data_3N42 # _model_server_result.job_id S5N2E0aLyaYW2fM7SUjzJA _model_server_result.datetime_utc '2025-07-07 22:34:57' _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 3n42 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1001}' # _entry.id 3N42 # _exptl.entry_id 3N42 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 5 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _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 3N42 _cell.length_a 58.391 _cell.length_b 90.678 _cell.length_c 178.41 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3N42 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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 5 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 4 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 4 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NDG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 4 n D NAG 1 C 1 NAG F 1001 NAG 4 n D NDG 2 C 2 NDG F 1002 NDG # 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 disulf ? disulf1 A SG CYS 9 A CYS 8 1_555 A SG CYS 18 A CYS 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf2 A SG CYS 23 A CYS 22 1_555 A SG CYS 27 A CYS 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf3 A SG CYS 26 A CYS 25 1_555 A SG CYS 58 A CYS 57 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf4 B SG CYS 19 B CYS 19 1_555 B SG CYS 125 B CYS 125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf5 B SG CYS 22 B CYS 22 1_555 B SG CYS 28 B CYS 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf6 B SG CYS 91 B CYS 91 1_555 B SG CYS 105 B CYS 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf7 B SG CYS 153 B CYS 153 1_555 B SG CYS 266 B CYS 266 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf8 B SG CYS 201 B CYS 201 1_555 B SG CYS 225 B CYS 225 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf9 B SG CYS 203 B CYS 203 1_555 B SG CYS 220 B CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf10 C SG CYS 71 F CYS 49 1_555 C SG CYS 136 F CYS 114 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf11 C SG CYS 84 F CYS 62 1_555 C SG CYS 116 F CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf12 C SG CYS 85 F CYS 63 1_555 C SG CYS 118 F CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf13 C SG CYS 90 F CYS 68 1_555 C SG CYS 100 F CYS 78 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf14 C SG CYS 281 F CYS 259 1_555 C SG CYS 293 F CYS 271 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf15 C SG CYS 323 F CYS 301 1_555 C SG CYS 398 F CYS 376 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf16 C SG CYS 328 F CYS 306 1_555 C SG CYS 402 F CYS 380 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf17 C SG CYS 350 F CYS 328 1_555 C SG CYS 392 F CYS 370 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? covale ? covale1 B ND2 ASN 263 B ASN 263 1_555 E C1 NAG . B NAG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.465 ? covale ? covale2 C ND2 ASN 163 F ASN 141 1_555 D C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale3 D O4 NAG . C NAG 1 1_555 D C1 NDG . C NDG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? # _chem_comp.formula 'C8 H15 N O6' _chem_comp.formula_weight 221.208 _chem_comp.id NAG _chem_comp.mon_nstd_flag . _chem_comp.name 2-acetamido-2-deoxy-beta-D-glucopyranose _chem_comp.type 'd-saccharide, beta linking' _chem_comp.pdbx_synonyms N-acetyl-beta-D-glucosamine;2-acetamido-2-deoxy-beta-D-glucose;2-acetamido-2-deoxy-D-glucose;2-acetamido-2-deoxy-glucose;N-ACETYL-D-GLUCOSAMINE # 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 C1 C2 NAG sing 237 n n C1 O1 NAG sing 238 n n C1 O5 NAG sing 239 n n C1 H1 NAG sing 240 n n C2 C3 NAG sing 241 n n C2 N2 NAG sing 242 n n C2 H2 NAG sing 243 n n C3 C4 NAG sing 244 n n C3 O3 NAG sing 245 n n C3 H3 NAG sing 246 n n C4 C5 NAG sing 247 n n C4 O4 NAG sing 248 n n C4 H4 NAG sing 249 n n C5 C6 NAG sing 250 n n C5 O5 NAG sing 251 n n C5 H5 NAG sing 252 n n C6 O6 NAG sing 253 n n C6 H61 NAG sing 254 n n C6 H62 NAG sing 255 n n C7 C8 NAG sing 256 n n C7 N2 NAG sing 257 n n C7 O7 NAG doub 258 n n C8 H81 NAG sing 259 n n C8 H82 NAG sing 260 n n C8 H83 NAG sing 261 n n N2 HN2 NAG sing 262 n n O1 HO1 NAG sing 263 n n O3 HO3 NAG sing 264 n n O4 HO4 NAG sing 265 n n O6 HO6 NAG sing 266 n n # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.identifier _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version NAG DGlcpNAcb 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 NAG N-acetyl-b-D-glucopyranosamine 'COMMON NAME' GMML 1 NAG b-D-GlcpNAc 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 NAG GlcNAc 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 3N42 _atom_sites.fract_transf_matrix[1][1] 0.017126 _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] 0.011028 _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] 0.005605 _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 E 5 NAG B 1 1001 1001 NAG NAG . F 6 HOH B 1 361 343 HOH HOH . F 6 HOH B 2 362 344 HOH HOH . F 6 HOH B 3 363 345 HOH HOH . F 6 HOH B 4 364 346 HOH HOH . F 6 HOH B 5 365 347 HOH HOH . F 6 HOH B 6 366 348 HOH HOH . F 6 HOH B 7 367 349 HOH HOH . F 6 HOH B 8 368 350 HOH HOH . F 6 HOH B 9 369 351 HOH HOH . F 6 HOH B 10 370 352 HOH HOH . F 6 HOH B 11 390 390 HOH HOH . F 6 HOH B 12 425 425 HOH HOH . F 6 HOH B 13 507 507 HOH HOH . F 6 HOH B 14 530 530 HOH HOH . F 6 HOH B 15 532 532 HOH HOH . F 6 HOH B 16 534 534 HOH HOH . F 6 HOH B 17 538 538 HOH HOH . F 6 HOH B 18 551 551 HOH HOH . F 6 HOH B 19 552 552 HOH HOH . F 6 HOH B 20 553 553 HOH HOH . F 6 HOH B 21 555 555 HOH HOH . F 6 HOH B 22 561 561 HOH HOH . F 6 HOH B 23 562 562 HOH HOH . F 6 HOH B 24 564 564 HOH HOH . F 6 HOH B 25 570 570 HOH HOH . F 6 HOH B 26 576 576 HOH HOH . G 6 HOH F 1 452 394 HOH HOH . G 6 HOH F 2 453 395 HOH HOH . G 6 HOH F 3 454 396 HOH HOH . G 6 HOH F 4 455 397 HOH HOH . G 6 HOH F 5 456 398 HOH HOH . G 6 HOH F 6 457 399 HOH HOH . G 6 HOH F 7 458 400 HOH HOH . G 6 HOH F 8 459 401 HOH HOH . G 6 HOH F 9 460 402 HOH HOH . G 6 HOH F 10 461 403 HOH HOH . G 6 HOH F 11 462 404 HOH HOH . G 6 HOH F 12 463 405 HOH HOH . G 6 HOH F 13 464 406 HOH HOH . G 6 HOH F 14 465 407 HOH HOH . G 6 HOH F 15 466 408 HOH HOH . G 6 HOH F 16 467 409 HOH HOH . G 6 HOH F 17 468 410 HOH HOH . G 6 HOH F 18 469 414 HOH HOH . G 6 HOH F 19 470 421 HOH HOH . G 6 HOH F 20 496 496 HOH HOH . G 6 HOH F 21 504 504 HOH HOH . G 6 HOH F 22 505 505 HOH HOH . G 6 HOH F 23 506 506 HOH HOH . G 6 HOH F 24 510 510 HOH HOH . G 6 HOH F 25 511 511 HOH HOH . G 6 HOH F 26 512 512 HOH HOH . G 6 HOH F 27 513 513 HOH HOH . G 6 HOH F 28 514 514 HOH HOH . G 6 HOH F 29 515 515 HOH HOH . G 6 HOH F 30 516 516 HOH HOH . G 6 HOH F 31 517 517 HOH HOH . G 6 HOH F 32 518 518 HOH HOH . G 6 HOH F 33 519 519 HOH HOH . G 6 HOH F 34 520 520 HOH HOH . G 6 HOH F 35 521 521 HOH HOH . G 6 HOH F 36 522 522 HOH HOH . G 6 HOH F 37 523 523 HOH HOH . G 6 HOH F 38 524 524 HOH HOH . G 6 HOH F 39 525 525 HOH HOH . G 6 HOH F 40 526 526 HOH HOH . G 6 HOH F 41 527 527 HOH HOH . G 6 HOH F 42 529 529 HOH HOH . G 6 HOH F 43 536 536 HOH HOH . G 6 HOH F 44 537 537 HOH HOH . G 6 HOH F 45 542 542 HOH HOH . G 6 HOH F 46 545 545 HOH HOH . G 6 HOH F 47 546 546 HOH HOH . G 6 HOH F 48 547 547 HOH HOH . G 6 HOH F 49 549 549 HOH HOH . G 6 HOH F 50 557 557 HOH HOH . G 6 HOH F 51 559 559 HOH HOH . G 6 HOH F 52 563 563 HOH HOH . G 6 HOH F 53 565 565 HOH HOH . G 6 HOH F 54 567 567 HOH HOH . G 6 HOH F 55 568 568 HOH HOH . G 6 HOH F 56 569 569 HOH HOH . G 6 HOH F 57 571 571 HOH HOH . G 6 HOH F 58 572 572 HOH HOH . G 6 HOH F 59 573 573 HOH HOH . G 6 HOH F 60 574 574 HOH HOH . G 6 HOH F 61 575 575 HOH HOH . G 6 HOH F 62 577 577 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 C C1 NAG . . . E 5 -30.694 4.545 -26.302 1 71.36 ? C1 NAG 1001 B 1 HETATM 2 C C2 NAG . . . E 5 -31.971 5.249 -26.908 1 73.08 ? C2 NAG 1001 B 1 HETATM 3 C C3 NAG . . . E 5 -31.585 6.175 -28.097 1 74.55 ? C3 NAG 1001 B 1 HETATM 4 C C4 NAG . . . E 5 -30.411 7.123 -27.74 1 75.12 ? C4 NAG 1001 B 1 HETATM 5 C C5 NAG . . . E 5 -29.203 6.336 -27.156 1 74.32 ? C5 NAG 1001 B 1 HETATM 6 C C6 NAG . . . E 5 -28.598 6.99 -25.897 1 75.57 ? C6 NAG 1001 B 1 HETATM 7 C C7 NAG . . . E 5 -33.725 3.466 -26.5 1 75.59 ? C7 NAG 1001 B 1 HETATM 8 C C8 NAG . . . E 5 -34.719 2.593 -27.219 1 76.4 ? C8 NAG 1001 B 1 HETATM 9 N N2 NAG . . . E 5 -33.008 4.291 -27.337 1 74.09 ? N2 NAG 1001 B 1 HETATM 10 O O3 NAG . . . E 5 -32.739 6.915 -28.55 1 76.64 ? O3 NAG 1001 B 1 HETATM 11 O O4 NAG . . . E 5 -29.992 7.817 -28.931 1 77.52 ? O4 NAG 1001 B 1 HETATM 12 O O5 NAG . . . E 5 -29.439 4.916 -26.924 1 72.66 ? O5 NAG 1001 B 1 HETATM 13 O O6 NAG . . . E 5 -27.323 6.426 -25.572 1 77.64 ? O6 NAG 1001 B 1 HETATM 14 O O7 NAG . . . E 5 -33.58 3.433 -25.276 1 77.61 ? O7 NAG 1001 B 1 # _model_server_stats.io_time_ms 72 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 280 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #