data_5GDS # _model_server_result.job_id 70cNLm4_BK57kKoihyKWsg _model_server_result.datetime_utc '2024-11-01 02:24:24' _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 5gds # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":400}' # _entry.id 5GDS # _exptl.entry_id 5GDS _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 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 100.7 _cell.angle_gamma 90 _cell.entry_id 5GDS _cell.length_a 71.9 _cell.length_b 72.8 _cell.length_c 73.3 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5GDS _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 # _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 # 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 9 L CYS 1 1_555 B SG CYS 119 H CYS 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.995 ? disulf ? disulf2 B SG CYS 28 H CYS 42 1_555 B SG CYS 44 H CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf3 B SG CYS 173 H CYS 168 1_555 B SG CYS 187 H CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf4 B SG CYS 201 H CYS 191 1_555 B SG CYS 231 H CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? covale ? covale1 B ND2 ASN 53 H ASN 60 1_555 D C1 NAG . H NAG 400 1_555 G ? ? ? ? ? ? ? ? ? ? ? 1.393 ? covale ? covale2 C C CHG 1 I CHG 1 1_555 C N VAL 2 I VAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.341 ? covale ? covale3 C C VAL 2 I VAL 2 1_555 C N NAL 3 I NAL 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale4 C C PRO 21 I PRO 21 1_555 C N AIB 22 I AIB 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.346 ? covale ? covale5 C C AIB 22 I AIB 22 1_555 C N AIB 23 I AIB 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale6 C C AIB 23 I AIB 23 1_555 C N TYR 24 I TYR 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.341 ? covale ? covale7 C C TYR 24 I TYR 24 1_555 C N ALC 25 I ALC 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale8 C C ALC 25 I ALC 25 1_555 C N DGL 26 I DGL 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? # _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_ _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 5GDS _atom_sites.fract_transf_matrix[1][1] 0.013908 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002628 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013736 _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] 0.013884 _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 H 1 400 400 NAG NAG . E 5 HOH L 1 436 436 HOH HOH . E 5 HOH L 2 446 446 HOH HOH . E 5 HOH L 3 449 449 HOH HOH . E 5 HOH L 4 451 451 HOH HOH . E 5 HOH L 5 456 456 HOH HOH . E 5 HOH L 6 484 484 HOH HOH . E 5 HOH L 7 505 505 HOH HOH . E 5 HOH L 8 517 517 HOH HOH . E 5 HOH L 9 520 520 HOH HOH . E 5 HOH L 10 528 528 HOH HOH . F 5 HOH H 1 401 401 HOH HOH . F 5 HOH H 2 402 402 HOH HOH . F 5 HOH H 3 403 403 HOH HOH . F 5 HOH H 4 404 404 HOH HOH . F 5 HOH H 5 405 405 HOH HOH . F 5 HOH H 6 406 406 HOH HOH . F 5 HOH H 7 407 407 HOH HOH . F 5 HOH H 8 408 408 HOH HOH . F 5 HOH H 9 409 409 HOH HOH . F 5 HOH H 10 410 410 HOH HOH . F 5 HOH H 11 411 411 HOH HOH . F 5 HOH H 12 412 412 HOH HOH . F 5 HOH H 13 413 413 HOH HOH . F 5 HOH H 14 414 414 HOH HOH . F 5 HOH H 15 415 415 HOH HOH . F 5 HOH H 16 416 416 HOH HOH . F 5 HOH H 17 417 417 HOH HOH . F 5 HOH H 18 418 418 HOH HOH . F 5 HOH H 19 419 419 HOH HOH . F 5 HOH H 20 420 420 HOH HOH . F 5 HOH H 21 421 421 HOH HOH . F 5 HOH H 22 422 422 HOH HOH . F 5 HOH H 23 423 423 HOH HOH . F 5 HOH H 24 424 424 HOH HOH . F 5 HOH H 25 425 425 HOH HOH . F 5 HOH H 26 426 426 HOH HOH . F 5 HOH H 27 427 427 HOH HOH . F 5 HOH H 28 428 428 HOH HOH . F 5 HOH H 29 429 429 HOH HOH . F 5 HOH H 30 430 430 HOH HOH . F 5 HOH H 31 431 431 HOH HOH . F 5 HOH H 32 432 432 HOH HOH . F 5 HOH H 33 433 433 HOH HOH . F 5 HOH H 34 434 434 HOH HOH . F 5 HOH H 35 435 435 HOH HOH . F 5 HOH H 36 437 437 HOH HOH . F 5 HOH H 37 438 438 HOH HOH . F 5 HOH H 38 439 439 HOH HOH . F 5 HOH H 39 440 440 HOH HOH . F 5 HOH H 40 441 441 HOH HOH . F 5 HOH H 41 442 442 HOH HOH . F 5 HOH H 42 443 443 HOH HOH . F 5 HOH H 43 444 444 HOH HOH . F 5 HOH H 44 445 445 HOH HOH . F 5 HOH H 45 447 447 HOH HOH . F 5 HOH H 46 448 448 HOH HOH . F 5 HOH H 47 450 450 HOH HOH . F 5 HOH H 48 452 452 HOH HOH . F 5 HOH H 49 453 453 HOH HOH . F 5 HOH H 50 454 454 HOH HOH . F 5 HOH H 51 455 455 HOH HOH . F 5 HOH H 52 457 457 HOH HOH . F 5 HOH H 53 458 458 HOH HOH . F 5 HOH H 54 459 459 HOH HOH . F 5 HOH H 55 460 460 HOH HOH . F 5 HOH H 56 461 461 HOH HOH . F 5 HOH H 57 462 462 HOH HOH . F 5 HOH H 58 463 463 HOH HOH . F 5 HOH H 59 464 464 HOH HOH . F 5 HOH H 60 465 465 HOH HOH . F 5 HOH H 61 466 466 HOH HOH . F 5 HOH H 62 467 467 HOH HOH . F 5 HOH H 63 468 468 HOH HOH . F 5 HOH H 64 469 469 HOH HOH . F 5 HOH H 65 470 470 HOH HOH . F 5 HOH H 66 471 471 HOH HOH . F 5 HOH H 67 472 472 HOH HOH . F 5 HOH H 68 473 473 HOH HOH . F 5 HOH H 69 474 474 HOH HOH . F 5 HOH H 70 475 475 HOH HOH . F 5 HOH H 71 476 476 HOH HOH . F 5 HOH H 72 477 477 HOH HOH . F 5 HOH H 73 478 478 HOH HOH . F 5 HOH H 74 479 479 HOH HOH . F 5 HOH H 75 480 480 HOH HOH . F 5 HOH H 76 481 481 HOH HOH . F 5 HOH H 77 482 482 HOH HOH . F 5 HOH H 78 483 483 HOH HOH . F 5 HOH H 79 485 485 HOH HOH . F 5 HOH H 80 486 486 HOH HOH . F 5 HOH H 81 487 487 HOH HOH . F 5 HOH H 82 488 488 HOH HOH . F 5 HOH H 83 489 489 HOH HOH . F 5 HOH H 84 490 490 HOH HOH . F 5 HOH H 85 491 491 HOH HOH . F 5 HOH H 86 493 493 HOH HOH . F 5 HOH H 87 495 495 HOH HOH . F 5 HOH H 88 496 496 HOH HOH . F 5 HOH H 89 497 497 HOH HOH . F 5 HOH H 90 498 498 HOH HOH . F 5 HOH H 91 499 499 HOH HOH . F 5 HOH H 92 500 500 HOH HOH . F 5 HOH H 93 501 501 HOH HOH . F 5 HOH H 94 502 502 HOH HOH . F 5 HOH H 95 503 503 HOH HOH . F 5 HOH H 96 504 504 HOH HOH . F 5 HOH H 97 506 506 HOH HOH . F 5 HOH H 98 507 507 HOH HOH . F 5 HOH H 99 508 508 HOH HOH . F 5 HOH H 100 509 509 HOH HOH . F 5 HOH H 101 510 510 HOH HOH . F 5 HOH H 102 511 511 HOH HOH . F 5 HOH H 103 512 512 HOH HOH . F 5 HOH H 104 513 513 HOH HOH . F 5 HOH H 105 515 515 HOH HOH . F 5 HOH H 106 516 516 HOH HOH . F 5 HOH H 107 518 518 HOH HOH . F 5 HOH H 108 519 519 HOH HOH . F 5 HOH H 109 521 521 HOH HOH . F 5 HOH H 110 522 522 HOH HOH . F 5 HOH H 111 523 523 HOH HOH . F 5 HOH H 112 524 524 HOH HOH . F 5 HOH H 113 525 525 HOH HOH . F 5 HOH H 114 526 526 HOH HOH . F 5 HOH H 115 529 529 HOH HOH . F 5 HOH H 116 530 530 HOH HOH . F 5 HOH H 117 531 531 HOH HOH . F 5 HOH H 118 532 532 HOH HOH . F 5 HOH H 119 533 533 HOH HOH . F 5 HOH H 120 534 534 HOH HOH . G 5 HOH I 1 494 494 HOH HOH . G 5 HOH I 2 514 514 HOH HOH . G 5 HOH I 3 527 527 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 31.987 -8.26 10.862 0 55 ? C1 NAG 400 H 1 HETATM 2 C C2 NAG . . . D 4 33.051 -8.574 11.874 0 55 ? C2 NAG 400 H 1 HETATM 3 C C3 NAG . . . D 4 34.425 -7.954 11.704 0 55 ? C3 NAG 400 H 1 HETATM 4 C C4 NAG . . . D 4 34.644 -7.408 10.319 0 55 ? C4 NAG 400 H 1 HETATM 5 C C5 NAG . . . D 4 33.46 -7.223 9.342 0 55 ? C5 NAG 400 H 1 HETATM 6 C C6 NAG . . . D 4 33.758 -6.574 7.993 0 55 ? C6 NAG 400 H 1 HETATM 7 C C7 NAG . . . D 4 33.411 -10.523 13.568 0 55 ? C7 NAG 400 H 1 HETATM 8 C C8 NAG . . . D 4 33.428 -11.772 12.709 0 55 ? C8 NAG 400 H 1 HETATM 9 N N2 NAG . . . D 4 32.686 -9.488 13.012 0 55 ? N2 NAG 400 H 1 HETATM 10 O O3 NAG . . . D 4 35.591 -8.494 12.375 0 55 ? O3 NAG 400 H 1 HETATM 11 O O4 NAG . . . D 4 35.934 -6.79 9.994 0 55 ? O4 NAG 400 H 1 HETATM 12 O O5 NAG . . . D 4 32.424 -8.192 9.495 0 55 ? O5 NAG 400 H 1 HETATM 13 O O6 NAG . . . D 4 32.772 -6.344 7.026 0 55 ? O6 NAG 400 H 1 HETATM 14 O O7 NAG . . . D 4 33.006 -10.762 14.706 0 55 ? O7 NAG 400 H 1 # _model_server_stats.io_time_ms 47 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 326 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 14 #