data_4Q56 # _model_server_result.job_id 5BI8GfXcAwJhEfoUg4rJdg _model_server_result.datetime_utc '2024-11-26 23:56:14' _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 4q56 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":202}' # _entry.id 4Q56 # _exptl.entry_id 4Q56 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 4 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-alpha-D-galactopyranose _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 4Q56 _cell.length_a 47.9 _cell.length_b 47.9 _cell.length_c 281.53 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4Q56 _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 1,2,3,4,5,6 # 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' 2_655 -y+1,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 47.9 0 0 3 'crystal symmetry operation' 3_665 -x+y+1,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 23.95 41.482617 0 4 'crystal symmetry operation' 16_545 y+1/3,x-1/3,-z+2/3 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 23.95 -13.827539 187.686667 5 'crystal symmetry operation' 17_555 x-y+1/3,-y+2/3,-z+2/3 1 0 0 0 -1 0 0 0 -1 0 27.655078 187.686667 6 'crystal symmetry operation' 18_655 -x+4/3,-x+y+2/3,-z+2/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 47.9 27.655078 187.686667 # _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 # _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 FUC NAG C1 O1 . O3 HO3 . sing 2 ? 2 3 2 GAL FUC C1 O1 . O4 HO4 . sing 3 ? 2 4 3 FUC GAL C1 O1 . O2 HO2 . sing 4 ? 2 5 1 NAG NAG C1 O1 . O4 HO4 . sing 5 ? 2 6 5 BMA NAG C1 O1 . O4 HO4 . 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 S 201 NAG 2 n B FUC 2 B 2 FUC S 204 FUC 2 n B GAL 3 B 3 GAL S 205 GAL 2 n B FUC 4 B 4 FUC S 206 FUC 2 n B NAG 5 B 5 NAG S 202 NAG 2 n B BMA 6 B 6 BMA S 203 BMA # 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 10 A CYS 10 1_555 A SG CYS 81 A CYS 81 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf2 A SG CYS 43 A CYS 43 1_555 A SG CYS 43 A CYS 43 5_556 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? covale ? covale1 A C PCA 1 A PCA 1 1_555 A N ARG 2 A ARG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale2 A ND2 ASN 35 A ASN 35 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.469 ? covale ? covale3 B O3 NAG . B NAG 1 1_555 B C1 FUC . B FUC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale4 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale5 B O4 FUC . B FUC 2 1_555 B C1 GAL . B GAL 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.42 ? covale ? covale6 B O2 GAL . B GAL 3 1_555 B C1 FUC . B FUC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale7 B O4 NAG . B NAG 5 1_555 B C1 BMA . B BMA 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? metalc ? metalc1 A O GLN 59 A GLN 59 1_555 E NA NA . A NA 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.478 ? metalc ? metalc2 A OE1 GLN 59 A GLN 59 1_555 E NA NA . A NA 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.526 ? metalc ? metalc3 A NE2 HIS 85 A HIS 85 1_555 F ZN ZN . A ZN 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? metalc ? metalc4 C O ACT . A ACT 201 1_555 F ZN ZN . A ZN 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.939 ? metalc ? metalc5 C OXT ACT . A ACT 201 1_555 F ZN ZN . A ZN 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.523 ? metalc ? metalc6 E NA NA . A NA 203 1_555 G O HOH . A HOH 337 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.473 ? metalc ? metalc7 E NA NA . A NA 203 1_555 G O HOH . A HOH 396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.724 ? # _chem_comp.formula 'C8 H15 N O6' _chem_comp.formula_weight 221.208 _chem_comp.id A2G _chem_comp.mon_nstd_flag . _chem_comp.name 2-acetamido-2-deoxy-alpha-D-galactopyranose _chem_comp.type 'd-saccharide, alpha linking' _chem_comp.pdbx_synonyms N-acetyl-alpha-D-galactosamine;2-acetamido-2-deoxy-alpha-D-galactose;2-acetamido-2-deoxy-D-galactose;2-acetamido-2-deoxy-galactose;N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE # 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 A2G sing 1 n n C1 O5 A2G sing 2 n n C1 C2 A2G sing 3 n n C1 H1 A2G sing 4 n n O1 C1 A2G sing 5 n n O1 HO1 A2G sing 6 n n C2 C3 A2G sing 7 n n C2 H2 A2G sing 8 n n N2 C2 A2G sing 9 n n N2 HN2 A2G sing 10 n n C3 C4 A2G sing 11 n n C3 O3 A2G sing 12 n n C3 H3 A2G sing 13 n n O3 HO3 A2G sing 14 n n C4 O4 A2G sing 15 n n C4 H4 A2G sing 16 n n O4 HO4 A2G sing 17 n n C5 C4 A2G sing 18 n n C5 C6 A2G sing 19 n n C5 H5 A2G sing 20 n n C6 O6 A2G sing 21 n n C6 H61 A2G sing 22 n n C7 N2 A2G sing 23 n n O7 C7 A2G doub 24 n n C8 C7 A2G sing 25 n n C8 H81 A2G sing 26 n n C8 H82 A2G sing 27 n n C8 H83 A2G sing 28 n n C6 H62 A2G sing 29 n n O6 HO6 A2G sing 30 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 A2G DGalpNAca 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 A2G N-acetyl-a-D-galactopyranosamine 'COMMON NAME' GMML 1 A2G a-D-GalpNAc 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 A2G GalNAc 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 4Q56 _atom_sites.fract_transf_matrix[1][1] 0.020877 _atom_sites.fract_transf_matrix[1][2] 0.012053 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.024106 _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] 0.003552 _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 ACT A 1 201 1 ACT ACT . D 4 A2G A 1 202 1 A2G A2G . E 5 NA A 1 203 1 NA NA . F 6 ZN A 1 210 1 ZN ZN . G 7 HOH A 1 301 1 HOH HOH . G 7 HOH A 2 302 2 HOH HOH . G 7 HOH A 3 303 3 HOH HOH . G 7 HOH A 4 304 4 HOH HOH . G 7 HOH A 5 305 5 HOH HOH . G 7 HOH A 6 306 6 HOH HOH . G 7 HOH A 7 307 7 HOH HOH . G 7 HOH A 8 308 8 HOH HOH . G 7 HOH A 9 309 9 HOH HOH . G 7 HOH A 10 310 10 HOH HOH . G 7 HOH A 11 311 11 HOH HOH . G 7 HOH A 12 312 12 HOH HOH . G 7 HOH A 13 313 13 HOH HOH . G 7 HOH A 14 314 14 HOH HOH . G 7 HOH A 15 315 15 HOH HOH . G 7 HOH A 16 316 16 HOH HOH . G 7 HOH A 17 317 17 HOH HOH . G 7 HOH A 18 318 18 HOH HOH . G 7 HOH A 19 319 19 HOH HOH . G 7 HOH A 20 320 20 HOH HOH . G 7 HOH A 21 321 21 HOH HOH . G 7 HOH A 22 322 22 HOH HOH . G 7 HOH A 23 323 23 HOH HOH . G 7 HOH A 24 324 24 HOH HOH . G 7 HOH A 25 325 25 HOH HOH . G 7 HOH A 26 326 26 HOH HOH . G 7 HOH A 27 327 27 HOH HOH . G 7 HOH A 28 328 28 HOH HOH . G 7 HOH A 29 329 29 HOH HOH . G 7 HOH A 30 330 30 HOH HOH . G 7 HOH A 31 331 31 HOH HOH . G 7 HOH A 32 332 32 HOH HOH . G 7 HOH A 33 333 33 HOH HOH . G 7 HOH A 34 334 34 HOH HOH . G 7 HOH A 35 335 35 HOH HOH . G 7 HOH A 36 336 36 HOH HOH . G 7 HOH A 37 337 37 HOH HOH . G 7 HOH A 38 338 38 HOH HOH . G 7 HOH A 39 339 39 HOH HOH . G 7 HOH A 40 340 40 HOH HOH . G 7 HOH A 41 341 41 HOH HOH . G 7 HOH A 42 342 42 HOH HOH . G 7 HOH A 43 343 43 HOH HOH . G 7 HOH A 44 344 44 HOH HOH . G 7 HOH A 45 345 45 HOH HOH . G 7 HOH A 46 346 46 HOH HOH . G 7 HOH A 47 347 47 HOH HOH . G 7 HOH A 48 348 48 HOH HOH . G 7 HOH A 49 349 49 HOH HOH . G 7 HOH A 50 350 50 HOH HOH . G 7 HOH A 51 351 51 HOH HOH . G 7 HOH A 52 352 52 HOH HOH . G 7 HOH A 53 353 53 HOH HOH . G 7 HOH A 54 354 54 HOH HOH . G 7 HOH A 55 355 55 HOH HOH . G 7 HOH A 56 356 56 HOH HOH . G 7 HOH A 57 357 57 HOH HOH . G 7 HOH A 58 358 58 HOH HOH . G 7 HOH A 59 359 59 HOH HOH . G 7 HOH A 60 360 60 HOH HOH . G 7 HOH A 61 361 61 HOH HOH . G 7 HOH A 62 362 62 HOH HOH . G 7 HOH A 63 363 63 HOH HOH . G 7 HOH A 64 364 64 HOH HOH . G 7 HOH A 65 365 65 HOH HOH . G 7 HOH A 66 366 66 HOH HOH . G 7 HOH A 67 367 67 HOH HOH . G 7 HOH A 68 368 68 HOH HOH . G 7 HOH A 69 369 69 HOH HOH . G 7 HOH A 70 370 70 HOH HOH . G 7 HOH A 71 371 71 HOH HOH . G 7 HOH A 72 372 72 HOH HOH . G 7 HOH A 73 373 73 HOH HOH . G 7 HOH A 74 374 74 HOH HOH . G 7 HOH A 75 375 75 HOH HOH . G 7 HOH A 76 376 76 HOH HOH . G 7 HOH A 77 377 77 HOH HOH . G 7 HOH A 78 378 78 HOH HOH . G 7 HOH A 79 379 79 HOH HOH . G 7 HOH A 80 380 80 HOH HOH . G 7 HOH A 81 381 81 HOH HOH . G 7 HOH A 82 382 82 HOH HOH . G 7 HOH A 83 383 83 HOH HOH . G 7 HOH A 84 384 84 HOH HOH . G 7 HOH A 85 385 85 HOH HOH . G 7 HOH A 86 386 86 HOH HOH . G 7 HOH A 87 387 87 HOH HOH . G 7 HOH A 88 388 88 HOH HOH . G 7 HOH A 89 389 89 HOH HOH . G 7 HOH A 90 390 90 HOH HOH . G 7 HOH A 91 391 91 HOH HOH . G 7 HOH A 92 392 92 HOH HOH . G 7 HOH A 93 393 93 HOH HOH . G 7 HOH A 94 394 94 HOH HOH . G 7 HOH A 95 395 95 HOH HOH . G 7 HOH A 96 396 96 HOH HOH . G 7 HOH A 97 397 97 HOH HOH . G 7 HOH A 98 398 98 HOH HOH . G 7 HOH A 99 399 99 HOH HOH . G 7 HOH A 100 400 100 HOH HOH . G 7 HOH A 101 401 101 HOH HOH . G 7 HOH A 102 402 102 HOH HOH . G 7 HOH A 103 403 103 HOH HOH . G 7 HOH A 104 404 104 HOH HOH . G 7 HOH A 105 405 105 HOH HOH . G 7 HOH A 106 406 106 HOH HOH . G 7 HOH A 107 407 107 HOH HOH . G 7 HOH A 108 408 108 HOH HOH . G 7 HOH A 109 409 109 HOH HOH . G 7 HOH A 110 410 110 HOH HOH . G 7 HOH A 111 411 111 HOH HOH . G 7 HOH A 112 412 112 HOH HOH . G 7 HOH A 113 413 113 HOH HOH . G 7 HOH A 114 414 114 HOH HOH . G 7 HOH A 115 415 115 HOH HOH . G 7 HOH A 116 416 116 HOH HOH . G 7 HOH A 117 417 117 HOH HOH . G 7 HOH A 118 418 118 HOH HOH . G 7 HOH A 119 419 119 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 A2G . . . D 4 8.256 -9.921 98.178 1 18.52 ? O5 A2G 202 A 1 HETATM 2 C C1 A2G . . . D 4 9.565 -10.374 97.78 1 18.77 ? C1 A2G 202 A 1 HETATM 3 O O1 A2G . . . D 4 9.377 -11.63 97.126 1 20.96 ? O1 A2G 202 A 1 HETATM 4 C C2 A2G . . . D 4 10.418 -10.566 99.037 1 19.17 ? C2 A2G 202 A 1 HETATM 5 N N2 A2G . . . D 4 11.693 -11.184 98.644 1 19.3 ? N2 A2G 202 A 1 HETATM 6 C C3 A2G . . . D 4 9.725 -11.465 100.052 1 18.7 ? C3 A2G 202 A 1 HETATM 7 O O3 A2G . . . D 4 10.437 -11.532 101.282 1 19.92 ? O3 A2G 202 A 1 HETATM 8 C C4 A2G . . . D 4 8.328 -10.934 100.392 1 17.78 ? C4 A2G 202 A 1 HETATM 9 O O4 A2G . . . D 4 8.422 -9.693 101.104 1 17.43 ? O4 A2G 202 A 1 HETATM 10 C C5 A2G . . . D 4 7.539 -10.777 99.097 1 18.24 ? C5 A2G 202 A 1 HETATM 11 C C6 A2G . . . D 4 6.144 -10.155 99.228 1 16.66 ? C6 A2G 202 A 1 HETATM 12 O O6 A2G . . . D 4 6.169 -8.757 99.51 1 16.58 ? O6 A2G 202 A 1 HETATM 13 C C7 A2G . . . D 4 12.857 -10.798 99.096 1 20.3 ? C7 A2G 202 A 1 HETATM 14 O O7 A2G . . . D 4 13.042 -9.905 99.908 1 19.33 ? O7 A2G 202 A 1 HETATM 15 C C8 A2G . . . D 4 14.024 -11.546 98.455 1 22.19 ? C8 A2G 202 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 266 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 15 #