data_7PYF # _model_server_result.job_id Wbdmax_tmmVrbJZmkaYwNg _model_server_result.datetime_utc '2024-11-24 13:06:11' _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 7pyf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":302}' # _entry.id 7PYF # _exptl.entry_id 7PYF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 4 _entity.src_method syn _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 7PYF _cell.length_a 125.62 _cell.length_b 125.62 _cell.length_c 125.62 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7PYF _symmetry.cell_setting ? _symmetry.Int_Tables_number 213 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 3 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,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 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 BGC BGC C1 O1 . O4 HO4 . sing 2 ? 2 3 2 BGC BGC C1 O1 . O4 HO4 . sing 3 ? 2 4 3 BGC BGC 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 BGC 1 B 1 BGC B 1 BGC 2 n B BGC 2 B 2 BGC B 402 BGC 2 n B BGC 3 B 3 BGC B 403 BGC 2 n B BGC 4 B 4 BGC B 404 BGC # 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 41 A CYS 41 1_555 A SG CYS 167 A CYS 167 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.01 ? covale ? covale1 A C HIC 1 A HIC 1 1_555 A N THR 2 A THR 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.351 ? covale ? covale2 A ND2 ASN 33 A ASN 33 1_555 D C1 NAG . A NAG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale3 B O4 BGC . B BGC 1 1_555 B C1 BGC . B BGC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale4 B O4 BGC . B BGC 2 1_555 B C1 BGC . B BGC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.413 ? covale ? covale5 B O4 BGC . B BGC 3 1_555 B C1 BGC . B BGC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.415 ? metalc ? metalc1 A N HIC 1 A HIC 1 1_555 C CU CU . A CU 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? metalc ? metalc2 A ND1 HIC 1 A HIC 1 1_555 C CU CU . A CU 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.98 ? metalc ? metalc3 A NE2 HIS 78 A HIS 78 1_555 C CU CU . A CU 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? metalc ? metalc4 A OH TYR 164 A TYR 164 1_555 C CU CU . A CU 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.544 ? # _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 284 n n C1 O1 NAG sing 285 n n C1 O5 NAG sing 286 n n C1 H1 NAG sing 287 n n C2 C3 NAG sing 288 n n C2 N2 NAG sing 289 n n C2 H2 NAG sing 290 n n C3 C4 NAG sing 291 n n C3 O3 NAG sing 292 n n C3 H3 NAG sing 293 n n C4 C5 NAG sing 294 n n C4 O4 NAG sing 295 n n C4 H4 NAG sing 296 n n C5 C6 NAG sing 297 n n C5 O5 NAG sing 298 n n C5 H5 NAG sing 299 n n C6 O6 NAG sing 300 n n C6 H61 NAG sing 301 n n C6 H62 NAG sing 302 n n C7 C8 NAG sing 303 n n C7 N2 NAG sing 304 n n C7 O7 NAG doub 305 n n C8 H81 NAG sing 306 n n C8 H82 NAG sing 307 n n C8 H83 NAG sing 308 n n N2 HN2 NAG sing 309 n n O1 HO1 NAG sing 310 n n O3 HO3 NAG sing 311 n n O4 HO4 NAG sing 312 n n O6 HO6 NAG sing 313 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 7PYF _atom_sites.fract_transf_matrix[1][1] 0.007961 _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] 0.007961 _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] 0.007961 _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 CU A 1 301 301 CU CU . D 4 NAG A 1 302 401 NAG NAG . E 5 CL A 1 303 1 CL CL . F 5 CL A 1 304 2 CL CL . G 6 HOH A 1 401 61 HOH HOH . G 6 HOH A 2 402 40 HOH HOH . G 6 HOH A 3 403 90 HOH HOH . G 6 HOH A 4 404 67 HOH HOH . G 6 HOH A 5 405 68 HOH HOH . G 6 HOH A 6 406 45 HOH HOH . G 6 HOH A 7 407 6 HOH HOH . G 6 HOH A 8 408 84 HOH HOH . G 6 HOH A 9 409 53 HOH HOH . G 6 HOH A 10 410 88 HOH HOH . G 6 HOH A 11 411 73 HOH HOH . G 6 HOH A 12 412 39 HOH HOH . G 6 HOH A 13 413 13 HOH HOH . G 6 HOH A 14 414 54 HOH HOH . G 6 HOH A 15 415 52 HOH HOH . G 6 HOH A 16 416 10 HOH HOH . G 6 HOH A 17 417 78 HOH HOH . G 6 HOH A 18 418 94 HOH HOH . G 6 HOH A 19 419 25 HOH HOH . G 6 HOH A 20 420 77 HOH HOH . G 6 HOH A 21 421 18 HOH HOH . G 6 HOH A 22 422 36 HOH HOH . G 6 HOH A 23 423 44 HOH HOH . G 6 HOH A 24 424 50 HOH HOH . G 6 HOH A 25 425 32 HOH HOH . G 6 HOH A 26 426 21 HOH HOH . G 6 HOH A 27 427 29 HOH HOH . G 6 HOH A 28 428 27 HOH HOH . G 6 HOH A 29 429 70 HOH HOH . G 6 HOH A 30 430 19 HOH HOH . G 6 HOH A 31 431 41 HOH HOH . G 6 HOH A 32 432 55 HOH HOH . G 6 HOH A 33 433 26 HOH HOH . G 6 HOH A 34 434 7 HOH HOH . G 6 HOH A 35 435 43 HOH HOH . G 6 HOH A 36 436 46 HOH HOH . G 6 HOH A 37 437 4 HOH HOH . G 6 HOH A 38 438 20 HOH HOH . G 6 HOH A 39 439 48 HOH HOH . G 6 HOH A 40 440 12 HOH HOH . G 6 HOH A 41 441 35 HOH HOH . G 6 HOH A 42 442 11 HOH HOH . G 6 HOH A 43 443 31 HOH HOH . G 6 HOH A 44 444 3 HOH HOH . G 6 HOH A 45 445 28 HOH HOH . G 6 HOH A 46 446 15 HOH HOH . G 6 HOH A 47 447 8 HOH HOH . G 6 HOH A 48 448 86 HOH HOH . G 6 HOH A 49 449 47 HOH HOH . G 6 HOH A 50 450 79 HOH HOH . G 6 HOH A 51 451 56 HOH HOH . G 6 HOH A 52 452 16 HOH HOH . G 6 HOH A 53 453 17 HOH HOH . G 6 HOH A 54 454 82 HOH HOH . G 6 HOH A 55 455 24 HOH HOH . G 6 HOH A 56 456 22 HOH HOH . G 6 HOH A 57 457 72 HOH HOH . G 6 HOH A 58 458 71 HOH HOH . G 6 HOH A 59 459 69 HOH HOH . G 6 HOH A 60 460 81 HOH HOH . G 6 HOH A 61 461 65 HOH HOH . G 6 HOH A 62 462 9 HOH HOH . G 6 HOH A 63 463 2 HOH HOH . G 6 HOH A 64 464 14 HOH HOH . G 6 HOH A 65 465 85 HOH HOH . G 6 HOH A 66 466 23 HOH HOH . G 6 HOH A 67 467 58 HOH HOH . G 6 HOH A 68 468 33 HOH HOH . G 6 HOH A 69 469 34 HOH HOH . G 6 HOH A 70 470 60 HOH HOH . G 6 HOH A 71 471 37 HOH HOH . G 6 HOH A 72 472 30 HOH HOH . G 6 HOH A 73 473 93 HOH HOH . G 6 HOH A 74 474 87 HOH HOH . G 6 HOH A 75 475 76 HOH HOH . G 6 HOH A 76 476 38 HOH HOH . G 6 HOH A 77 477 80 HOH HOH . G 6 HOH A 78 478 5 HOH HOH . G 6 HOH A 79 479 64 HOH HOH . G 6 HOH A 80 480 89 HOH HOH . G 6 HOH A 81 481 57 HOH HOH . G 6 HOH A 82 482 75 HOH HOH . G 6 HOH A 83 483 59 HOH HOH . G 6 HOH A 84 484 83 HOH HOH . G 6 HOH A 85 485 63 HOH HOH . G 6 HOH A 86 486 49 HOH HOH . G 6 HOH A 87 487 42 HOH HOH . G 6 HOH A 88 488 91 HOH HOH . G 6 HOH A 89 489 74 HOH HOH . G 6 HOH A 90 490 66 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 . . . D 4 -24.67 -5.53 12.128 1 46.42 ? C1 NAG 302 A 1 HETATM 2 C C2 NAG . . . D 4 -25.294 -4.169 11.99 1 47.53 ? C2 NAG 302 A 1 HETATM 3 C C3 NAG . . . D 4 -26.672 -4.284 11.372 1 52.11 ? C3 NAG 302 A 1 HETATM 4 C C4 NAG . . . D 4 -26.58 -5.109 10.088 1 53.18 ? C4 NAG 302 A 1 HETATM 5 C C5 NAG . . . D 4 -25.894 -6.461 10.307 1 49.51 ? C5 NAG 302 A 1 HETATM 6 C C6 NAG . . . D 4 -25.737 -7.264 9.007 1 44.53 ? C6 NAG 302 A 1 HETATM 7 C C7 NAG . . . D 4 -24.845 -2.201 13.349 1 44.49 ? C7 NAG 302 A 1 HETATM 8 C C8 NAG . . . D 4 -24.832 -1.521 14.68 1 43.64 ? C8 NAG 302 A 1 HETATM 9 N N2 NAG . . . D 4 -25.307 -3.464 13.268 1 45.5 ? N2 NAG 302 A 1 HETATM 10 O O3 NAG . . . D 4 -27.122 -2.98 10.987 1 47.02 ? O3 NAG 302 A 1 HETATM 11 O O4 NAG . . . D 4 -27.898 -5.236 9.547 1 55.08 ? O4 NAG 302 A 1 HETATM 12 O O5 NAG . . . D 4 -24.595 -6.163 10.84 1 47.69 ? O5 NAG 302 A 1 HETATM 13 O O6 NAG . . . D 4 -24.877 -6.585 8.066 1 41.92 ? O6 NAG 302 A 1 HETATM 14 O O7 NAG . . . D 4 -24.435 -1.597 12.371 1 50.97 ? O7 NAG 302 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 14 #