data_2YY8 # _model_server_result.job_id qVD8jI6yvASCwdOsw7Ga2A _model_server_result.datetime_utc '2025-02-28 07:19:46' _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 2yy8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":400}' # _entry.id 2YY8 # _exptl.entry_id 2YY8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 297.334 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-DEOXY-5'-METHYLTHIOADENOSINE" _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 2YY8 _cell.length_a 56.151 _cell.length_b 56.151 _cell.length_c 121.844 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2YY8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 145 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,E,F _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 2 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C11 H15 N5 O3 S' _chem_comp.formula_weight 297.334 _chem_comp.id MTA _chem_comp.mon_nstd_flag . _chem_comp.name "5'-DEOXY-5'-METHYLTHIOADENOSINE" _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 CS S5' MTA sing 224 n n CS HCS1 MTA sing 225 n n CS HCS2 MTA sing 226 n n CS HCS3 MTA sing 227 n n S5' C5' MTA sing 228 n n C5' C4' MTA sing 229 n n C5' "H5'1" MTA sing 230 n n C5' "H5'2" MTA sing 231 n n C4' O4' MTA sing 232 n n C4' C3' MTA sing 233 n n C4' H4' MTA sing 234 n n O4' C1' MTA sing 235 n n C2' O2' MTA sing 236 n n C2' C3' MTA sing 237 n n C2' C1' MTA sing 238 n n C2' H2' MTA sing 239 n n O2' HO2' MTA sing 240 n n C3' O3' MTA sing 241 n n C3' H3' MTA sing 242 n n O3' H3T MTA sing 243 n n C1' N9 MTA sing 244 n n C1' H1' MTA sing 245 n n N9 C8 MTA sing 246 n y N9 C4 MTA sing 247 n y C8 N7 MTA doub 248 n y C8 H8 MTA sing 249 n n N7 C5 MTA sing 250 n y C5 C6 MTA sing 251 n y C5 C4 MTA doub 252 n y C6 N6 MTA sing 253 n n C6 N1 MTA doub 254 n y N6 H61 MTA sing 255 n n N6 H62 MTA sing 256 n n N1 C2 MTA sing 257 n y C2 N3 MTA doub 258 n y C2 H2 MTA sing 259 n n N3 C4 MTA sing 260 n y # _atom_sites.entry_id 2YY8 _atom_sites.fract_transf_matrix[1][1] 0.017809 _atom_sites.fract_transf_matrix[1][2] 0.010282 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.020564 _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] 0.008207 _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 MTA A 1 400 400 MTA MTA . D 3 SAM B 1 500 500 SAM SAM . E 4 HOH A 1 401 1 HOH TIP . E 4 HOH A 2 402 2 HOH TIP . E 4 HOH A 3 403 4 HOH TIP . E 4 HOH A 4 404 6 HOH TIP . E 4 HOH A 5 405 9 HOH TIP . E 4 HOH A 6 406 10 HOH TIP . E 4 HOH A 7 407 11 HOH TIP . E 4 HOH A 8 408 12 HOH TIP . E 4 HOH A 9 409 13 HOH TIP . E 4 HOH A 10 410 19 HOH TIP . E 4 HOH A 11 411 23 HOH TIP . E 4 HOH A 12 412 24 HOH TIP . E 4 HOH A 13 413 25 HOH TIP . E 4 HOH A 14 414 29 HOH TIP . E 4 HOH A 15 415 31 HOH TIP . E 4 HOH A 16 416 32 HOH TIP . E 4 HOH A 17 417 33 HOH TIP . E 4 HOH A 18 418 36 HOH TIP . E 4 HOH A 19 419 39 HOH TIP . E 4 HOH A 20 420 42 HOH TIP . E 4 HOH A 21 421 43 HOH TIP . E 4 HOH A 22 422 45 HOH TIP . E 4 HOH A 23 423 46 HOH TIP . E 4 HOH A 24 424 47 HOH TIP . E 4 HOH A 25 425 48 HOH TIP . E 4 HOH A 26 426 50 HOH TIP . E 4 HOH A 27 427 52 HOH TIP . E 4 HOH A 28 428 53 HOH TIP . E 4 HOH A 29 429 55 HOH TIP . E 4 HOH A 30 430 57 HOH TIP . E 4 HOH A 31 431 58 HOH TIP . E 4 HOH A 32 432 59 HOH TIP . E 4 HOH A 33 433 60 HOH TIP . E 4 HOH A 34 434 63 HOH TIP . E 4 HOH A 35 435 64 HOH TIP . E 4 HOH A 36 436 65 HOH TIP . E 4 HOH A 37 437 66 HOH TIP . E 4 HOH A 38 438 74 HOH TIP . E 4 HOH A 39 439 75 HOH TIP . E 4 HOH A 40 440 76 HOH TIP . E 4 HOH A 41 441 79 HOH TIP . E 4 HOH A 42 442 85 HOH TIP . E 4 HOH A 43 443 86 HOH TIP . E 4 HOH A 44 444 87 HOH TIP . E 4 HOH A 45 445 90 HOH TIP . E 4 HOH A 46 446 91 HOH TIP . E 4 HOH A 47 447 93 HOH TIP . E 4 HOH A 48 448 95 HOH TIP . E 4 HOH A 49 449 96 HOH TIP . E 4 HOH A 50 450 99 HOH TIP . E 4 HOH A 51 451 100 HOH TIP . F 4 HOH B 1 501 3 HOH TIP . F 4 HOH B 2 502 5 HOH TIP . F 4 HOH B 3 503 7 HOH TIP . F 4 HOH B 4 504 8 HOH TIP . F 4 HOH B 5 505 14 HOH TIP . F 4 HOH B 6 506 15 HOH TIP . F 4 HOH B 7 507 16 HOH TIP . F 4 HOH B 8 508 17 HOH TIP . F 4 HOH B 9 509 18 HOH TIP . F 4 HOH B 10 510 20 HOH TIP . F 4 HOH B 11 511 21 HOH TIP . F 4 HOH B 12 512 22 HOH TIP . F 4 HOH B 13 513 26 HOH TIP . F 4 HOH B 14 514 27 HOH TIP . F 4 HOH B 15 515 28 HOH TIP . F 4 HOH B 16 516 30 HOH TIP . F 4 HOH B 17 517 34 HOH TIP . F 4 HOH B 18 518 35 HOH TIP . F 4 HOH B 19 519 37 HOH TIP . F 4 HOH B 20 520 38 HOH TIP . F 4 HOH B 21 521 40 HOH TIP . F 4 HOH B 22 522 41 HOH TIP . F 4 HOH B 23 523 44 HOH TIP . F 4 HOH B 24 524 49 HOH TIP . F 4 HOH B 25 525 51 HOH TIP . F 4 HOH B 26 526 54 HOH TIP . F 4 HOH B 27 527 56 HOH TIP . F 4 HOH B 28 528 61 HOH TIP . F 4 HOH B 29 529 62 HOH TIP . F 4 HOH B 30 530 67 HOH TIP . F 4 HOH B 31 531 68 HOH TIP . F 4 HOH B 32 532 69 HOH TIP . F 4 HOH B 33 533 70 HOH TIP . F 4 HOH B 34 534 71 HOH TIP . F 4 HOH B 35 535 72 HOH TIP . F 4 HOH B 36 536 73 HOH TIP . F 4 HOH B 37 537 77 HOH TIP . F 4 HOH B 38 538 78 HOH TIP . F 4 HOH B 39 539 80 HOH TIP . F 4 HOH B 40 540 81 HOH TIP . F 4 HOH B 41 541 82 HOH TIP . F 4 HOH B 42 542 83 HOH TIP . F 4 HOH B 43 543 84 HOH TIP . F 4 HOH B 44 544 88 HOH TIP . F 4 HOH B 45 545 89 HOH TIP . F 4 HOH B 46 546 92 HOH TIP . F 4 HOH B 47 547 94 HOH TIP . F 4 HOH B 48 548 97 HOH TIP . F 4 HOH B 49 549 98 HOH TIP . F 4 HOH B 50 550 101 HOH TIP . # 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 C CS MTA . . . C 2 11.362 -2.923 -3.424 1 45.86 ? CS MTA 400 A 1 HETATM 2 S S5' MTA . . . C 2 11.824 -1.232 -3.738 1 48.74 ? S5' MTA 400 A 1 HETATM 3 C C5' MTA . . . C 2 11.769 -0.854 -1.941 1 41.68 ? C5' MTA 400 A 1 HETATM 4 C C4' MTA . . . C 2 13.011 -0.887 -1.092 1 38.22 ? C4' MTA 400 A 1 HETATM 5 O O4' MTA . . . C 2 12.379 0.252 -0.501 1 35.42 ? O4' MTA 400 A 1 HETATM 6 C C2' MTA . . . C 2 12.483 -1.459 1.142 1 35.52 ? C2' MTA 400 A 1 HETATM 7 O O2' MTA . . . C 2 13.702 -1.293 1.876 1 35.75 ? O2' MTA 400 A 1 HETATM 8 C C3' MTA . . . C 2 12.822 -2.12 -0.199 1 35.78 ? C3' MTA 400 A 1 HETATM 9 O O3' MTA . . . C 2 14.049 -2.836 0.023 1 34.8 ? O3' MTA 400 A 1 HETATM 10 C C1' MTA . . . C 2 11.895 -0.085 0.801 1 32.54 ? C1' MTA 400 A 1 HETATM 11 N N9 MTA . . . C 2 10.416 -0.011 0.872 1 27.57 ? N9 MTA 400 A 1 HETATM 12 C C8 MTA . . . C 2 9.514 0.096 -0.097 1 26.21 ? C8 MTA 400 A 1 HETATM 13 N N7 MTA . . . C 2 8.303 0.202 0.451 1 28.34 ? N7 MTA 400 A 1 HETATM 14 C C5 MTA . . . C 2 8.436 0.153 1.779 1 27.02 ? C5 MTA 400 A 1 HETATM 15 C C6 MTA . . . C 2 7.586 0.148 2.886 1 25.19 ? C6 MTA 400 A 1 HETATM 16 N N6 MTA . . . C 2 6.267 0.154 2.72 1 25.62 ? N6 MTA 400 A 1 HETATM 17 N N1 MTA . . . C 2 8.095 0.028 4.124 1 25.81 ? N1 MTA 400 A 1 HETATM 18 C C2 MTA . . . C 2 9.398 -0.087 4.342 1 26.46 ? C2 MTA 400 A 1 HETATM 19 N N3 MTA . . . C 2 10.23 -0.097 3.311 1 25.3 ? N3 MTA 400 A 1 HETATM 20 C C4 MTA . . . C 2 9.79 0.016 2.046 1 26.23 ? C4 MTA 400 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 20 #