data_8VQL # _model_server_result.job_id tRkCyyFtrORLJHGYc1RVVA _model_server_result.datetime_utc '2024-10-17 19:31:33' _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 8vql # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":403}' # _entry.id 8VQL # _exptl.entry_id 8VQL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 3 _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 8VQL _cell.length_a 164.269 _cell.length_b 164.269 _cell.length_c 164.269 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8VQL _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_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 _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' 5_555 z,x,y 0 0 1 1 0 0 0 1 0 0 0 0 3 'crystal symmetry operation' 9_555 y,z,x 0 1 0 0 0 1 1 0 0 0 0 0 # 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 # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 3 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order 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 D 1 NAG D 1 NAG 3 n C 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 7 A CYS 14 1_555 B SG CYS 137 B CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf2 A SG CYS 45 A CYS 52 1_555 A SG CYS 277 A CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf3 A SG CYS 58 A CYS 64 1_555 A SG CYS 70 A CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf4 A SG CYS 93 A CYS 97 1_555 A SG CYS 138 A CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf5 A SG CYS 281 A CYS 281 1_555 A SG CYS 305 A CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf6 B SG CYS 144 B CYS 144 1_555 B SG CYS 148 B CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? covale ? covale1 A ND2 ASN 14 A ASN 21 1_555 D C1 NAG . A NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale2 A ND2 ASN 26 A ASN 33 1_555 F C1 NAG . A NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale3 A ND2 ASN 289 A ASN 289 1_555 E C1 NAG . A NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale4 B ND2 ASN 154 B ASN 154 1_555 C C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale5 C O4 NAG . D NAG 1 1_555 C C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? # _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 301 n n C1 O1 NAG sing 302 n n C1 O5 NAG sing 303 n n C1 H1 NAG sing 304 n n C2 C3 NAG sing 305 n n C2 N2 NAG sing 306 n n C2 H2 NAG sing 307 n n C3 C4 NAG sing 308 n n C3 O3 NAG sing 309 n n C3 H3 NAG sing 310 n n C4 C5 NAG sing 311 n n C4 O4 NAG sing 312 n n C4 H4 NAG sing 313 n n C5 C6 NAG sing 314 n n C5 O5 NAG sing 315 n n C5 H5 NAG sing 316 n n C6 O6 NAG sing 317 n n C6 H61 NAG sing 318 n n C6 H62 NAG sing 319 n n C7 C8 NAG sing 320 n n C7 N2 NAG sing 321 n n C7 O7 NAG doub 322 n n C8 H81 NAG sing 323 n n C8 H82 NAG sing 324 n n C8 H83 NAG sing 325 n n N2 HN2 NAG sing 326 n n O1 HO1 NAG sing 327 n n O3 HO3 NAG sing 328 n n O4 HO4 NAG sing 329 n n O6 HO6 NAG sing 330 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 8VQL _atom_sites.fract_transf_matrix[1][1] 0.006088 _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] 0.006088 _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] 0.006088 _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 1 401 326 NAG NAG . E 4 NAG A 1 402 329 NAG NAG . F 4 NAG A 1 403 330 NAG NAG . G 5 A1ADD B 1 301 201 A1ADD Y23 . H 6 HOH A 1 501 147 HOH HOH . H 6 HOH A 2 502 124 HOH HOH . H 6 HOH A 3 503 15 HOH HOH . H 6 HOH A 4 504 127 HOH HOH . H 6 HOH A 5 505 96 HOH HOH . H 6 HOH A 6 506 17 HOH HOH . H 6 HOH A 7 507 41 HOH HOH . H 6 HOH A 8 508 31 HOH HOH . H 6 HOH A 9 509 151 HOH HOH . H 6 HOH A 10 510 144 HOH HOH . H 6 HOH A 11 511 22 HOH HOH . H 6 HOH A 12 512 36 HOH HOH . H 6 HOH A 13 513 52 HOH HOH . H 6 HOH A 14 514 69 HOH HOH . H 6 HOH A 15 515 78 HOH HOH . H 6 HOH A 16 516 109 HOH HOH . H 6 HOH A 17 517 25 HOH HOH . H 6 HOH A 18 518 12 HOH HOH . H 6 HOH A 19 519 65 HOH HOH . H 6 HOH A 20 520 110 HOH HOH . H 6 HOH A 21 521 126 HOH HOH . H 6 HOH A 22 522 46 HOH HOH . H 6 HOH A 23 523 159 HOH HOH . H 6 HOH A 24 524 60 HOH HOH . H 6 HOH A 25 525 6 HOH HOH . H 6 HOH A 26 526 33 HOH HOH . H 6 HOH A 27 527 107 HOH HOH . H 6 HOH A 28 528 5 HOH HOH . H 6 HOH A 29 529 77 HOH HOH . H 6 HOH A 30 530 120 HOH HOH . H 6 HOH A 31 531 133 HOH HOH . H 6 HOH A 32 532 11 HOH HOH . H 6 HOH A 33 533 75 HOH HOH . H 6 HOH A 34 534 104 HOH HOH . H 6 HOH A 35 535 37 HOH HOH . H 6 HOH A 36 536 57 HOH HOH . H 6 HOH A 37 537 135 HOH HOH . H 6 HOH A 38 538 19 HOH HOH . H 6 HOH A 39 539 39 HOH HOH . H 6 HOH A 40 540 16 HOH HOH . H 6 HOH A 41 541 146 HOH HOH . H 6 HOH A 42 542 3 HOH HOH . H 6 HOH A 43 543 72 HOH HOH . H 6 HOH A 44 544 128 HOH HOH . H 6 HOH A 45 545 83 HOH HOH . H 6 HOH A 46 546 23 HOH HOH . H 6 HOH A 47 547 45 HOH HOH . H 6 HOH A 48 548 42 HOH HOH . H 6 HOH A 49 549 111 HOH HOH . H 6 HOH A 50 550 13 HOH HOH . H 6 HOH A 51 551 1 HOH HOH . H 6 HOH A 52 552 158 HOH HOH . H 6 HOH A 53 553 132 HOH HOH . H 6 HOH A 54 554 43 HOH HOH . H 6 HOH A 55 555 30 HOH HOH . H 6 HOH A 56 556 14 HOH HOH . H 6 HOH A 57 557 53 HOH HOH . H 6 HOH A 58 558 49 HOH HOH . H 6 HOH A 59 559 63 HOH HOH . H 6 HOH A 60 560 138 HOH HOH . H 6 HOH A 61 561 142 HOH HOH . H 6 HOH A 62 562 90 HOH HOH . H 6 HOH A 63 563 59 HOH HOH . H 6 HOH A 64 564 71 HOH HOH . H 6 HOH A 65 565 105 HOH HOH . H 6 HOH A 66 566 154 HOH HOH . H 6 HOH A 67 567 87 HOH HOH . H 6 HOH A 68 568 44 HOH HOH . H 6 HOH A 69 569 160 HOH HOH . H 6 HOH A 70 570 40 HOH HOH . H 6 HOH A 71 571 61 HOH HOH . H 6 HOH A 72 572 140 HOH HOH . H 6 HOH A 73 573 35 HOH HOH . H 6 HOH A 74 574 8 HOH HOH . H 6 HOH A 75 575 113 HOH HOH . H 6 HOH A 76 576 4 HOH HOH . H 6 HOH A 77 577 2 HOH HOH . H 6 HOH A 78 578 76 HOH HOH . H 6 HOH A 79 579 84 HOH HOH . H 6 HOH A 80 580 112 HOH HOH . H 6 HOH A 81 581 34 HOH HOH . H 6 HOH A 82 582 161 HOH HOH . H 6 HOH A 83 583 92 HOH HOH . H 6 HOH A 84 584 20 HOH HOH . H 6 HOH A 85 585 95 HOH HOH . H 6 HOH A 86 586 55 HOH HOH . H 6 HOH A 87 587 62 HOH HOH . H 6 HOH A 88 588 82 HOH HOH . H 6 HOH A 89 589 136 HOH HOH . H 6 HOH A 90 590 48 HOH HOH . H 6 HOH A 91 591 7 HOH HOH . H 6 HOH A 92 592 29 HOH HOH . H 6 HOH A 93 593 47 HOH HOH . H 6 HOH A 94 594 70 HOH HOH . H 6 HOH A 95 595 85 HOH HOH . H 6 HOH A 96 596 114 HOH HOH . H 6 HOH A 97 597 73 HOH HOH . H 6 HOH A 98 598 116 HOH HOH . H 6 HOH A 99 599 18 HOH HOH . H 6 HOH A 100 600 51 HOH HOH . H 6 HOH A 101 601 91 HOH HOH . H 6 HOH A 102 602 26 HOH HOH . H 6 HOH A 103 603 79 HOH HOH . H 6 HOH A 104 604 98 HOH HOH . H 6 HOH A 105 605 102 HOH HOH . H 6 HOH A 106 606 134 HOH HOH . H 6 HOH A 107 607 81 HOH HOH . H 6 HOH A 108 608 24 HOH HOH . H 6 HOH A 109 609 156 HOH HOH . H 6 HOH A 110 610 129 HOH HOH . H 6 HOH A 111 611 123 HOH HOH . H 6 HOH A 112 612 93 HOH HOH . H 6 HOH A 113 613 100 HOH HOH . H 6 HOH A 114 614 149 HOH HOH . H 6 HOH A 115 615 145 HOH HOH . H 6 HOH A 116 616 148 HOH HOH . H 6 HOH A 117 617 130 HOH HOH . H 6 HOH A 118 618 115 HOH HOH . H 6 HOH A 119 619 101 HOH HOH . H 6 HOH A 120 620 108 HOH HOH . H 6 HOH A 121 621 97 HOH HOH . H 6 HOH A 122 622 94 HOH HOH . H 6 HOH A 123 623 139 HOH HOH . H 6 HOH A 124 624 150 HOH HOH . I 6 HOH B 1 401 10 HOH HOH . I 6 HOH B 2 402 118 HOH HOH . I 6 HOH B 3 403 121 HOH HOH . I 6 HOH B 4 404 28 HOH HOH . I 6 HOH B 5 405 67 HOH HOH . I 6 HOH B 6 406 32 HOH HOH . I 6 HOH B 7 407 54 HOH HOH . I 6 HOH B 8 408 21 HOH HOH . I 6 HOH B 9 409 9 HOH HOH . I 6 HOH B 10 410 89 HOH HOH . I 6 HOH B 11 411 58 HOH HOH . I 6 HOH B 12 412 56 HOH HOH . I 6 HOH B 13 413 88 HOH HOH . I 6 HOH B 14 414 99 HOH HOH . I 6 HOH B 15 415 119 HOH HOH . I 6 HOH B 16 416 68 HOH HOH . I 6 HOH B 17 417 27 HOH HOH . I 6 HOH B 18 418 106 HOH HOH . I 6 HOH B 19 419 153 HOH HOH . I 6 HOH B 20 420 66 HOH HOH . I 6 HOH B 21 421 38 HOH HOH . I 6 HOH B 22 422 157 HOH HOH . I 6 HOH B 23 423 141 HOH HOH . I 6 HOH B 24 424 137 HOH HOH . I 6 HOH B 25 425 143 HOH HOH . I 6 HOH B 26 426 64 HOH HOH . I 6 HOH B 27 427 80 HOH HOH . I 6 HOH B 28 428 131 HOH HOH . I 6 HOH B 29 429 117 HOH HOH . I 6 HOH B 30 430 122 HOH HOH . I 6 HOH B 31 431 50 HOH HOH . I 6 HOH B 32 432 125 HOH HOH . I 6 HOH B 33 433 152 HOH HOH . I 6 HOH B 34 434 155 HOH HOH . I 6 HOH B 35 435 103 HOH HOH . I 6 HOH B 36 436 74 HOH HOH . I 6 HOH B 37 437 86 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 . . . F 4 -23.286 1.591 10.233 1 97.1 ? C1 NAG 403 A 1 HETATM 2 C C2 NAG . . . F 4 -24.288 0.888 11.154 1 98.44 ? C2 NAG 403 A 1 HETATM 3 C C3 NAG . . . F 4 -25.407 1.85 11.549 1 94.96 ? C3 NAG 403 A 1 HETATM 4 C C4 NAG . . . F 4 -24.825 3.117 12.162 1 101.28 ? C4 NAG 403 A 1 HETATM 5 C C5 NAG . . . F 4 -23.805 3.743 11.211 1 95.82 ? C5 NAG 403 A 1 HETATM 6 C C6 NAG . . . F 4 -23.1 4.946 11.8 1 89.65 ? C6 NAG 403 A 1 HETATM 7 C C7 NAG . . . F 4 -24.648 -1.542 10.998 1 97.51 ? C7 NAG 403 A 1 HETATM 8 C C8 NAG . . . F 4 -23.835 -1.651 12.253 1 87.6 ? C8 NAG 403 A 1 HETATM 9 N N2 NAG . . . F 4 -24.833 -0.304 10.522 1 105.1 ? N2 NAG 403 A 1 HETATM 10 O O3 NAG . . . F 4 -26.276 1.217 12.482 1 102.7 ? O3 NAG 403 A 1 HETATM 11 O O4 NAG . . . F 4 -25.864 4.052 12.432 1 94.73 ? O4 NAG 403 A 1 HETATM 12 O O5 NAG . . . F 4 -22.787 2.785 10.879 1 98.26 ? O5 NAG 403 A 1 HETATM 13 O O6 NAG . . . F 4 -22.341 4.609 12.953 1 95.86 ? O6 NAG 403 A 1 HETATM 14 O O7 NAG . . . F 4 -25.119 -2.53 10.44 1 92.14 ? O7 NAG 403 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 297 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #