data_5KY9 # _model_server_result.job_id UYnhRYOmBeQr5hthr6DiNA _model_server_result.datetime_utc '2024-11-23 01:29:17' _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 5ky9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 5KY9 # _exptl.entry_id 5KY9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 3 _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 90 _cell.angle_gamma 90 _cell.entry_id 5KY9 _cell.length_a 52.1 _cell.length_b 66.52 _cell.length_c 109.96 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5KY9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 3 _struct_asym.id C _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 14 A CYS 43 1_555 A SG CYS 16 A CYS 45 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf2 A SG CYS 102 A CYS 131 1_555 A SG CYS 116 A CYS 145 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf3 A SG CYS 225 A CYS 254 1_555 A SG CYS 259 A CYS 288 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? disulf ? disulf4 A SG CYS 243 A CYS 272 1_555 A SG CYS 330 A CYS 359 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf5 B SG CYS 5 B CYS 456 1_555 B SG CYS 16 B CYS 467 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf6 B SG CYS 10 B CYS 461 1_555 B SG CYS 25 B CYS 476 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf7 B SG CYS 27 B CYS 478 1_555 B SG CYS 36 B CYS 487 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? covale ? covale1 A ND2 ASN 38 A ASN 67 1_555 C C1 NAG . A NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? # _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 282 n n C1 O1 NAG sing 283 n n C1 O5 NAG sing 284 n n C1 H1 NAG sing 285 n n C2 C3 NAG sing 286 n n C2 N2 NAG sing 287 n n C2 H2 NAG sing 288 n n C3 C4 NAG sing 289 n n C3 O3 NAG sing 290 n n C3 H3 NAG sing 291 n n C4 C5 NAG sing 292 n n C4 O4 NAG sing 293 n n C4 H4 NAG sing 294 n n C5 C6 NAG sing 295 n n C5 O5 NAG sing 296 n n C5 H5 NAG sing 297 n n C6 O6 NAG sing 298 n n C6 H61 NAG sing 299 n n C6 H62 NAG sing 300 n n C7 C8 NAG sing 301 n n C7 N2 NAG sing 302 n n C7 O7 NAG doub 303 n n C8 H81 NAG sing 304 n n C8 H82 NAG sing 305 n n C8 H83 NAG sing 306 n n N2 HN2 NAG sing 307 n n O1 HO1 NAG sing 308 n n O3 HO3 NAG sing 309 n n O4 HO4 NAG sing 310 n n O6 HO6 NAG sing 311 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 5KY9 _atom_sites.fract_transf_matrix[1][1] 0.019194 _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] 0.015033 _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] 0.009094 _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 NAG A 1 401 401 NAG NAG . D 4 GDP A 1 402 1 GDP GDP . E 5 HOH A 1 501 149 HOH HOH . E 5 HOH A 2 502 94 HOH HOH . E 5 HOH A 3 503 17 HOH HOH . E 5 HOH A 4 504 152 HOH HOH . E 5 HOH A 5 505 57 HOH HOH . E 5 HOH A 6 506 110 HOH HOH . E 5 HOH A 7 507 54 HOH HOH . E 5 HOH A 8 508 9 HOH HOH . E 5 HOH A 9 509 97 HOH HOH . E 5 HOH A 10 510 58 HOH HOH . E 5 HOH A 11 511 103 HOH HOH . E 5 HOH A 12 512 68 HOH HOH . E 5 HOH A 13 513 120 HOH HOH . E 5 HOH A 14 514 40 HOH HOH . E 5 HOH A 15 515 77 HOH HOH . E 5 HOH A 16 516 21 HOH HOH . E 5 HOH A 17 517 61 HOH HOH . E 5 HOH A 18 518 4 HOH HOH . E 5 HOH A 19 519 19 HOH HOH . E 5 HOH A 20 520 34 HOH HOH . E 5 HOH A 21 521 13 HOH HOH . E 5 HOH A 22 522 99 HOH HOH . E 5 HOH A 23 523 30 HOH HOH . E 5 HOH A 24 524 23 HOH HOH . E 5 HOH A 25 525 37 HOH HOH . E 5 HOH A 26 526 113 HOH HOH . E 5 HOH A 27 527 3 HOH HOH . E 5 HOH A 28 528 24 HOH HOH . E 5 HOH A 29 529 55 HOH HOH . E 5 HOH A 30 530 16 HOH HOH . E 5 HOH A 31 531 90 HOH HOH . E 5 HOH A 32 532 111 HOH HOH . E 5 HOH A 33 533 35 HOH HOH . E 5 HOH A 34 534 31 HOH HOH . E 5 HOH A 35 535 115 HOH HOH . E 5 HOH A 36 536 80 HOH HOH . E 5 HOH A 37 537 8 HOH HOH . E 5 HOH A 38 538 49 HOH HOH . E 5 HOH A 39 539 109 HOH HOH . E 5 HOH A 40 540 81 HOH HOH . E 5 HOH A 41 541 1 HOH HOH . E 5 HOH A 42 542 12 HOH HOH . E 5 HOH A 43 543 28 HOH HOH . E 5 HOH A 44 544 5 HOH HOH . E 5 HOH A 45 545 67 HOH HOH . E 5 HOH A 46 546 117 HOH HOH . E 5 HOH A 47 547 27 HOH HOH . E 5 HOH A 48 548 29 HOH HOH . E 5 HOH A 49 549 107 HOH HOH . E 5 HOH A 50 550 104 HOH HOH . E 5 HOH A 51 551 10 HOH HOH . E 5 HOH A 52 552 79 HOH HOH . E 5 HOH A 53 553 133 HOH HOH . E 5 HOH A 54 554 132 HOH HOH . E 5 HOH A 55 555 39 HOH HOH . E 5 HOH A 56 556 14 HOH HOH . E 5 HOH A 57 557 52 HOH HOH . E 5 HOH A 58 558 20 HOH HOH . E 5 HOH A 59 559 114 HOH HOH . E 5 HOH A 60 560 129 HOH HOH . E 5 HOH A 61 561 83 HOH HOH . E 5 HOH A 62 562 139 HOH HOH . E 5 HOH A 63 563 123 HOH HOH . E 5 HOH A 64 564 15 HOH HOH . E 5 HOH A 65 565 64 HOH HOH . E 5 HOH A 66 566 140 HOH HOH . E 5 HOH A 67 567 18 HOH HOH . E 5 HOH A 68 568 72 HOH HOH . E 5 HOH A 69 569 101 HOH HOH . E 5 HOH A 70 570 46 HOH HOH . E 5 HOH A 71 571 73 HOH HOH . E 5 HOH A 72 572 22 HOH HOH . E 5 HOH A 73 573 91 HOH HOH . E 5 HOH A 74 574 142 HOH HOH . E 5 HOH A 75 575 51 HOH HOH . E 5 HOH A 76 576 25 HOH HOH . E 5 HOH A 77 577 147 HOH HOH . E 5 HOH A 78 578 50 HOH HOH . E 5 HOH A 79 579 125 HOH HOH . E 5 HOH A 80 580 89 HOH HOH . E 5 HOH A 81 581 122 HOH HOH . E 5 HOH A 82 582 6 HOH HOH . E 5 HOH A 83 583 11 HOH HOH . E 5 HOH A 84 584 70 HOH HOH . E 5 HOH A 85 585 116 HOH HOH . E 5 HOH A 86 586 2 HOH HOH . E 5 HOH A 87 587 42 HOH HOH . E 5 HOH A 88 588 71 HOH HOH . E 5 HOH A 89 589 135 HOH HOH . E 5 HOH A 90 590 119 HOH HOH . E 5 HOH A 91 591 45 HOH HOH . E 5 HOH A 92 592 82 HOH HOH . E 5 HOH A 93 593 86 HOH HOH . E 5 HOH A 94 594 7 HOH HOH . E 5 HOH A 95 595 41 HOH HOH . E 5 HOH A 96 596 48 HOH HOH . E 5 HOH A 97 597 69 HOH HOH . E 5 HOH A 98 598 102 HOH HOH . E 5 HOH A 99 599 143 HOH HOH . E 5 HOH A 100 600 38 HOH HOH . E 5 HOH A 101 601 63 HOH HOH . E 5 HOH A 102 602 106 HOH HOH . E 5 HOH A 103 603 47 HOH HOH . E 5 HOH A 104 604 128 HOH HOH . E 5 HOH A 105 605 87 HOH HOH . E 5 HOH A 106 606 108 HOH HOH . E 5 HOH A 107 607 33 HOH HOH . E 5 HOH A 108 608 75 HOH HOH . E 5 HOH A 109 609 153 HOH HOH . E 5 HOH A 110 610 92 HOH HOH . E 5 HOH A 111 611 76 HOH HOH . E 5 HOH A 112 612 32 HOH HOH . E 5 HOH A 113 613 148 HOH HOH . E 5 HOH A 114 614 85 HOH HOH . E 5 HOH A 115 615 105 HOH HOH . E 5 HOH A 116 616 60 HOH HOH . E 5 HOH A 117 617 74 HOH HOH . E 5 HOH A 118 618 93 HOH HOH . E 5 HOH A 119 619 62 HOH HOH . E 5 HOH A 120 620 66 HOH HOH . E 5 HOH A 121 621 65 HOH HOH . E 5 HOH A 122 622 26 HOH HOH . E 5 HOH A 123 623 146 HOH HOH . E 5 HOH A 124 624 126 HOH HOH . E 5 HOH A 125 625 88 HOH HOH . E 5 HOH A 126 626 78 HOH HOH . E 5 HOH A 127 627 56 HOH HOH . E 5 HOH A 128 628 36 HOH HOH . E 5 HOH A 129 629 130 HOH HOH . E 5 HOH A 130 630 95 HOH HOH . E 5 HOH A 131 631 136 HOH HOH . E 5 HOH A 132 632 131 HOH HOH . E 5 HOH A 133 633 145 HOH HOH . E 5 HOH A 134 634 100 HOH HOH . E 5 HOH A 135 635 43 HOH HOH . E 5 HOH A 136 636 84 HOH HOH . E 5 HOH A 137 637 134 HOH HOH . E 5 HOH A 138 638 144 HOH HOH . E 5 HOH A 139 639 127 HOH HOH . E 5 HOH A 140 640 151 HOH HOH . E 5 HOH A 141 641 138 HOH HOH . E 5 HOH A 142 642 124 HOH HOH . E 5 HOH A 143 643 59 HOH HOH . E 5 HOH A 144 644 112 HOH HOH . E 5 HOH A 145 645 150 HOH HOH . E 5 HOH A 146 646 98 HOH HOH . E 5 HOH A 147 647 44 HOH HOH . E 5 HOH A 148 648 53 HOH HOH . F 5 HOH B 1 501 121 HOH HOH . F 5 HOH B 2 502 118 HOH HOH . F 5 HOH B 3 503 96 HOH HOH . F 5 HOH B 4 504 141 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 . . . C 3 24.811 45.677 35.517 1 30.21 ? C1 NAG 401 A 1 HETATM 2 C C2 NAG . . . C 3 25.869 46.297 36.44 1 36.8 ? C2 NAG 401 A 1 HETATM 3 C C3 NAG . . . C 3 25.804 45.675 37.826 1 40.23 ? C3 NAG 401 A 1 HETATM 4 C C4 NAG . . . C 3 24.389 45.745 38.376 1 37.95 ? C4 NAG 401 A 1 HETATM 5 C C5 NAG . . . C 3 23.391 45.156 37.379 1 37.48 ? C5 NAG 401 A 1 HETATM 6 C C6 NAG . . . C 3 21.96 45.377 37.811 1 40.22 ? C6 NAG 401 A 1 HETATM 7 C C7 NAG . . . C 3 27.834 47.037 35.16 1 42.44 ? C7 NAG 401 A 1 HETATM 8 C C8 NAG . . . C 3 29.19 46.652 34.663 1 40.4 ? C8 NAG 401 A 1 HETATM 9 N N2 NAG . . . C 3 27.19 46.108 35.876 1 39.92 ? N2 NAG 401 A 1 HETATM 10 O O3 NAG . . . C 3 26.691 46.392 38.68 1 39.82 ? O3 NAG 401 A 1 HETATM 11 O O4 NAG . . . C 3 24.293 45.028 39.601 1 39.23 ? O4 NAG 401 A 1 HETATM 12 O O5 NAG . . . C 3 23.535 45.8 36.101 1 34.4 ? O5 NAG 401 A 1 HETATM 13 O O6 NAG . . . C 3 21.048 44.544 37.103 1 41.89 ? O6 NAG 401 A 1 HETATM 14 O O7 NAG . . . C 3 27.343 48.135 34.922 1 42.16 ? O7 NAG 401 A 1 HETATM 15 H H1 NAG . . . C 3 25.015 44.732 35.383 1 36.25 ? H1 NAG 401 A 1 HETATM 16 H H2 NAG . . . C 3 25.692 47.253 36.522 1 44.15 ? H2 NAG 401 A 1 HETATM 17 H H3 NAG . . . C 3 26.086 44.742 37.776 1 48.28 ? H3 NAG 401 A 1 HETATM 18 H H4 NAG . . . C 3 24.159 46.68 38.537 1 45.54 ? H4 NAG 401 A 1 HETATM 19 H H5 NAG . . . C 3 23.557 44.199 37.281 1 44.97 ? H5 NAG 401 A 1 HETATM 20 H H61 NAG . . . C 3 21.885 45.187 38.766 1 48.27 ? H61 NAG 401 A 1 HETATM 21 H H62 NAG . . . C 3 21.723 46.31 37.655 1 48.27 ? H62 NAG 401 A 1 HETATM 22 H H81 NAG . . . C 3 29.115 45.868 34.087 1 48.48 ? H81 NAG 401 A 1 HETATM 23 H H82 NAG . . . C 3 29.768 46.445 35.422 1 48.48 ? H82 NAG 401 A 1 HETATM 24 H H83 NAG . . . C 3 29.573 47.393 34.155 1 48.48 ? H83 NAG 401 A 1 HETATM 25 H HN2 NAG . . . C 3 27.608 45.31 36.018 1 47.91 ? HN2 NAG 401 A 1 HETATM 26 H HO3 NAG . . . C 3 26.486 46.225 39.528 1 47.79 ? HO3 NAG 401 A 1 HETATM 27 H HO4 NAG . . . C 3 25.016 45.185 40.093 1 47.07 ? HO4 NAG 401 A 1 HETATM 28 H HO6 NAG . . . C 3 21.36 43.713 37.083 1 50.27 ? HO6 NAG 401 A 1 # _model_server_stats.io_time_ms 52 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 231 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #