data_1B8N # _model_server_result.job_id bnE0iIOpLiBNb-6I38OZlA _model_server_result.datetime_utc '2025-02-26 18:00:09' _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 1b8n # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":600}' # _entry.id 1B8N # _exptl.entry_id 1B8N _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 281.268 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1,4-DIDEOXY-1,4-IMINO-1-(S)-(9-DEAZAGUANIN-9-YL)-D-RIBITOL _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 1B8N _cell.length_a 90.32 _cell.length_b 90.32 _cell.length_c 90.32 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1B8N _symmetry.cell_setting cubic _symmetry.Int_Tables_number 198 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 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 ? monomeric 1 author_defined_assembly 1 PISA,PQS trimeric 3 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,B,C,D,E 1 1 A,B,C,D,E 2 1,2,3 # 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' 6_357 z-3/2,-x+1/2,-y+2 0 0 1 -1 0 0 0 -1 0 -135.48 45.16 180.64 3 'crystal symmetry operation' 12_576 -y+1/2,-z+2,x+3/2 0 -1 0 0 0 -1 1 0 0 45.16 180.64 135.48 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _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 E O HOH . A HOH 305 1_555 B MG MG . A MG 598 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.233 ? metalc ? metalc2 E O HOH . A HOH 321 1_555 B MG MG . A MG 598 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? metalc ? metalc3 E O HOH . A HOH 327 1_555 B MG MG . A MG 598 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? metalc ? metalc4 E O HOH . A HOH 331 1_555 B MG MG . A MG 598 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? metalc ? metalc5 E O HOH . A HOH 341 1_555 B MG MG . A MG 598 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.273 ? metalc ? metalc6 E O HOH . A HOH 357 1_555 B MG MG . A MG 598 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? # _chem_comp.formula 'C11 H15 N5 O4' _chem_comp.formula_weight 281.268 _chem_comp.id IMG _chem_comp.mon_nstd_flag . _chem_comp.name 1,4-DIDEOXY-1,4-IMINO-1-(S)-(9-DEAZAGUANIN-9-YL)-D-RIBITOL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms IMMUCILLIN-G # 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 O5' C5' IMG sing 173 n n O5' "HO'5" IMG sing 174 n n C5' C4' IMG sing 175 n n C5' "H5'1" IMG sing 176 n n C5' "H5'2" IMG sing 177 n n C4' N4' IMG sing 178 n n C4' C3' IMG sing 179 n n C4' H4' IMG sing 180 n n N4' C1' IMG sing 181 n n N4' "HN'4" IMG sing 182 n n C3' O3' IMG sing 183 n n C3' C2' IMG sing 184 n n C3' H3' IMG sing 185 n n O3' "HO'3" IMG sing 186 n n C2' O2' IMG sing 187 n n C2' C1' IMG sing 188 n n C2' H2' IMG sing 189 n n O2' "HO'2" IMG sing 190 n n C1' C9 IMG sing 191 n n C1' H1' IMG sing 192 n n C9 C8 IMG doub 193 n y C9 C4 IMG sing 194 n y C8 N7 IMG sing 195 n y C8 H8 IMG sing 196 n n N7 C5 IMG sing 197 n y N7 H7 IMG sing 198 n n C5 C6 IMG sing 199 n n C5 C4 IMG doub 200 n y C6 O6 IMG doub 201 n n C6 N1 IMG sing 202 n n N1 C2 IMG sing 203 n n N1 H1 IMG sing 204 n n N2 C2 IMG sing 205 n n N2 H21 IMG sing 206 n n N2 H22 IMG sing 207 n n C2 N3 IMG doub 208 n n N3 C4 IMG sing 209 n n # _atom_sites.entry_id 1B8N _atom_sites.fract_transf_matrix[1][1] 0.011072 _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] 0.011072 _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] 0.011072 _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 MG A 1 598 598 MG MG . C 3 PO4 A 1 599 599 PO4 PO4 . D 4 IMG A 1 600 600 IMG IMG . E 5 HOH A 1 301 301 HOH HOH . E 5 HOH A 2 302 302 HOH HOH . E 5 HOH A 3 303 303 HOH HOH . E 5 HOH A 4 304 304 HOH HOH . E 5 HOH A 5 305 305 HOH HOH . E 5 HOH A 6 306 306 HOH HOH . E 5 HOH A 7 307 307 HOH HOH . E 5 HOH A 8 308 308 HOH HOH . E 5 HOH A 9 309 309 HOH HOH . E 5 HOH A 10 310 310 HOH HOH . E 5 HOH A 11 311 311 HOH HOH . E 5 HOH A 12 312 312 HOH HOH . E 5 HOH A 13 313 313 HOH HOH . E 5 HOH A 14 314 314 HOH HOH . E 5 HOH A 15 315 315 HOH HOH . E 5 HOH A 16 316 316 HOH HOH . E 5 HOH A 17 317 317 HOH HOH . E 5 HOH A 18 318 318 HOH HOH . E 5 HOH A 19 319 319 HOH HOH . E 5 HOH A 20 320 320 HOH HOH . E 5 HOH A 21 321 321 HOH HOH . E 5 HOH A 22 322 322 HOH HOH . E 5 HOH A 23 323 323 HOH HOH . E 5 HOH A 24 324 324 HOH HOH . E 5 HOH A 25 325 325 HOH HOH . E 5 HOH A 26 326 326 HOH HOH . E 5 HOH A 27 327 327 HOH HOH . E 5 HOH A 28 328 328 HOH HOH . E 5 HOH A 29 329 329 HOH HOH . E 5 HOH A 30 330 330 HOH HOH . E 5 HOH A 31 331 331 HOH HOH . E 5 HOH A 32 332 332 HOH HOH . E 5 HOH A 33 333 333 HOH HOH . E 5 HOH A 34 334 334 HOH HOH . E 5 HOH A 35 335 335 HOH HOH . E 5 HOH A 36 336 336 HOH HOH . E 5 HOH A 37 337 337 HOH HOH . E 5 HOH A 38 338 338 HOH HOH . E 5 HOH A 39 339 339 HOH HOH . E 5 HOH A 40 340 340 HOH HOH . E 5 HOH A 41 341 341 HOH HOH . E 5 HOH A 42 342 342 HOH HOH . E 5 HOH A 43 343 343 HOH HOH . E 5 HOH A 44 344 344 HOH HOH . E 5 HOH A 45 345 345 HOH HOH . E 5 HOH A 46 346 346 HOH HOH . E 5 HOH A 47 347 347 HOH HOH . E 5 HOH A 48 348 348 HOH HOH . E 5 HOH A 49 349 349 HOH HOH . E 5 HOH A 50 350 350 HOH HOH . E 5 HOH A 51 351 351 HOH HOH . E 5 HOH A 52 352 352 HOH HOH . E 5 HOH A 53 353 353 HOH HOH . E 5 HOH A 54 354 354 HOH HOH . E 5 HOH A 55 355 355 HOH HOH . E 5 HOH A 56 356 356 HOH HOH . E 5 HOH A 57 357 357 HOH HOH . E 5 HOH A 58 358 358 HOH HOH . E 5 HOH A 59 359 359 HOH HOH . E 5 HOH A 60 360 360 HOH HOH . E 5 HOH A 61 361 361 HOH HOH . E 5 HOH A 62 362 362 HOH HOH . E 5 HOH A 63 363 363 HOH HOH . E 5 HOH A 64 364 364 HOH HOH . E 5 HOH A 65 365 365 HOH HOH . E 5 HOH A 66 366 366 HOH HOH . E 5 HOH A 67 367 367 HOH HOH . E 5 HOH A 68 368 368 HOH HOH . E 5 HOH A 69 369 369 HOH HOH . E 5 HOH A 70 370 370 HOH HOH . E 5 HOH A 71 371 371 HOH HOH . E 5 HOH A 72 372 372 HOH HOH . E 5 HOH A 73 373 373 HOH HOH . E 5 HOH A 74 374 374 HOH HOH . E 5 HOH A 75 375 375 HOH HOH . E 5 HOH A 76 376 376 HOH HOH . E 5 HOH A 77 377 377 HOH HOH . E 5 HOH A 78 378 378 HOH HOH . E 5 HOH A 79 379 379 HOH HOH . E 5 HOH A 80 380 380 HOH HOH . E 5 HOH A 81 381 381 HOH HOH . E 5 HOH A 82 382 382 HOH HOH . E 5 HOH A 83 383 383 HOH HOH . E 5 HOH A 84 384 384 HOH HOH . E 5 HOH A 85 385 385 HOH HOH . E 5 HOH A 86 387 387 HOH HOH . E 5 HOH A 87 388 388 HOH HOH . E 5 HOH A 88 389 389 HOH HOH . E 5 HOH A 89 390 390 HOH HOH . E 5 HOH A 90 391 391 HOH HOH . E 5 HOH A 91 392 392 HOH HOH . E 5 HOH A 92 393 393 HOH HOH . E 5 HOH A 93 394 394 HOH HOH . E 5 HOH A 94 395 395 HOH HOH . E 5 HOH A 95 396 396 HOH HOH . E 5 HOH A 96 398 398 HOH HOH . E 5 HOH A 97 399 399 HOH HOH . E 5 HOH A 98 400 400 HOH HOH . E 5 HOH A 99 401 401 HOH HOH . E 5 HOH A 100 402 402 HOH HOH . E 5 HOH A 101 403 403 HOH HOH . E 5 HOH A 102 404 404 HOH HOH . E 5 HOH A 103 405 405 HOH HOH . E 5 HOH A 104 406 406 HOH HOH . E 5 HOH A 105 407 407 HOH HOH . E 5 HOH A 106 408 408 HOH HOH . E 5 HOH A 107 410 410 HOH HOH . E 5 HOH A 108 411 411 HOH HOH . E 5 HOH A 109 413 413 HOH HOH . E 5 HOH A 110 414 414 HOH HOH . E 5 HOH A 111 415 415 HOH HOH . E 5 HOH A 112 416 416 HOH HOH . E 5 HOH A 113 417 417 HOH HOH . E 5 HOH A 114 418 418 HOH HOH . E 5 HOH A 115 419 419 HOH HOH . E 5 HOH A 116 420 420 HOH HOH . E 5 HOH A 117 421 421 HOH HOH . E 5 HOH A 118 422 422 HOH HOH . E 5 HOH A 119 424 424 HOH HOH . E 5 HOH A 120 425 425 HOH HOH . E 5 HOH A 121 426 426 HOH HOH . E 5 HOH A 122 427 427 HOH HOH . E 5 HOH A 123 428 428 HOH HOH . E 5 HOH A 124 429 429 HOH HOH . E 5 HOH A 125 430 430 HOH HOH . E 5 HOH A 126 431 431 HOH HOH . E 5 HOH A 127 433 433 HOH HOH . E 5 HOH A 128 434 434 HOH HOH . E 5 HOH A 129 435 435 HOH HOH . E 5 HOH A 130 436 436 HOH HOH . E 5 HOH A 131 437 437 HOH HOH . E 5 HOH A 132 438 438 HOH HOH . E 5 HOH A 133 439 439 HOH HOH . E 5 HOH A 134 440 440 HOH HOH . E 5 HOH A 135 441 441 HOH HOH . E 5 HOH A 136 442 442 HOH HOH . E 5 HOH A 137 443 443 HOH HOH . E 5 HOH A 138 444 444 HOH HOH . E 5 HOH A 139 445 445 HOH HOH . E 5 HOH A 140 446 446 HOH HOH . E 5 HOH A 141 447 447 HOH HOH . E 5 HOH A 142 448 448 HOH HOH . E 5 HOH A 143 449 449 HOH HOH . E 5 HOH A 144 450 450 HOH HOH . E 5 HOH A 145 451 451 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 O5' IMG . . . D 4 -66.69 90.381 97.605 1 17.25 ? O5' IMG 600 A 1 HETATM 2 C C5' IMG . . . D 4 -65.386 90.255 97.023 1 12.45 ? C5' IMG 600 A 1 HETATM 3 C C4' IMG . . . D 4 -65.023 88.898 96.361 1 19.39 ? C4' IMG 600 A 1 HETATM 4 N N4' IMG . . . D 4 -66.087 88.744 95.366 1 16.74 ? N4' IMG 600 A 1 HETATM 5 C C3' IMG . . . D 4 -63.713 88.806 95.51 1 19.16 ? C3' IMG 600 A 1 HETATM 6 O O3' IMG . . . D 4 -63.189 87.458 95.344 1 20.06 ? O3' IMG 600 A 1 HETATM 7 C C2' IMG . . . D 4 -64.121 89.351 94.098 1 16.45 ? C2' IMG 600 A 1 HETATM 8 O O2' IMG . . . D 4 -63.597 88.538 93.04 1 14.48 ? O2' IMG 600 A 1 HETATM 9 C C1' IMG . . . D 4 -65.664 89.291 94.08 1 15.81 ? C1' IMG 600 A 1 HETATM 10 C C9 IMG . . . D 4 -66.369 90.742 93.876 1 19.4 ? C9 IMG 600 A 1 HETATM 11 C C8 IMG . . . D 4 -67.647 91.032 94.155 1 17.02 ? C8 IMG 600 A 1 HETATM 12 N N7 IMG . . . D 4 -67.901 92.414 93.843 1 21.11 ? N7 IMG 600 A 1 HETATM 13 C C5 IMG . . . D 4 -66.663 92.903 93.371 1 19.45 ? C5 IMG 600 A 1 HETATM 14 C C6 IMG . . . D 4 -66.387 94.271 92.902 1 18.38 ? C6 IMG 600 A 1 HETATM 15 O O6 IMG . . . D 4 -67.128 95.267 92.889 1 19.52 ? O6 IMG 600 A 1 HETATM 16 N N1 IMG . . . D 4 -65.07 94.336 92.508 1 15.71 ? N1 IMG 600 A 1 HETATM 17 N N2 IMG . . . D 4 -62.904 93.518 91.937 1 19.95 ? N2 IMG 600 A 1 HETATM 18 C C2 IMG . . . D 4 -64.139 93.3 92.52 1 17.89 ? C2 IMG 600 A 1 HETATM 19 N N3 IMG . . . D 4 -64.469 92.093 92.949 1 18.3 ? N3 IMG 600 A 1 HETATM 20 C C4 IMG . . . D 4 -65.733 91.94 93.361 1 19.78 ? C4 IMG 600 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 236 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 20 #