data_2DF3 # _model_server_result.job_id raZzd5oxJtIHk9kgQVX7YA _model_server_result.datetime_utc '2025-02-05 11:49:56' _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 2df3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":301}' # _entry.id 2DF3 # _exptl.entry_id 2DF3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 3 _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 2DF3 _cell.length_a 53.07 _cell.length_b 53.07 _cell.length_c 92.88 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2DF3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _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 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 2 1 GAL NAG C1 O1 . O3 HO3 . sing 2 ? 2 3 2 SIA GAL C2 O2 . O3 HO3 . sing 3 ? 2 4 1 SIA NAG C2 O2 . O6 HO6 . 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 2 n B NAG 1 B 1 NAG D 201 NAG 2 n B GAL 2 B 2 GAL D 202 GAL 2 n B SIA 3 B 3 SIA D 203 SIA 2 n B SIA 4 B 4 SIA D 200 SIA # 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 29 A CYS 46 1_555 A SG CYS 89 A CYS 106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? covale ? covale1 A ND2 ASN 88 A ASN 105 1_555 C C1 NAG . A NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale2 B O3 NAG . B NAG 1 1_555 B C1 GAL . B GAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.408 ? covale ? covale3 B O6 NAG . B NAG 1 1_555 B C2 SIA . B SIA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.427 sing covale ? covale4 B O3 GAL . B GAL 2 1_555 B C2 SIA . B SIA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 sing # _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 261 n n C1 O1 NAG sing 262 n n C1 O5 NAG sing 263 n n C1 H1 NAG sing 264 n n C2 C3 NAG sing 265 n n C2 N2 NAG sing 266 n n C2 H2 NAG sing 267 n n C3 C4 NAG sing 268 n n C3 O3 NAG sing 269 n n C3 H3 NAG sing 270 n n C4 C5 NAG sing 271 n n C4 O4 NAG sing 272 n n C4 H4 NAG sing 273 n n C5 C6 NAG sing 274 n n C5 O5 NAG sing 275 n n C5 H5 NAG sing 276 n n C6 O6 NAG sing 277 n n C6 H61 NAG sing 278 n n C6 H62 NAG sing 279 n n C7 C8 NAG sing 280 n n C7 N2 NAG sing 281 n n C7 O7 NAG doub 282 n n C8 H81 NAG sing 283 n n C8 H82 NAG sing 284 n n C8 H83 NAG sing 285 n n N2 HN2 NAG sing 286 n n O1 HO1 NAG sing 287 n n O3 HO3 NAG sing 288 n n O4 HO4 NAG sing 289 n n O6 HO6 NAG sing 290 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 2DF3 _atom_sites.fract_transf_matrix[1][1] 0.01884 _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] 0.01884 _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] 0.01077 _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 3 NAG A 1 301 301 NAG NAG . D 4 CYS A 1 310 201 CYS CYS . E 5 HOH A 1 401 1 HOH HOH . E 5 HOH A 2 402 2 HOH HOH . E 5 HOH A 3 403 3 HOH HOH . E 5 HOH A 4 404 5 HOH HOH . E 5 HOH A 5 405 6 HOH HOH . E 5 HOH A 6 406 7 HOH HOH . E 5 HOH A 7 407 8 HOH HOH . E 5 HOH A 8 408 9 HOH HOH . E 5 HOH A 9 409 10 HOH HOH . E 5 HOH A 10 410 11 HOH HOH . E 5 HOH A 11 411 12 HOH HOH . E 5 HOH A 12 412 13 HOH HOH . E 5 HOH A 13 413 14 HOH HOH . E 5 HOH A 14 414 15 HOH HOH . E 5 HOH A 15 415 16 HOH HOH . E 5 HOH A 16 416 17 HOH HOH . E 5 HOH A 17 417 18 HOH HOH . E 5 HOH A 18 418 19 HOH HOH . E 5 HOH A 19 419 20 HOH HOH . E 5 HOH A 20 420 21 HOH HOH . E 5 HOH A 21 421 22 HOH HOH . E 5 HOH A 22 422 23 HOH HOH . E 5 HOH A 23 423 24 HOH HOH . E 5 HOH A 24 424 25 HOH HOH . E 5 HOH A 25 425 29 HOH HOH . E 5 HOH A 26 426 31 HOH HOH . E 5 HOH A 27 427 32 HOH HOH . E 5 HOH A 28 428 34 HOH HOH . E 5 HOH A 29 429 35 HOH HOH . E 5 HOH A 30 430 36 HOH HOH . E 5 HOH A 31 431 38 HOH HOH . E 5 HOH A 32 432 40 HOH HOH . E 5 HOH A 33 433 41 HOH HOH . E 5 HOH A 34 434 43 HOH HOH . E 5 HOH A 35 435 44 HOH HOH . E 5 HOH A 36 436 46 HOH HOH . E 5 HOH A 37 437 49 HOH HOH . E 5 HOH A 38 438 50 HOH HOH . E 5 HOH A 39 439 51 HOH HOH . E 5 HOH A 40 440 52 HOH HOH . E 5 HOH A 41 441 53 HOH HOH . E 5 HOH A 42 442 57 HOH HOH . E 5 HOH A 43 443 58 HOH HOH . E 5 HOH A 44 444 60 HOH HOH . E 5 HOH A 45 445 61 HOH HOH . E 5 HOH A 46 446 65 HOH HOH . E 5 HOH A 47 447 68 HOH HOH . E 5 HOH A 48 448 69 HOH HOH . E 5 HOH A 49 449 70 HOH HOH . E 5 HOH A 50 450 72 HOH HOH . E 5 HOH A 51 451 73 HOH HOH . E 5 HOH A 52 452 75 HOH HOH . E 5 HOH A 53 453 76 HOH HOH . E 5 HOH A 54 454 77 HOH HOH . E 5 HOH A 55 455 78 HOH HOH . E 5 HOH A 56 456 79 HOH HOH . E 5 HOH A 57 457 81 HOH HOH . E 5 HOH A 58 458 82 HOH HOH . E 5 HOH A 59 459 83 HOH HOH . E 5 HOH A 60 460 84 HOH HOH . E 5 HOH A 61 461 85 HOH HOH . E 5 HOH A 62 462 86 HOH HOH . E 5 HOH A 63 463 87 HOH HOH . E 5 HOH A 64 464 89 HOH HOH . E 5 HOH A 65 465 90 HOH HOH . E 5 HOH A 66 466 92 HOH HOH . E 5 HOH A 67 467 93 HOH HOH . E 5 HOH A 68 468 94 HOH HOH . E 5 HOH A 69 469 95 HOH HOH . E 5 HOH A 70 470 96 HOH HOH . E 5 HOH A 71 471 99 HOH HOH . E 5 HOH A 72 472 100 HOH HOH . E 5 HOH A 73 473 101 HOH HOH . E 5 HOH A 74 474 102 HOH HOH . E 5 HOH A 75 475 103 HOH HOH . E 5 HOH A 76 476 104 HOH HOH . E 5 HOH A 77 477 105 HOH HOH . E 5 HOH A 78 478 106 HOH HOH . E 5 HOH A 79 479 107 HOH HOH . E 5 HOH A 80 480 108 HOH HOH . E 5 HOH A 81 481 109 HOH HOH . E 5 HOH A 82 482 110 HOH HOH . E 5 HOH A 83 483 111 HOH HOH . E 5 HOH A 84 484 114 HOH HOH . E 5 HOH A 85 485 115 HOH HOH . E 5 HOH A 86 486 116 HOH HOH . E 5 HOH A 87 487 119 HOH HOH . E 5 HOH A 88 488 125 HOH HOH . E 5 HOH A 89 489 126 HOH HOH . E 5 HOH A 90 490 127 HOH HOH . E 5 HOH A 91 491 131 HOH HOH . E 5 HOH A 92 492 133 HOH HOH . E 5 HOH A 93 493 134 HOH HOH . E 5 HOH A 94 494 146 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 . . . C 3 7.338 7.782 23.585 1 28.05 ? C1 NAG 301 A 1 HETATM 2 C C2 NAG . . . C 3 5.953 7.153 23.423 1 32.43 ? C2 NAG 301 A 1 HETATM 3 C C3 NAG . . . C 3 5.687 6.058 24.464 1 32.74 ? C3 NAG 301 A 1 HETATM 4 C C4 NAG . . . C 3 6.866 5.101 24.619 1 33.64 ? C4 NAG 301 A 1 HETATM 5 C C5 NAG . . . C 3 8.115 5.954 24.829 1 33.2 ? C5 NAG 301 A 1 HETATM 6 C C6 NAG . . . C 3 9.349 5.118 25.16 1 33.29 ? C6 NAG 301 A 1 HETATM 7 C C7 NAG . . . C 3 3.913 8.316 22.738 1 33.48 ? C7 NAG 301 A 1 HETATM 8 C C8 NAG . . . C 3 3.011 9.488 23 1 33.52 ? C8 NAG 301 A 1 HETATM 9 N N2 NAG . . . C 3 4.951 8.19 23.562 1 32.77 ? N2 NAG 301 A 1 HETATM 10 O O3 NAG . . . C 3 4.525 5.346 24.112 1 35.81 ? O3 NAG 301 A 1 HETATM 11 O O4 NAG . . . C 3 6.664 4.253 25.734 1 34.64 ? O4 NAG 301 A 1 HETATM 12 O O5 NAG . . . C 3 8.299 6.75 23.665 1 30.07 ? O5 NAG 301 A 1 HETATM 13 O O6 NAG . . . C 3 10.033 4.762 23.98 1 37.56 ? O6 NAG 301 A 1 HETATM 14 O O7 NAG . . . C 3 3.677 7.544 21.806 1 34.05 ? O7 NAG 301 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 345 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #