data_2VIU # _model_server_result.job_id Z7fWK5ySOVEKwL22F3axQA _model_server_result.datetime_utc '2024-12-02 21:06:07' _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 2viu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":410}' # _entry.id 2VIU # _exptl.entry_id 2VIU _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-beta-D-glucopyranose _entity.pdbx_number_of_molecules 5 _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 2VIU _cell.length_a 144.4 _cell.length_b 144.4 _cell.length_c 144.4 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2VIU _symmetry.cell_setting ? _symmetry.Int_Tables_number 198 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 3' # _pdbx_struct_assembly.method_details PISA,PQS _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,H,I,J _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # 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' 6_456 z-1/2,-x+1/2,-y+1 0 0 1 -1 0 0 0 -1 0 -72.2 72.2 144.4 3 'crystal symmetry operation' 12_565 -y+1/2,-z+1,x+1/2 0 -1 0 0 0 -1 1 0 0 72.2 144.4 72.2 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 D N N ? 4 E N N ? 4 F N N ? 4 G N N ? 4 H N N # _pdbx_entity_branch.entity_id 3 _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 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 3 2 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 3 n C NAG 1 C 1 NAG A 450 NAG 3 n C NAG 2 C 2 NAG A 451 NAG 3 n C BMA 3 C 3 BMA A 452 MAN # 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 14 A CYS 14 1_555 B SG CYS 137 B CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? disulf ? disulf2 A SG CYS 52 A CYS 52 1_555 A SG CYS 277 A CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf3 A SG CYS 64 A CYS 64 1_555 A SG CYS 76 A CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.006 ? disulf ? disulf4 A SG CYS 97 A CYS 97 1_555 A SG CYS 139 A CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? disulf ? disulf5 A SG CYS 281 A CYS 281 1_555 A SG CYS 305 A CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? disulf ? disulf6 B SG CYS 144 B CYS 144 1_555 B SG CYS 148 B CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? covale ? covale1 A ND2 ASN 81 A ASN 81 1_555 E C1 NAG . A NAG 440 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale2 A ND2 ASN 165 A ASN 165 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale3 A ND2 ASN 285 A ASN 285 1_555 G C1 NAG . A NAG 460 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale4 B ND2 ASN 154 B ASN 154 1_555 H C1 NAG . B NAG 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale5 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.387 ? covale ? covale6 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.38 ? # _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 2VIU _atom_sites.fract_transf_matrix[1][1] 0.006925 _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] 0.006925 _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] 0.006925 _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 D 4 NAG A 1 430 430 NAG NAG . E 4 NAG A 1 440 440 NAG NAG . F 4 NAG A 1 441 441 NAG NAG . G 4 NAG A 1 460 460 NAG NAG . H 4 NAG B 1 410 410 NAG NAG . I 5 HOH A 1 461 3 HOH HOH . I 5 HOH A 2 462 4 HOH HOH . I 5 HOH A 3 463 5 HOH HOH . I 5 HOH A 4 464 8 HOH HOH . I 5 HOH A 5 465 9 HOH HOH . I 5 HOH A 6 466 12 HOH HOH . I 5 HOH A 7 467 17 HOH HOH . I 5 HOH A 8 468 22 HOH HOH . I 5 HOH A 9 469 24 HOH HOH . I 5 HOH A 10 470 25 HOH HOH . I 5 HOH A 11 471 28 HOH HOH . I 5 HOH A 12 472 29 HOH HOH . I 5 HOH A 13 473 30 HOH HOH . I 5 HOH A 14 474 31 HOH HOH . I 5 HOH A 15 475 32 HOH HOH . I 5 HOH A 16 476 34 HOH HOH . I 5 HOH A 17 477 35 HOH HOH . I 5 HOH A 18 478 40 HOH HOH . I 5 HOH A 19 479 42 HOH HOH . I 5 HOH A 20 480 46 HOH HOH . I 5 HOH A 21 481 47 HOH HOH . I 5 HOH A 22 482 48 HOH HOH . I 5 HOH A 23 483 49 HOH HOH . I 5 HOH A 24 484 50 HOH HOH . I 5 HOH A 25 485 52 HOH HOH . I 5 HOH A 26 486 53 HOH HOH . I 5 HOH A 27 487 57 HOH HOH . I 5 HOH A 28 488 58 HOH HOH . I 5 HOH A 29 489 59 HOH HOH . I 5 HOH A 30 490 61 HOH HOH . I 5 HOH A 31 491 62 HOH HOH . I 5 HOH A 32 492 64 HOH HOH . I 5 HOH A 33 493 65 HOH HOH . I 5 HOH A 34 494 66 HOH HOH . I 5 HOH A 35 495 67 HOH HOH . I 5 HOH A 36 496 68 HOH HOH . I 5 HOH A 37 497 71 HOH HOH . I 5 HOH A 38 498 75 HOH HOH . I 5 HOH A 39 499 76 HOH HOH . I 5 HOH A 40 500 77 HOH HOH . I 5 HOH A 41 501 80 HOH HOH . I 5 HOH A 42 502 81 HOH HOH . I 5 HOH A 43 503 82 HOH HOH . I 5 HOH A 44 504 84 HOH HOH . I 5 HOH A 45 505 86 HOH HOH . I 5 HOH A 46 506 91 HOH HOH . I 5 HOH A 47 507 93 HOH HOH . I 5 HOH A 48 508 97 HOH HOH . I 5 HOH A 49 509 98 HOH HOH . I 5 HOH A 50 510 101 HOH HOH . I 5 HOH A 51 511 103 HOH HOH . J 5 HOH B 1 411 1 HOH HOH . J 5 HOH B 2 412 2 HOH HOH . J 5 HOH B 3 413 6 HOH HOH . J 5 HOH B 4 414 7 HOH HOH . J 5 HOH B 5 415 10 HOH HOH . J 5 HOH B 6 416 11 HOH HOH . J 5 HOH B 7 417 13 HOH HOH . J 5 HOH B 8 418 14 HOH HOH . J 5 HOH B 9 419 15 HOH HOH . J 5 HOH B 10 420 16 HOH HOH . J 5 HOH B 11 421 18 HOH HOH . J 5 HOH B 12 422 19 HOH HOH . J 5 HOH B 13 423 20 HOH HOH . J 5 HOH B 14 424 21 HOH HOH . J 5 HOH B 15 425 23 HOH HOH . J 5 HOH B 16 426 26 HOH HOH . J 5 HOH B 17 427 27 HOH HOH . J 5 HOH B 18 428 33 HOH HOH . J 5 HOH B 19 429 36 HOH HOH . J 5 HOH B 20 430 37 HOH HOH . J 5 HOH B 21 431 38 HOH HOH . J 5 HOH B 22 432 39 HOH HOH . J 5 HOH B 23 433 41 HOH HOH . J 5 HOH B 24 434 43 HOH HOH . J 5 HOH B 25 435 44 HOH HOH . J 5 HOH B 26 436 45 HOH HOH . J 5 HOH B 27 437 51 HOH HOH . J 5 HOH B 28 438 54 HOH HOH . J 5 HOH B 29 439 55 HOH HOH . J 5 HOH B 30 440 56 HOH HOH . J 5 HOH B 31 441 60 HOH HOH . J 5 HOH B 32 442 63 HOH HOH . J 5 HOH B 33 443 69 HOH HOH . J 5 HOH B 34 444 70 HOH HOH . J 5 HOH B 35 445 72 HOH HOH . J 5 HOH B 36 446 73 HOH HOH . J 5 HOH B 37 447 74 HOH HOH . J 5 HOH B 38 448 78 HOH HOH . J 5 HOH B 39 449 79 HOH HOH . J 5 HOH B 40 450 83 HOH HOH . J 5 HOH B 41 451 85 HOH HOH . J 5 HOH B 42 452 87 HOH HOH . J 5 HOH B 43 453 88 HOH HOH . J 5 HOH B 44 454 89 HOH HOH . J 5 HOH B 45 455 90 HOH HOH . J 5 HOH B 46 456 92 HOH HOH . J 5 HOH B 47 457 94 HOH HOH . J 5 HOH B 48 458 95 HOH HOH . J 5 HOH B 49 459 96 HOH HOH . J 5 HOH B 50 460 99 HOH HOH . J 5 HOH B 51 461 100 HOH HOH . J 5 HOH B 52 462 102 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 . . . H 4 -35.16 79.93 70.76 1 56.09 ? C1 NAG 410 B 1 HETATM 2 C C2 NAG . . . H 4 -36.078 78.781 71.256 1 59.21 ? C2 NAG 410 B 1 HETATM 3 C C3 NAG . . . H 4 -37.543 78.986 70.852 1 61.63 ? C3 NAG 410 B 1 HETATM 4 C C4 NAG . . . H 4 -38.006 80.401 71.185 1 62.23 ? C4 NAG 410 B 1 HETATM 5 C C5 NAG . . . H 4 -37.06 81.389 70.498 1 60.41 ? C5 NAG 410 B 1 HETATM 6 C C6 NAG . . . H 4 -37.443 82.846 70.704 1 60.57 ? C6 NAG 410 B 1 HETATM 7 C C7 NAG . . . H 4 -35.104 76.557 71.444 1 62.82 ? C7 NAG 410 B 1 HETATM 8 C C8 NAG . . . H 4 -34.657 75.286 70.734 1 62.77 ? C8 NAG 410 B 1 HETATM 9 N N2 NAG . . . H 4 -35.621 77.521 70.682 1 61.39 ? N2 NAG 410 B 1 HETATM 10 O O3 NAG . . . H 4 -38.379 78.044 71.519 1 63.34 ? O3 NAG 410 B 1 HETATM 11 O O4 NAG . . . H 4 -39.351 80.576 70.734 1 64.36 ? O4 NAG 410 B 1 HETATM 12 O O5 NAG . . . H 4 -35.733 81.223 71.02 1 56.75 ? O5 NAG 410 B 1 HETATM 13 O O6 NAG . . . H 4 -37.198 83.261 72.04 1 61.98 ? O6 NAG 410 B 1 HETATM 14 O O7 NAG . . . H 4 -35.001 76.649 72.671 1 64.39 ? O7 NAG 410 B 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 14 #