data_3H65 # _model_server_result.job_id jM3xApluWFMxG1WSYCoKOQ _model_server_result.datetime_utc '2024-11-07 20:41:54' _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 3h65 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":359}' # _entry.id 3H65 # _exptl.entry_id 3H65 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 526.394 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-O-[(S)-hydroxy{[2-hydroxy-3,5-dimethyl-6-(2-oxoethyl)pyridin-4-yl]oxy}phosphoryl]guanosine" _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 90 _cell.entry_id 3H65 _cell.length_a 97.63 _cell.length_b 97.63 _cell.length_c 165.75 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3H65 _symmetry.cell_setting ? _symmetry.Int_Tables_number 98 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 41 2 2' # _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,G,H _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' 15_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _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 B N1 I2C . A I2C 359 1_555 C FE FE2 . A FE2 360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? metalc ? metalc2 B C8 I2C . A I2C 359 1_555 C FE FE2 . A FE2 360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.909 ? metalc ? metalc3 C FE FE2 . A FE2 360 1_555 D C CMO . A CMO 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.812 ? metalc ? metalc4 C FE FE2 . A FE2 360 1_555 E C CMO . A CMO 362 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.843 ? metalc ? metalc5 C FE FE2 . A FE2 360 1_555 F O2 DTV . A DTV 363 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? metalc ? metalc6 C FE FE2 . A FE2 360 1_555 F S1 DTV . A DTV 363 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.31 ? # _chem_comp.formula 'C19 H23 N6 O10 P' _chem_comp.formula_weight 526.394 _chem_comp.id I2C _chem_comp.mon_nstd_flag . _chem_comp.name "5'-O-[(S)-hydroxy{[2-hydroxy-3,5-dimethyl-6-(2-oxoethyl)pyridin-4-yl]oxy}phosphoryl]guanosine" _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 O8 C8 I2C doub 273 n n C8 C7 I2C sing 274 n n N1 C2 I2C doub 275 n y N1 C6 I2C sing 276 n y C2 O2 I2C sing 277 n n C2 C3 I2C sing 278 n y C3 C3M I2C sing 279 n n C3 C4 I2C doub 280 n y C7 C6 I2C sing 281 n n C6 C5 I2C doub 282 n y C5 C5M I2C sing 283 n n C5 C4 I2C sing 284 n y C4 O3P I2C sing 285 n n O3P P1 I2C sing 286 n n P1 O2P I2C sing 287 n n P1 O1P I2C doub 288 n n P1 O5' I2C sing 289 n n O5' C5' I2C sing 290 n n C5' C4' I2C sing 291 n n C4' O4' I2C sing 292 n n C4' C3' I2C sing 293 n n O4' C1' I2C sing 294 n n C3' O3' I2C sing 295 n n C3' C2' I2C sing 296 n n C2' O2' I2C sing 297 n n C2' C1' I2C sing 298 n n C1' N9A I2C sing 299 n n N9A C4A I2C sing 300 n y N9A C8A I2C sing 301 n y C4A N3A I2C sing 302 n n C4A C5A I2C doub 303 n y N3A C2A I2C doub 304 n n C2A N2A I2C sing 305 n n C2A N1A I2C sing 306 n n N1A C6A I2C sing 307 n n C8A N7A I2C doub 308 n y N7A C5A I2C sing 309 n y C5A C6A I2C sing 310 n n C6A O6A I2C doub 311 n n C8 H8 I2C sing 312 n n O2 HO2 I2C sing 313 n n C3M H3M I2C sing 314 n n C3M H3MA I2C sing 315 n n C3M H3MB I2C sing 316 n n C7 H7 I2C sing 317 n n C7 H7A I2C sing 318 n n C5M H5M I2C sing 319 n n C5M H5MA I2C sing 320 n n C5M H5MB I2C sing 321 n n O2P HO2P I2C sing 322 n n C5' H5' I2C sing 323 n n C5' "H5'A" I2C sing 324 n n C4' H4' I2C sing 325 n n C3' H3' I2C sing 326 n n O3' HO3' I2C sing 327 n n C2' H2' I2C sing 328 n n O2' HO2' I2C sing 329 n n C1' H1' I2C sing 330 n n N2A HN2A I2C sing 331 n n N2A HN2B I2C sing 332 n n N1A HN1A I2C sing 333 n n C8A H8A I2C sing 334 n n # _atom_sites.entry_id 3H65 _atom_sites.fract_transf_matrix[1][1] 0.010243 _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] 0.010243 _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] 0.006033 _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 I2C A 1 359 359 I2C I2C . C 3 FE2 A 1 360 360 FE2 FE2 . D 4 CMO A 1 361 361 CMO CMO . E 4 CMO A 1 362 362 CMO CMO . F 5 DTV A 1 363 363 DTV DTV . G 6 H4M A 1 364 364 H4M H4M . H 7 HOH A 1 365 365 HOH HOH . H 7 HOH A 2 366 366 HOH HOH . H 7 HOH A 3 367 367 HOH HOH . H 7 HOH A 4 368 368 HOH HOH . H 7 HOH A 5 369 369 HOH HOH . H 7 HOH A 6 370 370 HOH HOH . H 7 HOH A 7 371 371 HOH HOH . H 7 HOH A 8 372 372 HOH HOH . H 7 HOH A 9 373 373 HOH HOH . H 7 HOH A 10 374 374 HOH HOH . H 7 HOH A 11 375 375 HOH HOH . H 7 HOH A 12 376 376 HOH HOH . H 7 HOH A 13 377 377 HOH HOH . H 7 HOH A 14 378 378 HOH HOH . H 7 HOH A 15 379 379 HOH HOH . H 7 HOH A 16 380 380 HOH HOH . H 7 HOH A 17 381 381 HOH HOH . H 7 HOH A 18 382 382 HOH HOH . H 7 HOH A 19 383 383 HOH HOH . H 7 HOH A 20 384 384 HOH HOH . H 7 HOH A 21 385 385 HOH HOH . H 7 HOH A 22 386 386 HOH HOH . H 7 HOH A 23 387 387 HOH HOH . H 7 HOH A 24 388 388 HOH HOH . H 7 HOH A 25 389 389 HOH HOH . H 7 HOH A 26 390 390 HOH HOH . H 7 HOH A 27 391 391 HOH HOH . H 7 HOH A 28 392 392 HOH HOH . H 7 HOH A 29 393 393 HOH HOH . H 7 HOH A 30 394 394 HOH HOH . H 7 HOH A 31 395 395 HOH HOH . H 7 HOH A 32 396 396 HOH HOH . H 7 HOH A 33 397 397 HOH HOH . H 7 HOH A 34 398 398 HOH HOH . H 7 HOH A 35 399 399 HOH HOH . H 7 HOH A 36 400 400 HOH HOH . H 7 HOH A 37 401 401 HOH HOH . H 7 HOH A 38 402 402 HOH HOH . H 7 HOH A 39 403 403 HOH HOH . H 7 HOH A 40 404 404 HOH HOH . H 7 HOH A 41 405 405 HOH HOH . H 7 HOH A 42 406 406 HOH HOH . H 7 HOH A 43 407 407 HOH HOH . H 7 HOH A 44 408 408 HOH HOH . H 7 HOH A 45 409 409 HOH HOH . H 7 HOH A 46 410 410 HOH HOH . H 7 HOH A 47 411 411 HOH HOH . H 7 HOH A 48 412 412 HOH HOH . H 7 HOH A 49 413 413 HOH HOH . H 7 HOH A 50 414 414 HOH HOH . H 7 HOH A 51 415 415 HOH HOH . H 7 HOH A 52 416 416 HOH HOH . H 7 HOH A 53 417 417 HOH HOH . H 7 HOH A 54 418 418 HOH HOH . H 7 HOH A 55 419 419 HOH HOH . H 7 HOH A 56 420 420 HOH HOH . H 7 HOH A 57 421 421 HOH HOH . H 7 HOH A 58 422 422 HOH HOH . H 7 HOH A 59 423 423 HOH HOH . H 7 HOH A 60 424 424 HOH HOH . H 7 HOH A 61 425 425 HOH HOH . H 7 HOH A 62 426 426 HOH HOH . H 7 HOH A 63 427 427 HOH HOH . H 7 HOH A 64 428 428 HOH HOH . H 7 HOH A 65 429 429 HOH HOH . H 7 HOH A 66 430 430 HOH HOH . H 7 HOH A 67 431 431 HOH HOH . H 7 HOH A 68 432 432 HOH HOH . H 7 HOH A 69 433 433 HOH HOH . H 7 HOH A 70 434 434 HOH HOH . H 7 HOH A 71 435 435 HOH HOH . H 7 HOH A 72 436 436 HOH HOH . H 7 HOH A 73 437 437 HOH HOH . H 7 HOH A 74 438 438 HOH HOH . H 7 HOH A 75 439 439 HOH HOH . H 7 HOH A 76 440 440 HOH HOH . H 7 HOH A 77 441 441 HOH HOH . H 7 HOH A 78 442 442 HOH HOH . H 7 HOH A 79 443 443 HOH HOH . H 7 HOH A 80 444 444 HOH HOH . H 7 HOH A 81 445 445 HOH HOH . H 7 HOH A 82 446 446 HOH HOH . H 7 HOH A 83 447 447 HOH HOH . H 7 HOH A 84 448 448 HOH HOH . H 7 HOH A 85 449 449 HOH HOH . H 7 HOH A 86 450 450 HOH HOH . H 7 HOH A 87 451 451 HOH HOH . H 7 HOH A 88 452 452 HOH HOH . H 7 HOH A 89 453 453 HOH HOH . H 7 HOH A 90 454 454 HOH HOH . H 7 HOH A 91 455 455 HOH HOH . H 7 HOH A 92 456 456 HOH HOH . H 7 HOH A 93 457 457 HOH HOH . H 7 HOH A 94 458 458 HOH HOH . H 7 HOH A 95 459 459 HOH HOH . H 7 HOH A 96 460 460 HOH HOH . H 7 HOH A 97 461 461 HOH HOH . H 7 HOH A 98 462 462 HOH HOH . H 7 HOH A 99 463 463 HOH HOH . H 7 HOH A 100 464 464 HOH HOH . H 7 HOH A 101 465 465 HOH HOH . H 7 HOH A 102 466 466 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 O O8 I2C . . . B 2 21.756 6.894 23.178 1 38.32 ? O8 I2C 359 A 1 HETATM 2 C C8 I2C . . . B 2 21.154 7.322 24.164 1 38.29 ? C8 I2C 359 A 1 HETATM 3 N N1 I2C . . . B 2 19.678 7.769 26.192 1 37.66 ? N1 I2C 359 A 1 HETATM 4 C C2 I2C . . . B 2 18.744 7.869 27.148 1 34.7 ? C2 I2C 359 A 1 HETATM 5 O O2 I2C . . . B 2 17.489 7.436 26.943 1 36.28 ? O2 I2C 359 A 1 HETATM 6 C C3 I2C . . . B 2 19.028 8.401 28.397 1 36.24 ? C3 I2C 359 A 1 HETATM 7 C C3M I2C . . . B 2 17.925 8.51 29.401 1 35.19 ? C3M I2C 359 A 1 HETATM 8 C C7 I2C . . . B 2 21.922 8.017 25.323 1 36.84 ? C7 I2C 359 A 1 HETATM 9 C C6 I2C . . . B 2 20.942 8.172 26.457 1 34.49 ? C6 I2C 359 A 1 HETATM 10 C C5 I2C . . . B 2 21.307 8.68 27.721 1 35.42 ? C5 I2C 359 A 1 HETATM 11 C C5M I2C . . . B 2 22.725 9.134 28.027 1 34.14 ? C5M I2C 359 A 1 HETATM 12 C C4 I2C . . . B 2 20.319 8.787 28.704 1 37.01 ? C4 I2C 359 A 1 HETATM 13 O O3P I2C . . . B 2 20.585 9.376 29.941 1 39.88 ? O3P I2C 359 A 1 HETATM 14 P P1 I2C . . . B 2 20.499 8.764 31.393 1 38.53 ? P1 I2C 359 A 1 HETATM 15 O O2P I2C . . . B 2 19.752 7.491 31.358 1 36.32 ? O2P I2C 359 A 1 HETATM 16 O O1P I2C . . . B 2 19.983 9.87 32.303 1 45.25 ? O1P I2C 359 A 1 HETATM 17 O O5' I2C . . . B 2 22.048 8.489 31.568 1 37.02 ? O5' I2C 359 A 1 HETATM 18 C C5' I2C . . . B 2 23.052 9.498 31.801 1 34.87 ? C5' I2C 359 A 1 HETATM 19 C C4' I2C . . . B 2 23.907 8.976 32.967 1 35.34 ? C4' I2C 359 A 1 HETATM 20 O O4' I2C . . . B 2 25.076 9.768 33.193 1 40.86 ? O4' I2C 359 A 1 HETATM 21 C C3' I2C . . . B 2 23.147 8.99 34.274 1 37.93 ? C3' I2C 359 A 1 HETATM 22 O O3' I2C . . . B 2 23.07 7.664 34.792 1 39.03 ? O3' I2C 359 A 1 HETATM 23 C C2' I2C . . . B 2 23.919 9.92 35.211 1 39.8 ? C2' I2C 359 A 1 HETATM 24 O O2' I2C . . . B 2 23.897 9.448 36.567 1 41.46 ? O2' I2C 359 A 1 HETATM 25 C C1' I2C . . . B 2 25.29 9.813 34.603 1 41.51 ? C1' I2C 359 A 1 HETATM 26 N N9A I2C . . . B 2 26.237 10.881 35.009 1 42.31 ? N9A I2C 359 A 1 HETATM 27 C C4A I2C . . . B 2 27.544 10.626 35.065 1 42.03 ? C4A I2C 359 A 1 HETATM 28 N N3A I2C . . . B 2 28.253 9.491 34.825 1 39.16 ? N3A I2C 359 A 1 HETATM 29 C C2A I2C . . . B 2 29.59 9.507 34.98 1 40.41 ? C2A I2C 359 A 1 HETATM 30 N N2A I2C . . . B 2 30.317 8.397 34.737 1 41.23 ? N2A I2C 359 A 1 HETATM 31 N N1A I2C . . . B 2 30.228 10.64 35.379 1 41.27 ? N1A I2C 359 A 1 HETATM 32 C C8A I2C . . . B 2 25.998 12.157 35.393 1 40.32 ? C8A I2C 359 A 1 HETATM 33 N N7A I2C . . . B 2 27.179 12.704 35.695 1 41.42 ? N7A I2C 359 A 1 HETATM 34 C C5A I2C . . . B 2 28.166 11.794 35.523 1 42.09 ? C5A I2C 359 A 1 HETATM 35 C C6A I2C . . . B 2 29.562 11.774 35.683 1 42.79 ? C6A I2C 359 A 1 HETATM 36 O O6A I2C . . . B 2 30.224 12.773 36.046 1 42.99 ? O6A I2C 359 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 334 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 36 #