 HOH A 21 322 21 HOH HOH . F 5 HOH A 22 323 22 HOH HOH . F 5 HOH A 23 324 23 HOH HOH . F 5 HOH A 24 325 24 HOH HOH . F 5 HOH A 25 326 25 HOH HOH . F 5 HOH A 26 327 26 HOH HOH . F 5 HOH A 27 328 27 HOH HOH . F 5 HOH A 28 329 28 HOH HOH . F 5 HOH A 29 330 29 HOH HOH . F 5 HOH A 30 331 30 HOH HOH . F 5 HOH A 31 332 31 HOH HOH . F 5 HOH A 32 333 32 HOH HOH . F 5 HOH A 33 334 33 HOH HOH . F 5 HOH A 34 335 34 HOH HOH . F 5 HOH A 35 336 35 HOH HOH . F 5 HOH A 36 337 36 HOH HOH . F 5 HOH A 37 338 37 HOH HOH . F 5 HOH A 38 339 38 HOH HOH . F 5 HOH A 39 340 39 HOH HOH . F 5 HOH A 40 341 40 HOH HOH . F 5 HOH A 41 342 41 HOH HOH . F 5 HOH A 42 343 42 HOH HOH . F 5 HOH A 43 344 43 HOH HOH . F 5 HOH A 44 345 44 HOH HOH . F 5 HOH A 45 346 45 HOH HOH . F 5 HOH A 46 347 46 HOH HOH . F 5 HOH A 47 348 47 HOH HOH . F 5 HOH A 48 349 48 HOH HOH . F 5 HOH A 49 350 49 HOH HOH . F 5 HOH A 50 351 50 HOH HOH . F 5 HOH A 51 352 51 HOH HOH . F 5 HOH A 52 353 52 HOH HOH . F 5 HOH A 53 354 53 HOH HOH . F 5 HOH A 54 355 54 HOH HOH . F 5 HOH A 55 356 55 HOH HOH . F 5 HOH A 56 357 56 HOH HOH . F 5 HOH A 57 358 57 HOH HOH . F 5 HOH A 58 359 58 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 N N1B T5A . . . E 4 24.111 9.625 9.212 1 26.91 ? N1B T5A 301 A 1 HETATM 2 C C6B T5A . . . E 4 25.449 9.953 9.314 1 23.99 ? C6B T5A 301 A 1 HETATM 3 C C2B T5A . . . E 4 23.623 8.35 9.476 1 24.92 ? C2B T5A 301 A 1 HETATM 4 O O2B T5A . . . E 4 22.43 7.955 9.39 1 23.28 ? O2B T5A 301 A 1 HETATM 5 N N3B T5A . . . E 4 24.622 7.452 9.857 1 24.21 ? N3B T5A 301 A 1 HETATM 6 C C4B T5A . . . E 4 26.001 7.698 9.984 1 23.17 ? C4B T5A 301 A 1 HETATM 7 O O4B T5A . . . E 4 26.816 6.792 10.333 1 23.44 ? O4B T5A 301 A 1 HETATM 8 C C5B T5A . . . E 4 26.404 9.071 9.679 1 21.47 ? C5B T5A 301 A 1 HETATM 9 C C7B T5A . . . E 4 27.894 9.42 9.791 1 18.95 ? C7B T5A 301 A 1 HETATM 10 C C5E T5A . . . E 4 24.226 13.399 6.761 1 33.17 ? C5E T5A 301 A 1 HETATM 11 C C4E T5A . . . E 4 23.162 12.487 7.376 1 30.49 ? C4E T5A 301 A 1 HETATM 12 O O4E T5A . . . E 4 23.738 11.181 7.552 1 29.32 ? O4E T5A 301 A 1 HETATM 13 C C1E T5A . . . E 4 23.175 10.643 8.786 1 27.11 ? C1E T5A 301 A 1 HETATM 14 C C2E T5A . . . E 4 23.071 11.925 9.646 1 29.01 ? C2E T5A 301 A 1 HETATM 15 C C3E T5A . . . E 4 22.682 13.041 8.7 1 30.14 ? C3E T5A 301 A 1 HETATM 16 O O3E T5A . . . E 4 21.28 13.256 8.619 1 32.12 ? O3E T5A 301 A 1 HETATM 17 P PA T5A . . . E 4 25.804 14.829 8.255 1 36.33 ? PA T5A 301 A 1 HETATM 18 O O1A T5A . . . E 4 27.227 14.981 8.368 1 39.71 ? O1A T5A 301 A 1 HETATM 19 O O2A T5A . . . E 4 25.042 14.979 9.508 1 40.05 ? O2A T5A 301 A 1 HETATM 20 O O5E T5A . . . E 4 25.321 13.409 7.591 1 34.49 ? O5E T5A 301 A 1 HETATM 21 O O3A T5A . . . E 4 25.243 15.961 7.637 1 41.25 ? O3A T5A 301 A 1 HETATM 22 P PB T5A . . . E 4 25.427 16.769 6.226 1 41.36 ? PB T5A 301 A 1 HETATM 23 O O1B T5A . . . E 4 24.219 17.613 5.988 1 43.36 ? O1B T5A 301 A 1 HETATM 24 O O2X T5A . . . E 4 25.748 15.767 5.177 1 41.65 ? O2X T5A 301 A 1 HETATM 25 O O3B T5A . . . E 4 26.778 17.517 6.465 1 45.84 ? O3B T5A 301 A 1 HETATM 26 P PC T5A . . . E 4 27.259 18.929 6.366 1 47.01 ? PC T5A 301 A 1 HETATM 27 O O1C T5A . . . E 4 27.191 19.487 7.72 1 47.2 ? O1C T5A 301 A 1 HETATM 28 O O2C T5A . . . E 4 28.562 18.875 5.702 1 48.47 ? O2C T5A 301 A 1 HETATM 29 O O3C T5A . . . E 4 26.233 19.635 5.33 1 47.43 ? O3C T5A 301 A 1 HETATM 30 P PD T5A . . . E 4 26.306 20.859 4.208 1 47.42 ? PD T5A 301 A 1 HETATM 31 O O1D T5A . . . E 4 26.979 22.046 4.821 1 49.06 ? O1D T5A 301 A 1 HETATM 32 O O2D T5A . . . E 4 24.932 20.898 3.713 1 47.29 ? O2D T5A 301 A 1 HETATM 33 O O3D T5A . . . E 4 27.411 20.402 3.133 1 47.84 ? O3D T5A 301 A 1 HETATM 34 P PE T5A . . . E 4 27.465 19.665 1.668 1 49.3 ? PE T5A 301 A 1 HETATM 35 O O1E T5A . . . E 4 26.545 20.375 0.721 1 49.68 ? O1E T5A 301 A 1 HETATM 36 O O2E T5A . . . E 4 28.908 19.679 1.392 1 51.26 ? O2E T5A 301 A 1 HETATM 37 O O5F T5A . . . E 4 26.996 18.222 2.035 1 50.31 ? O5F T5A 301 A 1 HETATM 38 C C5F T5A . . . E 4 25.971 17.514 1.316 1 48.4 ? C5F T5A 301 A 1 HETATM 39 C C4F T5A . . . E 4 26.468 16.342 0.529 1 47.24 ? C4F T5A 301 A 1 HETATM 40 O O4F T5A . . . E 4 25.31 15.772 -0.065 1 48.52 ? O4F T5A 301 A 1 HETATM 41 C C1F T5A . . . E 4 25.395 15.66 -1.513 1 47.53 ? C1F T5A 301 A 1 HETATM 42 C C2F T5A . . . E 4 26.892 15.706 -1.801 1 47.59 ? C2F T5A 301 A 1 HETATM 43 O O2F T5A . . . E 4 27.334 14.355 -1.758 1 47.58 ? O2F T5A 301 A 1 HETATM 44 C C3F T5A . . . E 4 27.461 16.653 -0.689 1 46.67 ? C3F T5A 301 A 1 HETATM 45 O O3F T5A . . . E 4 28.76 16.242 -0.231 1 46.12 ? O3F T5A 301 A 1 HETATM 46 N N9A T5A . . . E 4 24.748 16.79 -2.242 1 47.67 ? N9A T5A 301 A 1 HETATM 47 C C4A T5A . . . E 4 24.128 16.691 -3.48 1 47.64 ? C4A T5A 301 A 1 HETATM 48 N N3A T5A . . . E 4 23.99 15.538 -4.254 1 46.11 ? N3A T5A 301 A 1 HETATM 49 C C2A T5A . . . E 4 23.338 15.767 -5.422 1 47.36 ? C2A T5A 301 A 1 HETATM 50 N N1A T5A . . . E 4 22.845 16.984 -5.847 1 47.6 ? N1A T5A 301 A 1 HETATM 51 C C6A T5A . . . E 4 22.99 18.111 -5.068 1 47.22 ? C6A T5A 301 A 1 HETATM 52 N N6A T5A . . . E 4 22.483 19.226 -5.567 1 47.93 ? N6A T5A 301 A 1 HETATM 53 C C5A T5A . . . E 4 23.67 17.973 -3.8 1 47.39 ? C5A T5A 301 A 1 HETATM 54 N N7A T5A . . . E 4 23.995 18.839 -2.786 1 47.62 ? N7A T5A 301 A 1 HETATM 55 C C8A T5A . . . E 4 24.618 18.123 -1.899 1 46.32 ? C8A T5A 301 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 392 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 55 #