data_5D4Q # _model_server_result.job_id n27TT8MAYYPs0H_ZG4Hg9w _model_server_result.datetime_utc '2024-12-25 17:02:41' _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 5d4q # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":509}' # _entry.id 5D4Q # _exptl.entry_id 5D4Q _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 164.156 _entity.id 3 _entity.src_method man _entity.type non-polymer _entity.pdbx_description alpha-L-fucopyranose _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 5D4Q _cell.length_a 49.32 _cell.length_b 79.13 _cell.length_c 137.62 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5D4Q _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,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 3 _struct_asym.id E _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 . O6 HO6 . sing 4 ? 2 5 4 NAG MAN C1 O1 . O2 HO2 . sing 5 ? 2 6 5 GAL NAG C1 O1 . O4 HO4 . sing 6 ? 2 7 3 MAN BMA C1 O1 . O3 HO3 . sing 7 ? 2 8 7 NAG MAN C1 O1 . O2 HO2 . 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 C NAG 1 C 1 NAG A 1 NAG 2 n C NAG 2 C 2 NAG A 2 NAG 2 n C BMA 3 C 3 BMA A 3 BMA 2 n C MAN 4 C 4 MAN A 4 MAN 2 n C NAG 5 C 5 NAG A 5 NAG 2 n C GAL 6 C 6 GAL A 7 GAL 2 n C MAN 7 C 7 MAN A 6 MAN 2 n C NAG 8 C 8 NAG A 9 NAG 2 n D NAG 1 D 1 NAG B 1 NAG 2 n D NAG 2 D 2 NAG B 2 NAG 2 n D BMA 3 D 3 BMA B 3 BMA 2 n D MAN 4 D 4 MAN B 4 MAN 2 n D NAG 5 D 5 NAG B 5 NAG 2 n D GAL 6 D 6 GAL B 7 GAL 2 n D MAN 7 D 7 MAN B 6 MAN 2 n D NAG 8 D 8 NAG B 9 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 36 A CYS 261 1_555 A SG CYS 96 A CYS 321 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? disulf ? disulf2 A SG CYS 142 A CYS 367 1_555 A SG CYS 200 A CYS 425 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf3 B SG CYS 36 B CYS 261 1_555 B SG CYS 96 B CYS 321 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? disulf ? disulf4 B SG CYS 142 B CYS 367 1_555 B SG CYS 200 B CYS 425 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? covale ? covale1 A ND2 ASN 72 A ASN 297 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.216 ? covale ? covale2 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.387 ? covale ? covale3 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.384 ? covale ? covale4 C O6 BMA . C BMA 3 1_555 C C1 MAN . C MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.396 ? covale ? covale5 C O3 BMA . C BMA 3 1_555 C C1 MAN . C MAN 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.39 ? covale ? covale6 C O2 MAN . C MAN 4 1_555 C C1 NAG . C NAG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.388 ? covale ? covale7 C O4 NAG . C NAG 5 1_555 C C1 GAL . C GAL 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.391 ? covale ? covale8 C O2 MAN . C MAN 7 1_555 C C1 NAG . C NAG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.402 ? covale ? covale9 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.386 ? covale ? covale10 D O4 NAG . D NAG 2 1_555 D C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.393 ? covale ? covale11 D O6 BMA . D BMA 3 1_555 D C1 MAN . D MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale12 D O3 BMA . D BMA 3 1_555 D C1 MAN . D MAN 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.377 ? covale ? covale13 D O2 MAN . D MAN 4 1_555 D C1 NAG . D NAG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.389 ? covale ? covale14 D O4 NAG . D NAG 5 1_555 D C1 GAL . D GAL 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.39 ? covale ? covale15 D O2 MAN . D MAN 7 1_555 D C1 NAG . D NAG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.392 ? # _chem_comp.formula 'C6 H12 O5' _chem_comp.formula_weight 164.156 _chem_comp.id FUC _chem_comp.mon_nstd_flag . _chem_comp.name alpha-L-fucopyranose _chem_comp.type 'l-saccharide, alpha linking' _chem_comp.pdbx_synonyms alpha-L-fucose;6-deoxy-alpha-L-galactopyranose;L-fucose;fucose # 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 FUC sing 107 n n C1 O1 FUC sing 108 n n C1 O5 FUC sing 109 n n C1 H1 FUC sing 110 n n C2 C3 FUC sing 111 n n C2 O2 FUC sing 112 n n C2 H2 FUC sing 113 n n C3 C4 FUC sing 114 n n C3 O3 FUC sing 115 n n C3 H3 FUC sing 116 n n C4 C5 FUC sing 117 n n C4 O4 FUC sing 118 n n C4 H4 FUC sing 119 n n C5 C6 FUC sing 120 n n C5 O5 FUC sing 121 n n C5 H5 FUC sing 122 n n C6 H61 FUC sing 123 n n C6 H62 FUC sing 124 n n C6 H63 FUC sing 125 n n O1 HO1 FUC sing 126 n n O2 HO2 FUC sing 127 n n O3 HO3 FUC sing 128 n n O4 HO4 FUC sing 129 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 FUC LFucpa 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 FUC a-L-fucopyranose 'COMMON NAME' GMML 1 FUC a-L-Fucp 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 FUC Fuc 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 5D4Q _atom_sites.fract_transf_matrix[1][1] 0.020276 _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] 0.012637 _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] 0.007266 _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 E 3 FUC B 1 509 11 FUC FUC . F 4 HOH A 1 601 67 HOH HOH . F 4 HOH A 2 602 16 HOH HOH . F 4 HOH A 3 603 44 HOH HOH . F 4 HOH A 4 604 13 HOH HOH . F 4 HOH A 5 605 25 HOH HOH . F 4 HOH A 6 606 86 HOH HOH . F 4 HOH A 7 607 7 HOH HOH . F 4 HOH A 8 608 102 HOH HOH . F 4 HOH A 9 609 94 HOH HOH . F 4 HOH A 10 610 53 HOH HOH . F 4 HOH A 11 611 43 HOH HOH . F 4 HOH A 12 612 57 HOH HOH . F 4 HOH A 13 613 98 HOH HOH . F 4 HOH A 14 614 82 HOH HOH . F 4 HOH A 15 615 3 HOH HOH . F 4 HOH A 16 616 60 HOH HOH . F 4 HOH A 17 617 48 HOH HOH . F 4 HOH A 18 618 80 HOH HOH . F 4 HOH A 19 619 15 HOH HOH . F 4 HOH A 20 620 85 HOH HOH . F 4 HOH A 21 621 2 HOH HOH . F 4 HOH A 22 622 34 HOH HOH . F 4 HOH A 23 623 21 HOH HOH . F 4 HOH A 24 624 56 HOH HOH . F 4 HOH A 25 625 46 HOH HOH . F 4 HOH A 26 626 41 HOH HOH . F 4 HOH A 27 627 51 HOH HOH . F 4 HOH A 28 628 72 HOH HOH . F 4 HOH A 29 629 26 HOH HOH . F 4 HOH A 30 630 29 HOH HOH . F 4 HOH A 31 631 20 HOH HOH . F 4 HOH A 32 632 18 HOH HOH . F 4 HOH A 33 633 4 HOH HOH . F 4 HOH A 34 634 35 HOH HOH . F 4 HOH A 35 635 17 HOH HOH . F 4 HOH A 36 636 10 HOH HOH . F 4 HOH A 37 637 101 HOH HOH . F 4 HOH A 38 638 71 HOH HOH . F 4 HOH A 39 639 30 HOH HOH . F 4 HOH A 40 640 104 HOH HOH . F 4 HOH A 41 641 42 HOH HOH . F 4 HOH A 42 642 24 HOH HOH . F 4 HOH A 43 643 106 HOH HOH . F 4 HOH A 44 644 68 HOH HOH . F 4 HOH A 45 645 55 HOH HOH . F 4 HOH A 46 646 70 HOH HOH . F 4 HOH A 47 647 32 HOH HOH . F 4 HOH A 48 648 63 HOH HOH . F 4 HOH A 49 649 93 HOH HOH . F 4 HOH A 50 650 91 HOH HOH . F 4 HOH A 51 651 61 HOH HOH . F 4 HOH A 52 652 76 HOH HOH . F 4 HOH A 53 653 87 HOH HOH . F 4 HOH A 54 654 77 HOH HOH . F 4 HOH A 55 655 100 HOH HOH . G 4 HOH B 1 601 6 HOH HOH . G 4 HOH B 2 602 65 HOH HOH . G 4 HOH B 3 603 9 HOH HOH . G 4 HOH B 4 604 97 HOH HOH . G 4 HOH B 5 605 28 HOH HOH . G 4 HOH B 6 606 19 HOH HOH . G 4 HOH B 7 607 58 HOH HOH . G 4 HOH B 8 608 14 HOH HOH . G 4 HOH B 9 609 78 HOH HOH . G 4 HOH B 10 610 5 HOH HOH . G 4 HOH B 11 611 79 HOH HOH . G 4 HOH B 12 612 12 HOH HOH . G 4 HOH B 13 613 90 HOH HOH . G 4 HOH B 14 614 8 HOH HOH . G 4 HOH B 15 615 22 HOH HOH . G 4 HOH B 16 616 69 HOH HOH . G 4 HOH B 17 617 95 HOH HOH . G 4 HOH B 18 618 52 HOH HOH . G 4 HOH B 19 619 92 HOH HOH . G 4 HOH B 20 620 40 HOH HOH . G 4 HOH B 21 621 88 HOH HOH . G 4 HOH B 22 622 96 HOH HOH . G 4 HOH B 23 623 36 HOH HOH . G 4 HOH B 24 624 103 HOH HOH . G 4 HOH B 25 625 50 HOH HOH . G 4 HOH B 26 626 84 HOH HOH . G 4 HOH B 27 627 74 HOH HOH . G 4 HOH B 28 628 107 HOH HOH . G 4 HOH B 29 629 27 HOH HOH . G 4 HOH B 30 630 81 HOH HOH . G 4 HOH B 31 631 66 HOH HOH . G 4 HOH B 32 632 108 HOH HOH . G 4 HOH B 33 633 31 HOH HOH . G 4 HOH B 34 634 45 HOH HOH . G 4 HOH B 35 635 11 HOH HOH . G 4 HOH B 36 636 62 HOH HOH . G 4 HOH B 37 637 99 HOH HOH . G 4 HOH B 38 638 105 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 FUC . . . E 3 113.864 148.19 148.512 1 101.2 ? C1 FUC 509 B 1 HETATM 2 C C2 FUC . . . E 3 114.34 149.551 149.043 1 102.23 ? C2 FUC 509 B 1 HETATM 3 C C3 FUC . . . E 3 113.538 150.687 148.386 1 103.27 ? C3 FUC 509 B 1 HETATM 4 C C4 FUC . . . E 3 112.032 150.417 148.441 1 106.05 ? C4 FUC 509 B 1 HETATM 5 C C5 FUC . . . E 3 111.695 149.008 147.943 1 106.52 ? C5 FUC 509 B 1 HETATM 6 C C6 FUC . . . E 3 110.199 148.706 148.033 1 108.92 ? C6 FUC 509 B 1 HETATM 7 O O2 FUC . . . E 3 115.74 149.726 148.841 1 99.82 ? O2 FUC 509 B 1 HETATM 8 O O3 FUC . . . E 3 113.821 151.933 148.992 1 102.74 ? O3 FUC 509 B 1 HETATM 9 O O4 FUC . . . E 3 111.581 150.559 149.769 1 109.04 ? O4 FUC 509 B 1 HETATM 10 O O5 FUC . . . E 3 112.455 148.047 148.667 1 104.99 ? O5 FUC 509 B 1 # _model_server_stats.io_time_ms 25 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 277 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 10 #