data_6RYM # _model_server_result.job_id q7NWZGMe0ndLzm5-btSN8A _model_server_result.datetime_utc '2024-11-09 02:24:13' _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 6rym # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":404}' # _entry.id 6RYM # _exptl.entry_id 6RYM _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 90 _cell.angle_gamma 90 _cell.entry_id 6RYM _cell.length_a 50.225 _cell.length_b 50.225 _cell.length_c 51.925 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6RYM _symmetry.cell_setting ? _symmetry.Int_Tables_number 78 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 4 _struct_asym.id E _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 32 A CYS 255 1_555 A SG CYS 126 A CYS 349 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 A SG CYS 104 A CYS 327 1_555 A SG CYS 118 A CYS 341 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? metalc ? metalc1 A OD1 ASP 68 A ASP 291 1_555 C CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.662 ? metalc ? metalc2 A OD2 ASP 68 A ASP 291 1_555 C CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? metalc ? metalc3 A OE1 GLU 72 A GLU 295 1_555 C CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.567 ? metalc ? metalc4 A OE2 GLU 72 A GLU 295 1_555 C CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.565 ? metalc ? metalc5 A OE1 GLU 92 A GLU 315 1_555 B CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.62 ? metalc ? metalc6 A OD1 ASN 94 A ASN 317 1_555 B CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.435 ? metalc ? metalc7 A OD1 ASN 95 A ASN 318 1_555 C CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.652 ? metalc ? metalc8 A OE1 GLU 102 A GLU 325 1_555 B CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.393 ? metalc ? metalc9 A O GLU 102 A GLU 325 1_555 C CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.642 ? metalc ? metalc10 A OD1 ASN 103 A ASN 326 1_555 C CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.793 ? metalc ? metalc11 A OD1 ASN 114 A ASN 337 1_555 B CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? metalc ? metalc12 A O ASP 115 A ASP 338 1_555 B CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.479 ? metalc ? metalc13 A OD1 ASP 115 A ASP 338 1_555 B CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? metalc ? metalc14 B CA CA . A CA 401 1_555 D O3 NDG . A NDG 403 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.76 ? metalc ? metalc15 B CA CA . A CA 401 1_555 D O4 NDG . A NDG 403 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.517 ? metalc ? metalc16 B CA CA . A CA 401 1_555 E O3 NAG . A NAG 404 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.409 ? metalc ? metalc17 B CA CA . A CA 401 1_555 E O4 NAG . A NAG 404 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.368 ? metalc ? metalc18 C CA CA . A CA 402 1_555 F O HOH . A HOH 528 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? # _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_ _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 216 n n C1 O1 NAG sing 217 n n C1 O5 NAG sing 218 n n C1 H1 NAG sing 219 n n C2 C3 NAG sing 220 n n C2 N2 NAG sing 221 n n C2 H2 NAG sing 222 n n C3 C4 NAG sing 223 n n C3 O3 NAG sing 224 n n C3 H3 NAG sing 225 n n C4 C5 NAG sing 226 n n C4 O4 NAG sing 227 n n C4 H4 NAG sing 228 n n C5 C6 NAG sing 229 n n C5 O5 NAG sing 230 n n C5 H5 NAG sing 231 n n C6 O6 NAG sing 232 n n C6 H61 NAG sing 233 n n C6 H62 NAG sing 234 n n C7 C8 NAG sing 235 n n C7 N2 NAG sing 236 n n C7 O7 NAG doub 237 n n C8 H81 NAG sing 238 n n C8 H82 NAG sing 239 n n C8 H83 NAG sing 240 n n N2 HN2 NAG sing 241 n n O1 HO1 NAG sing 242 n n O3 HO3 NAG sing 243 n n O4 HO4 NAG sing 244 n n O6 HO6 NAG sing 245 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 6RYM _atom_sites.fract_transf_matrix[1][1] 0.01991 _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] 0.01991 _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] 0.019259 _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 B 2 CA A 1 401 401 CA CA . C 2 CA A 1 402 402 CA CA . D 3 NDG A 1 403 403 NDG NG3 . E 4 NAG A 1 404 403 NAG NAG . F 5 HOH A 1 501 127 HOH HOH . F 5 HOH A 2 502 115 HOH HOH . F 5 HOH A 3 503 99 HOH HOH . F 5 HOH A 4 504 67 HOH HOH . F 5 HOH A 5 505 32 HOH HOH . F 5 HOH A 6 506 96 HOH HOH . F 5 HOH A 7 507 44 HOH HOH . F 5 HOH A 8 508 132 HOH HOH . F 5 HOH A 9 509 68 HOH HOH . F 5 HOH A 10 510 38 HOH HOH . F 5 HOH A 11 511 119 HOH HOH . F 5 HOH A 12 512 102 HOH HOH . F 5 HOH A 13 513 143 HOH HOH . F 5 HOH A 14 514 117 HOH HOH . F 5 HOH A 15 515 75 HOH HOH . F 5 HOH A 16 516 3 HOH HOH . F 5 HOH A 17 517 39 HOH HOH . F 5 HOH A 18 518 31 HOH HOH . F 5 HOH A 19 519 136 HOH HOH . F 5 HOH A 20 520 71 HOH HOH . F 5 HOH A 21 521 73 HOH HOH . F 5 HOH A 22 522 65 HOH HOH . F 5 HOH A 23 523 40 HOH HOH . F 5 HOH A 24 524 4 HOH HOH . F 5 HOH A 25 525 18 HOH HOH . F 5 HOH A 26 526 28 HOH HOH . F 5 HOH A 27 527 2 HOH HOH . F 5 HOH A 28 528 45 HOH HOH . F 5 HOH A 29 529 14 HOH HOH . F 5 HOH A 30 530 113 HOH HOH . F 5 HOH A 31 531 46 HOH HOH . F 5 HOH A 32 532 48 HOH HOH . F 5 HOH A 33 533 62 HOH HOH . F 5 HOH A 34 534 103 HOH HOH . F 5 HOH A 35 535 11 HOH HOH . F 5 HOH A 36 536 74 HOH HOH . F 5 HOH A 37 537 61 HOH HOH . F 5 HOH A 38 538 121 HOH HOH . F 5 HOH A 39 539 19 HOH HOH . F 5 HOH A 40 540 114 HOH HOH . F 5 HOH A 41 541 63 HOH HOH . F 5 HOH A 42 542 52 HOH HOH . F 5 HOH A 43 543 12 HOH HOH . F 5 HOH A 44 544 13 HOH HOH . F 5 HOH A 45 545 76 HOH HOH . F 5 HOH A 46 546 149 HOH HOH . F 5 HOH A 47 547 29 HOH HOH . F 5 HOH A 48 548 1 HOH HOH . F 5 HOH A 49 549 15 HOH HOH . F 5 HOH A 50 550 125 HOH HOH . F 5 HOH A 51 551 54 HOH HOH . F 5 HOH A 52 552 86 HOH HOH . F 5 HOH A 53 553 95 HOH HOH . F 5 HOH A 54 554 56 HOH HOH . F 5 HOH A 55 555 21 HOH HOH . F 5 HOH A 56 556 6 HOH HOH . F 5 HOH A 57 557 25 HOH HOH . F 5 HOH A 58 558 51 HOH HOH . F 5 HOH A 59 559 8 HOH HOH . F 5 HOH A 60 560 58 HOH HOH . F 5 HOH A 61 561 7 HOH HOH . F 5 HOH A 62 562 55 HOH HOH . F 5 HOH A 63 563 77 HOH HOH . F 5 HOH A 64 564 53 HOH HOH . F 5 HOH A 65 565 50 HOH HOH . F 5 HOH A 66 566 144 HOH HOH . F 5 HOH A 67 567 47 HOH HOH . F 5 HOH A 68 568 81 HOH HOH . F 5 HOH A 69 569 80 HOH HOH . F 5 HOH A 70 570 35 HOH HOH . F 5 HOH A 71 571 64 HOH HOH . F 5 HOH A 72 572 20 HOH HOH . F 5 HOH A 73 573 30 HOH HOH . F 5 HOH A 74 574 72 HOH HOH . F 5 HOH A 75 575 59 HOH HOH . F 5 HOH A 76 576 9 HOH HOH . F 5 HOH A 77 577 123 HOH HOH . F 5 HOH A 78 578 145 HOH HOH . F 5 HOH A 79 579 94 HOH HOH . F 5 HOH A 80 580 109 HOH HOH . F 5 HOH A 81 581 41 HOH HOH . F 5 HOH A 82 582 79 HOH HOH . F 5 HOH A 83 583 60 HOH HOH . F 5 HOH A 84 584 122 HOH HOH . F 5 HOH A 85 585 120 HOH HOH . F 5 HOH A 86 586 146 HOH HOH . F 5 HOH A 87 587 22 HOH HOH . F 5 HOH A 88 588 17 HOH HOH . F 5 HOH A 89 589 66 HOH HOH . F 5 HOH A 90 590 43 HOH HOH . F 5 HOH A 91 591 24 HOH HOH . F 5 HOH A 92 592 148 HOH HOH . F 5 HOH A 93 593 69 HOH HOH . F 5 HOH A 94 594 97 HOH HOH . F 5 HOH A 95 595 34 HOH HOH . F 5 HOH A 96 596 37 HOH HOH . F 5 HOH A 97 597 10 HOH HOH . F 5 HOH A 98 598 116 HOH HOH . F 5 HOH A 99 599 57 HOH HOH . F 5 HOH A 100 600 16 HOH HOH . F 5 HOH A 101 601 78 HOH HOH . F 5 HOH A 102 602 107 HOH HOH . F 5 HOH A 103 603 42 HOH HOH . F 5 HOH A 104 604 36 HOH HOH . F 5 HOH A 105 605 98 HOH HOH . F 5 HOH A 106 606 70 HOH HOH . F 5 HOH A 107 607 124 HOH HOH . F 5 HOH A 108 608 26 HOH HOH . F 5 HOH A 109 609 27 HOH HOH . F 5 HOH A 110 610 5 HOH HOH . F 5 HOH A 111 611 23 HOH HOH . F 5 HOH A 112 612 139 HOH HOH . F 5 HOH A 113 613 49 HOH HOH . F 5 HOH A 114 614 106 HOH HOH . F 5 HOH A 115 615 141 HOH HOH . F 5 HOH A 116 616 33 HOH HOH . F 5 HOH A 117 617 118 HOH HOH . F 5 HOH A 118 618 105 HOH HOH . F 5 HOH A 119 619 128 HOH HOH . F 5 HOH A 120 620 92 HOH HOH . F 5 HOH A 121 621 91 HOH HOH . F 5 HOH A 122 622 147 HOH HOH . F 5 HOH A 123 623 100 HOH HOH . F 5 HOH A 124 624 111 HOH HOH . F 5 HOH A 125 625 88 HOH HOH . F 5 HOH A 126 626 138 HOH HOH . F 5 HOH A 127 627 137 HOH HOH . F 5 HOH A 128 628 129 HOH HOH . F 5 HOH A 129 629 101 HOH HOH . F 5 HOH A 130 630 134 HOH HOH . F 5 HOH A 131 631 89 HOH HOH . F 5 HOH A 132 632 85 HOH HOH . F 5 HOH A 133 633 104 HOH HOH . F 5 HOH A 134 634 108 HOH HOH . F 5 HOH A 135 635 130 HOH HOH . F 5 HOH A 136 636 110 HOH HOH . F 5 HOH A 137 637 140 HOH HOH . F 5 HOH A 138 638 87 HOH HOH . F 5 HOH A 139 639 126 HOH HOH . F 5 HOH A 140 640 131 HOH HOH . F 5 HOH A 141 641 93 HOH HOH . F 5 HOH A 142 642 82 HOH HOH . F 5 HOH A 143 643 142 HOH HOH . F 5 HOH A 144 644 84 HOH HOH . F 5 HOH A 145 645 83 HOH HOH . F 5 HOH A 146 646 90 HOH HOH . F 5 HOH A 147 647 112 HOH HOH . F 5 HOH A 148 648 135 HOH HOH . F 5 HOH A 149 649 133 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 . B . E 4 50.36 22.201 -9.559 0.5 16.63 ? C1 NAG 404 A 1 HETATM 2 C C2 NAG . B . E 4 49.255 22.509 -8.556 0.5 15.53 ? C2 NAG 404 A 1 HETATM 3 C C3 NAG . B . E 4 47.935 22.239 -9.257 0.5 14.84 ? C3 NAG 404 A 1 HETATM 4 C C4 NAG . B . E 4 47.849 23.107 -10.502 0.5 15.15 ? C4 NAG 404 A 1 HETATM 5 C C5 NAG . B . E 4 49.038 22.855 -11.431 0.5 16.39 ? C5 NAG 404 A 1 HETATM 6 C C6 NAG . B . E 4 49.057 23.784 -12.644 0.5 17 ? C6 NAG 404 A 1 HETATM 7 C C7 NAG . B . E 4 49.506 22.235 -6.13 0.5 17.03 ? C7 NAG 404 A 1 HETATM 8 C C8 NAG . B . E 4 49.773 21.272 -5.006 0.5 17.28 ? C8 NAG 404 A 1 HETATM 9 N N2 NAG . B . E 4 49.438 21.697 -7.354 0.5 16.11 ? N2 NAG 404 A 1 HETATM 10 O O1 NAG . B . E 4 51.625 22.419 -8.924 0.5 17.79 ? O1 NAG 404 A 1 HETATM 11 O O3 NAG . B . E 4 46.808 22.562 -8.434 0.5 13.65 ? O3 NAG 404 A 1 HETATM 12 O O4 NAG . B . E 4 46.596 22.821 -11.104 0.5 13.26 ? O4 NAG 404 A 1 HETATM 13 O O5 NAG . B . E 4 50.229 23.076 -10.68 0.5 16.62 ? O5 NAG 404 A 1 HETATM 14 O O6 NAG . B . E 4 50.257 23.588 -13.423 0.5 18.49 ? O6 NAG 404 A 1 HETATM 15 O O7 NAG . B . E 4 49.383 23.426 -5.925 0.5 15.92 ? O7 NAG 404 A 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 15 #