data_4DW1 # _model_server_result.job_id 26v6GHa19L8Rl_IsUrNBPg _model_server_result.datetime_utc '2024-12-03 19:00:24' _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 4dw1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":507}' # _entry.id 4DW1 # _exptl.entry_id 4DW1 _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 120 _cell.entry_id 4DW1 _cell.length_a 128.791 _cell.length_b 128.791 _cell.length_c 252.074 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4DW1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # _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 1,2,3 # 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' 2_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 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 # _pdbx_entity_branch.entity_id 2 _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 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 2 4 3 MAN BMA C1 O1 . O3 HO3 . sing 4 ? 2 5 4 MAN MAN C1 O1 . O3 HO3 . sing 5 ? 2 6 3 MAN BMA C1 O1 . O6 HO6 . 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 2 n B NAG 1 B 1 NAG A 501 NAG 2 n B NAG 2 B 2 NAG A 502 NAG 2 n B BMA 3 B 3 BMA A 503 BMA 2 n B MAN 4 B 4 MAN A 505 MAN 2 n B MAN 5 B 5 MAN A 506 MAN 2 n B MAN 6 B 6 MAN A 504 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 94 A CYS 119 1_555 A SG CYS 143 A CYS 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? disulf ? disulf2 A SG CYS 104 A CYS 129 1_555 A SG CYS 127 A CYS 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf3 A SG CYS 110 A CYS 135 1_555 A SG CYS 137 A CYS 162 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf4 A SG CYS 195 A CYS 220 1_555 A SG CYS 205 A CYS 230 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? disulf ? disulf5 A SG CYS 239 A CYS 264 1_555 A SG CYS 248 A CYS 273 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? covale ? covale1 A ND2 ASN 88 A ASN 113 1_555 C C1 NAG . A NAG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.427 ? covale ? covale2 A ND2 ASN 188 A ASN 213 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale3 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.426 ? covale ? covale4 B O4 NAG . B NAG 2 1_555 B C1 BMA . B BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale5 B O3 BMA . B BMA 3 1_555 B C1 MAN . B MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.466 ? covale ? covale6 B O6 BMA . B BMA 3 1_555 B C1 MAN . B MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale7 B O3 MAN . B MAN 4 1_555 B C1 MAN . B MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? # _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 347 n n C1 O1 NAG sing 348 n n C1 O5 NAG sing 349 n n C1 H1 NAG sing 350 n n C2 C3 NAG sing 351 n n C2 N2 NAG sing 352 n n C2 H2 NAG sing 353 n n C3 C4 NAG sing 354 n n C3 O3 NAG sing 355 n n C3 H3 NAG sing 356 n n C4 C5 NAG sing 357 n n C4 O4 NAG sing 358 n n C4 H4 NAG sing 359 n n C5 C6 NAG sing 360 n n C5 O5 NAG sing 361 n n C5 H5 NAG sing 362 n n C6 O6 NAG sing 363 n n C6 H61 NAG sing 364 n n C6 H62 NAG sing 365 n n C7 C8 NAG sing 366 n n C7 N2 NAG sing 367 n n C7 O7 NAG doub 368 n n C8 H81 NAG sing 369 n n C8 H82 NAG sing 370 n n C8 H83 NAG sing 371 n n N2 HN2 NAG sing 372 n n O1 HO1 NAG sing 373 n n O3 HO3 NAG sing 374 n n O4 HO4 NAG sing 375 n n O6 HO6 NAG sing 376 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 4DW1 _atom_sites.fract_transf_matrix[1][1] 0.007765 _atom_sites.fract_transf_matrix[1][2] 0.004483 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008966 _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] 0.003967 _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 1 507 511 NAG NAG . D 4 ATP A 1 508 1 ATP ATP . E 5 GOL A 1 509 1 GOL GOL . F 5 GOL A 1 510 2 GOL GOL . G 6 HOH A 1 601 1 HOH HOH . G 6 HOH A 2 602 2 HOH HOH . G 6 HOH A 3 603 3 HOH HOH . G 6 HOH A 4 604 4 HOH HOH . G 6 HOH A 5 605 5 HOH HOH . G 6 HOH A 6 606 6 HOH HOH . G 6 HOH A 7 607 7 HOH HOH . G 6 HOH A 8 608 8 HOH HOH . G 6 HOH A 9 609 9 HOH HOH . G 6 HOH A 10 610 10 HOH HOH . G 6 HOH A 11 611 11 HOH HOH . G 6 HOH A 12 612 12 HOH HOH . G 6 HOH A 13 613 13 HOH HOH . G 6 HOH A 14 614 14 HOH HOH . G 6 HOH A 15 615 15 HOH HOH . G 6 HOH A 16 616 16 HOH HOH . G 6 HOH A 17 617 17 HOH HOH . G 6 HOH A 18 618 18 HOH HOH . G 6 HOH A 19 619 19 HOH HOH . G 6 HOH A 20 620 20 HOH HOH . G 6 HOH A 21 621 21 HOH HOH . G 6 HOH A 22 622 22 HOH HOH . G 6 HOH A 23 623 23 HOH HOH . G 6 HOH A 24 624 24 HOH HOH . G 6 HOH A 25 625 25 HOH HOH . G 6 HOH A 26 626 26 HOH HOH . G 6 HOH A 27 627 27 HOH HOH . G 6 HOH A 28 628 28 HOH HOH . G 6 HOH A 29 629 29 HOH HOH . G 6 HOH A 30 630 30 HOH HOH . G 6 HOH A 31 631 31 HOH HOH . G 6 HOH A 32 632 32 HOH HOH . G 6 HOH A 33 633 33 HOH HOH . G 6 HOH A 34 634 34 HOH HOH . G 6 HOH A 35 635 35 HOH HOH . G 6 HOH A 36 636 36 HOH HOH . G 6 HOH A 37 637 37 HOH HOH . G 6 HOH A 38 638 38 HOH HOH . G 6 HOH A 39 639 39 HOH HOH . G 6 HOH A 40 640 40 HOH HOH . G 6 HOH A 41 641 41 HOH HOH . G 6 HOH A 42 642 42 HOH HOH . G 6 HOH A 43 643 43 HOH HOH . G 6 HOH A 44 644 44 HOH HOH . G 6 HOH A 45 645 45 HOH HOH . G 6 HOH A 46 646 46 HOH HOH . G 6 HOH A 47 647 47 HOH HOH . G 6 HOH A 48 648 48 HOH HOH . G 6 HOH A 49 649 49 HOH HOH . G 6 HOH A 50 650 50 HOH HOH . G 6 HOH A 51 651 51 HOH HOH . G 6 HOH A 52 652 52 HOH HOH . G 6 HOH A 53 653 53 HOH HOH . G 6 HOH A 54 654 54 HOH HOH . G 6 HOH A 55 655 55 HOH HOH . G 6 HOH A 56 656 56 HOH HOH . G 6 HOH A 57 657 57 HOH HOH . G 6 HOH A 58 658 58 HOH HOH . G 6 HOH A 59 659 59 HOH HOH . G 6 HOH A 60 660 60 HOH HOH . G 6 HOH A 61 661 61 HOH HOH . G 6 HOH A 62 662 62 HOH HOH . G 6 HOH A 63 663 63 HOH HOH . G 6 HOH A 64 664 64 HOH HOH . G 6 HOH A 65 665 65 HOH HOH . G 6 HOH A 66 666 66 HOH HOH . G 6 HOH A 67 667 67 HOH HOH . G 6 HOH A 68 668 68 HOH HOH . G 6 HOH A 69 669 69 HOH HOH . G 6 HOH A 70 670 70 HOH HOH . G 6 HOH A 71 671 71 HOH HOH . G 6 HOH A 72 672 72 HOH HOH . G 6 HOH A 73 673 73 HOH HOH . G 6 HOH A 74 674 74 HOH HOH . G 6 HOH A 75 675 75 HOH HOH . G 6 HOH A 76 676 76 HOH HOH . G 6 HOH A 77 677 77 HOH HOH . G 6 HOH A 78 678 78 HOH HOH . G 6 HOH A 79 679 82 HOH HOH . G 6 HOH A 80 680 83 HOH HOH . G 6 HOH A 81 681 84 HOH HOH . G 6 HOH A 82 682 85 HOH HOH . G 6 HOH A 83 683 86 HOH HOH . G 6 HOH A 84 684 87 HOH HOH . G 6 HOH A 85 685 88 HOH HOH . G 6 HOH A 86 686 89 HOH HOH . G 6 HOH A 87 687 90 HOH HOH . G 6 HOH A 88 688 91 HOH HOH . G 6 HOH A 89 689 92 HOH HOH . G 6 HOH A 90 690 93 HOH HOH . G 6 HOH A 91 691 94 HOH HOH . G 6 HOH A 92 692 95 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 -13.369 -1.602 24.122 1 119.1 ? C1 NAG 507 A 1 HETATM 2 C C2 NAG . . . C 3 -14.126 -2.934 23.932 1 124.03 ? C2 NAG 507 A 1 HETATM 3 C C3 NAG . . . C 3 -15.086 -2.928 22.748 1 127.59 ? C3 NAG 507 A 1 HETATM 4 C C4 NAG . . . C 3 -15.84 -1.603 22.731 1 127.21 ? C4 NAG 507 A 1 HETATM 5 C C5 NAG . . . C 3 -14.857 -0.447 22.559 1 127.42 ? C5 NAG 507 A 1 HETATM 6 C C6 NAG . . . C 3 -15.545 0.912 22.516 1 125.82 ? C6 NAG 507 A 1 HETATM 7 C C7 NAG . . . C 3 -12.942 -4.904 24.869 1 120.98 ? C7 NAG 507 A 1 HETATM 8 C C8 NAG . . . C 3 -11.53 -4.86 25.389 1 107.58 ? C8 NAG 507 A 1 HETATM 9 N N2 NAG . . . C 3 -13.215 -4.078 23.836 1 120.45 ? N2 NAG 507 A 1 HETATM 10 O O3 NAG . . . C 3 -15.992 -4.005 22.873 1 125.31 ? O3 NAG 507 A 1 HETATM 11 O O4 NAG . . . C 3 -16.795 -1.606 21.691 1 127.53 ? O4 NAG 507 A 1 HETATM 12 O O5 NAG . . . C 3 -13.92 -0.393 23.617 1 124.18 ? O5 NAG 507 A 1 HETATM 13 O O6 NAG . . . C 3 -14.582 1.874 22.888 1 120.28 ? O6 NAG 507 A 1 HETATM 14 O O7 NAG . . . C 3 -13.766 -5.673 25.392 1 123.22 ? O7 NAG 507 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 338 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #