data_8VQM # _model_server_result.job_id T4_s19D32Vs13x1xz2CfAA _model_server_result.datetime_utc '2024-10-17 19:35:01' _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 8vqm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":401}' # _entry.id 8VQM # _exptl.entry_id 8VQM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 5 _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 8VQM _cell.length_a 159.471 _cell.length_b 159.471 _cell.length_c 159.471 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8VQM _symmetry.cell_setting ? _symmetry.Int_Tables_number 199 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 21 3' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # 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,F,G,H 1 1,2,3 A,B,C,D,E,F,G,H 1 4 A,B,C,D,E,F,G,H 1 5 # 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 'point symmetry operation' ? ? 0 0 1 1 0 0 0 1 0 0 0 0 3 'point symmetry operation' ? ? 0 1 0 0 0 1 1 0 0 0 0 0 4 'point symmetry operation' ? ? 0 0 1 1 0 0 0 1 0 0 0 0 5 'point symmetry operation' ? ? 0 1 0 0 0 1 1 0 0 0 0 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 # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 3 oligosaccharide 4 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 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 4 2 1 NAG 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 3 n C NAG 1 C 1 NAG C 1 NAG 3 n C NAG 2 C 2 NAG C 2 NAG 3 n C BMA 3 C 3 BMA C 3 BMA 4 n D NAG 1 D 1 NAG D 1 NAG 4 n D NAG 2 D 2 NAG D 2 NAG # 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 4 A CYS 14 1_555 B SG CYS 137 B CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf2 A SG CYS 42 A CYS 52 1_555 A SG CYS 274 A CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf3 A SG CYS 55 A CYS 64 1_555 A SG CYS 67 A CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf4 A SG CYS 90 A CYS 97 1_555 A SG CYS 135 A CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf5 A SG CYS 278 A CYS 281 1_555 A SG CYS 302 A CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? covale ? covale1 A ND2 ASN 23 A ASN 33 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale2 A ND2 ASN 268 A ASN 271 1_555 E C1 NAG . A NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale3 B ND2 ASN 154 B ASN 154 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale4 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? covale ? covale5 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.465 ? covale ? covale6 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? # _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 325 n n C1 O1 NAG sing 326 n n C1 O5 NAG sing 327 n n C1 H1 NAG sing 328 n n C2 C3 NAG sing 329 n n C2 N2 NAG sing 330 n n C2 H2 NAG sing 331 n n C3 C4 NAG sing 332 n n C3 O3 NAG sing 333 n n C3 H3 NAG sing 334 n n C4 C5 NAG sing 335 n n C4 O4 NAG sing 336 n n C4 H4 NAG sing 337 n n C5 C6 NAG sing 338 n n C5 O5 NAG sing 339 n n C5 H5 NAG sing 340 n n C6 O6 NAG sing 341 n n C6 H61 NAG sing 342 n n C6 H62 NAG sing 343 n n C7 C8 NAG sing 344 n n C7 N2 NAG sing 345 n n C7 O7 NAG doub 346 n n C8 H81 NAG sing 347 n n C8 H82 NAG sing 348 n n C8 H83 NAG sing 349 n n N2 HN2 NAG sing 350 n n O1 HO1 NAG sing 351 n n O3 HO3 NAG sing 352 n n O4 HO4 NAG sing 353 n n O6 HO6 NAG sing 354 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 8VQM _atom_sites.fract_transf_matrix[1][1] 0.006271 _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] 0.006271 _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] 0.006271 _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 A 1 401 326 NAG NAG . F 6 A1ADU B 1 301 201 A1ADU Y25 . G 7 HOH A 1 501 22 HOH HOH . G 7 HOH A 2 502 17 HOH HOH . G 7 HOH A 3 503 9 HOH HOH . G 7 HOH A 4 504 28 HOH HOH . G 7 HOH A 5 505 68 HOH HOH . G 7 HOH A 6 506 24 HOH HOH . G 7 HOH A 7 507 61 HOH HOH . G 7 HOH A 8 508 73 HOH HOH . G 7 HOH A 9 509 7 HOH HOH . G 7 HOH A 10 510 62 HOH HOH . G 7 HOH A 11 511 4 HOH HOH . G 7 HOH A 12 512 10 HOH HOH . G 7 HOH A 13 513 106 HOH HOH . G 7 HOH A 14 514 8 HOH HOH . G 7 HOH A 15 515 13 HOH HOH . G 7 HOH A 16 516 51 HOH HOH . G 7 HOH A 17 517 126 HOH HOH . G 7 HOH A 18 518 38 HOH HOH . G 7 HOH A 19 519 48 HOH HOH . G 7 HOH A 20 520 121 HOH HOH . G 7 HOH A 21 521 88 HOH HOH . G 7 HOH A 22 522 37 HOH HOH . G 7 HOH A 23 523 26 HOH HOH . G 7 HOH A 24 524 1 HOH HOH . G 7 HOH A 25 525 96 HOH HOH . G 7 HOH A 26 526 112 HOH HOH . G 7 HOH A 27 527 31 HOH HOH . G 7 HOH A 28 528 34 HOH HOH . G 7 HOH A 29 529 60 HOH HOH . G 7 HOH A 30 530 14 HOH HOH . G 7 HOH A 31 531 50 HOH HOH . G 7 HOH A 32 532 25 HOH HOH . G 7 HOH A 33 533 58 HOH HOH . G 7 HOH A 34 534 18 HOH HOH . G 7 HOH A 35 535 71 HOH HOH . G 7 HOH A 36 536 94 HOH HOH . G 7 HOH A 37 537 67 HOH HOH . G 7 HOH A 38 538 53 HOH HOH . G 7 HOH A 39 539 46 HOH HOH . G 7 HOH A 40 540 75 HOH HOH . G 7 HOH A 41 541 54 HOH HOH . G 7 HOH A 42 542 134 HOH HOH . G 7 HOH A 43 543 113 HOH HOH . G 7 HOH A 44 544 87 HOH HOH . G 7 HOH A 45 545 81 HOH HOH . G 7 HOH A 46 546 41 HOH HOH . G 7 HOH A 47 547 20 HOH HOH . G 7 HOH A 48 548 43 HOH HOH . G 7 HOH A 49 549 104 HOH HOH . G 7 HOH A 50 550 52 HOH HOH . G 7 HOH A 51 551 15 HOH HOH . G 7 HOH A 52 552 103 HOH HOH . G 7 HOH A 53 553 21 HOH HOH . G 7 HOH A 54 554 78 HOH HOH . G 7 HOH A 55 555 63 HOH HOH . G 7 HOH A 56 556 27 HOH HOH . G 7 HOH A 57 557 65 HOH HOH . G 7 HOH A 58 558 101 HOH HOH . G 7 HOH A 59 559 49 HOH HOH . G 7 HOH A 60 560 44 HOH HOH . G 7 HOH A 61 561 30 HOH HOH . G 7 HOH A 62 562 29 HOH HOH . G 7 HOH A 63 563 115 HOH HOH . G 7 HOH A 64 564 57 HOH HOH . G 7 HOH A 65 565 84 HOH HOH . G 7 HOH A 66 566 70 HOH HOH . G 7 HOH A 67 567 97 HOH HOH . G 7 HOH A 68 568 95 HOH HOH . G 7 HOH A 69 569 66 HOH HOH . G 7 HOH A 70 570 76 HOH HOH . G 7 HOH A 71 571 139 HOH HOH . G 7 HOH A 72 572 116 HOH HOH . G 7 HOH A 73 573 64 HOH HOH . G 7 HOH A 74 574 3 HOH HOH . G 7 HOH A 75 575 92 HOH HOH . G 7 HOH A 76 576 91 HOH HOH . G 7 HOH A 77 577 124 HOH HOH . G 7 HOH A 78 578 83 HOH HOH . G 7 HOH A 79 579 56 HOH HOH . G 7 HOH A 80 580 108 HOH HOH . G 7 HOH A 81 581 107 HOH HOH . G 7 HOH A 82 582 12 HOH HOH . G 7 HOH A 83 583 6 HOH HOH . G 7 HOH A 84 584 131 HOH HOH . G 7 HOH A 85 585 99 HOH HOH . G 7 HOH A 86 586 129 HOH HOH . G 7 HOH A 87 587 35 HOH HOH . G 7 HOH A 88 588 33 HOH HOH . G 7 HOH A 89 589 82 HOH HOH . G 7 HOH A 90 590 137 HOH HOH . G 7 HOH A 91 591 72 HOH HOH . G 7 HOH A 92 592 42 HOH HOH . G 7 HOH A 93 593 110 HOH HOH . G 7 HOH A 94 594 102 HOH HOH . G 7 HOH A 95 595 127 HOH HOH . G 7 HOH A 96 596 133 HOH HOH . G 7 HOH A 97 597 130 HOH HOH . G 7 HOH A 98 598 86 HOH HOH . G 7 HOH A 99 599 128 HOH HOH . G 7 HOH A 100 600 109 HOH HOH . G 7 HOH A 101 601 125 HOH HOH . G 7 HOH A 102 602 98 HOH HOH . H 7 HOH B 1 401 85 HOH HOH . H 7 HOH B 2 402 80 HOH HOH . H 7 HOH B 3 403 111 HOH HOH . H 7 HOH B 4 404 2 HOH HOH . H 7 HOH B 5 405 32 HOH HOH . H 7 HOH B 6 406 40 HOH HOH . H 7 HOH B 7 407 11 HOH HOH . H 7 HOH B 8 408 122 HOH HOH . H 7 HOH B 9 409 138 HOH HOH . H 7 HOH B 10 410 89 HOH HOH . H 7 HOH B 11 411 77 HOH HOH . H 7 HOH B 12 412 39 HOH HOH . H 7 HOH B 13 413 16 HOH HOH . H 7 HOH B 14 414 23 HOH HOH . H 7 HOH B 15 415 79 HOH HOH . H 7 HOH B 16 416 136 HOH HOH . H 7 HOH B 17 417 118 HOH HOH . H 7 HOH B 18 418 142 HOH HOH . H 7 HOH B 19 419 55 HOH HOH . H 7 HOH B 20 420 143 HOH HOH . H 7 HOH B 21 421 45 HOH HOH . H 7 HOH B 22 422 140 HOH HOH . H 7 HOH B 23 423 47 HOH HOH . H 7 HOH B 24 424 105 HOH HOH . H 7 HOH B 25 425 90 HOH HOH . H 7 HOH B 26 426 100 HOH HOH . H 7 HOH B 27 427 141 HOH HOH . H 7 HOH B 28 428 59 HOH HOH . H 7 HOH B 29 429 117 HOH HOH . H 7 HOH B 30 430 119 HOH HOH . H 7 HOH B 31 431 36 HOH HOH . H 7 HOH B 32 432 19 HOH HOH . H 7 HOH B 33 433 114 HOH HOH . H 7 HOH B 34 434 74 HOH HOH . H 7 HOH B 35 435 93 HOH HOH . H 7 HOH B 36 436 135 HOH HOH . H 7 HOH B 37 437 132 HOH HOH . H 7 HOH B 38 438 69 HOH HOH . H 7 HOH B 39 439 123 HOH HOH . H 7 HOH B 40 440 120 HOH HOH . H 7 HOH B 41 441 5 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 -47.778 -9.605 -11.984 1 92.39 ? C1 NAG 401 A 1 HETATM 2 C C2 NAG . . . E 5 -48.621 -8.847 -10.953 1 96.79 ? C2 NAG 401 A 1 HETATM 3 C C3 NAG . . . E 5 -47.989 -8.959 -9.568 1 103.97 ? C3 NAG 401 A 1 HETATM 4 C C4 NAG . . . E 5 -47.784 -10.422 -9.199 1 96.91 ? C4 NAG 401 A 1 HETATM 5 C C5 NAG . . . E 5 -46.972 -11.129 -10.28 1 96.43 ? C5 NAG 401 A 1 HETATM 6 C C6 NAG . . . E 5 -46.838 -12.613 -10.032 1 92.58 ? C6 NAG 401 A 1 HETATM 7 C C7 NAG . . . E 5 -49.852 -7.001 -12.007 1 92.48 ? C7 NAG 401 A 1 HETATM 8 C C8 NAG . . . E 5 -49.86 -5.533 -12.314 1 80.72 ? C8 NAG 401 A 1 HETATM 9 N N2 NAG . . . E 5 -48.789 -7.453 -11.332 1 96.73 ? N2 NAG 401 A 1 HETATM 10 O O3 NAG . . . E 5 -48.826 -8.331 -8.602 1 102.96 ? O3 NAG 401 A 1 HETATM 11 O O4 NAG . . . E 5 -47.104 -10.526 -7.953 1 93.47 ? O4 NAG 401 A 1 HETATM 12 O O5 NAG . . . E 5 -47.611 -10.977 -11.559 1 100.36 ? O5 NAG 401 A 1 HETATM 13 O O6 NAG . . . E 5 -46.808 -13.342 -11.252 1 94.78 ? O6 NAG 401 A 1 HETATM 14 O O7 NAG . . . E 5 -50.765 -7.744 -12.355 1 94.7 ? O7 NAG 401 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 417 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #