data_8WRY # _model_server_result.job_id 1Fnv_WXK44YDYo9-9ARDiw _model_server_result.datetime_utc '2025-03-01 19:27:04' _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 8wry # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"CA","auth_seq_id":701}' # _entry.id 8WRY # _exptl.entry_id 8WRY _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 188.135 _entity.id 8 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-(hydroxymethyl)-5-methoxy-3,6-bis(oxidanyl)pyran-4-one _entity.pdbx_number_of_molecules 2 _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 8WRY _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8WRY _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 8 V N N ? 8 CA 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 E NAG 1 E 1 NAG E 1 NAG 3 n E NAG 2 E 2 NAG E 2 NAG 3 n F NAG 1 F 1 NAG F 1 NAG 3 n F NAG 2 F 2 NAG F 2 NAG 3 n G NAG 1 G 1 NAG G 1 NAG 3 n G NAG 2 G 2 NAG G 2 NAG 3 n H NAG 1 H 1 NAG H 1 NAG 3 n H NAG 2 H 2 NAG H 2 NAG 3 n I NAG 1 I 1 NAG I 1 NAG 3 n I NAG 2 I 2 NAG I 2 NAG 3 n J NAG 1 J 1 NAG J 1 NAG 3 n J NAG 2 J 2 NAG J 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 19 C CYS 37 1_555 A SG CYS 130 C CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf2 A SG CYS 77 C CYS 95 1_555 A SG CYS 87 C CYS 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf3 B SG CYS 19 D CYS 37 1_555 B SG CYS 130 D CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf4 B SG CYS 77 D CYS 95 1_555 B SG CYS 87 D CYS 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf5 C SG CYS 3 B CYS 28 1_555 C SG CYS 14 B CYS 39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? disulf ? disulf6 C SG CYS 255 B CYS 280 1_555 C SG CYS 279 B CYS 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf7 C SG CYS 363 B CYS 388 1_555 C SG CYS 364 B CYS 389 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.166 ? disulf ? disulf8 C SG CYS 555 B CYS 580 1_555 C SG CYS 581 B CYS 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf9 D SG CYS 3 A CYS 28 1_555 D SG CYS 14 A CYS 39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? disulf ? disulf10 D SG CYS 255 A CYS 280 1_555 D SG CYS 279 A CYS 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf11 D SG CYS 363 A CYS 388 1_555 D SG CYS 364 A CYS 389 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.166 ? disulf ? disulf12 D SG CYS 555 A CYS 580 1_555 D SG CYS 581 A CYS 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? covale ? covale1 A ND2 ASN 96 C ASN 114 1_555 N C1 NAG . C NAG 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale2 A ND2 ASN 132 C ASN 150 1_555 O C1 NAG . C NAG 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale3 K C1 2IL . C 2IL 201 1_555 U N2 GP4 . B GP4 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.291 ? covale ? covale4 L O3E 0IL . C 0IL 202 1_555 U C3 GP4 . B GP4 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.423 ? covale ? covale5 M O1 2IL . C 2IL 203 1_555 CA C4 XIQ . A XIQ 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.425 ? covale ? covale6 B ND2 ASN 96 D ASN 114 1_555 S C1 NAG . D NAG 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale7 B ND2 ASN 132 D ASN 150 1_555 T C1 NAG . D NAG 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale8 P C1 2IL . D 2IL 201 1_555 DA N2 GP4 . A GP4 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.291 ? covale ? covale9 Q O3E 0IL . D 0IL 202 1_555 DA C3 GP4 . A GP4 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.422 ? covale ? covale10 R O1 2IL . D 2IL 203 1_555 V C4 XIQ . B XIQ 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.426 ? covale ? covale11 C ND2 ASN 9 B ASN 34 1_555 Y C1 NAG . B NAG 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale12 C ND2 ASN 50 B ASN 75 1_555 X C1 NAG . B NAG 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale13 C ND2 ASN 147 B ASN 172 1_555 W C1 NAG . B NAG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale14 C ND2 ASN 179 B ASN 204 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.471 ? covale ? covale15 C ND2 ASN 212 B ASN 237 1_555 AA C1 NAG . B NAG 707 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale16 C ND2 ASN 282 B ASN 307 1_555 BA C1 NAG . B NAG 708 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale17 C ND2 ASN 467 B ASN 492 1_555 Z C1 NAG . B NAG 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale18 C ND2 ASN 499 B ASN 524 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.463 ? covale ? covale19 C ND2 ASN 547 B ASN 572 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.419 ? covale ? covale20 U C1 GP4 . B GP4 701 1_555 CA OXT XIQ . A XIQ 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? covale ? covale21 V OXT XIQ . B XIQ 702 1_555 DA C1 GP4 . A GP4 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale22 D ND2 ASN 9 A ASN 34 1_555 GA C1 NAG . A NAG 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale23 D ND2 ASN 50 A ASN 75 1_555 FA C1 NAG . A NAG 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale24 D ND2 ASN 147 A ASN 172 1_555 EA C1 NAG . A NAG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale25 D ND2 ASN 179 A ASN 204 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.471 ? covale ? covale26 D ND2 ASN 212 A ASN 237 1_555 IA C1 NAG . A NAG 707 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale27 D ND2 ASN 282 A ASN 307 1_555 JA C1 NAG . A NAG 708 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale28 D ND2 ASN 467 A ASN 492 1_555 HA C1 NAG . A NAG 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale29 D ND2 ASN 499 A ASN 524 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.463 ? covale ? covale30 D ND2 ASN 547 A ASN 572 1_555 J C1 NAG . J NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.42 ? covale ? covale31 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale32 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale33 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale34 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale35 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale36 J O4 NAG . J NAG 1 1_555 J C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? # _chem_comp.formula 'C7 H8 O6' _chem_comp.formula_weight 188.135 _chem_comp.id XIQ _chem_comp.mon_nstd_flag . _chem_comp.name 2-(hydroxymethyl)-5-methoxy-3,6-bis(oxidanyl)pyran-4-one _chem_comp.type 'd-saccharide, alpha linking' _chem_comp.pdbx_synonyms ? # 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 O3 C3 XIQ doub 598 n n C3 C2 XIQ sing 599 n n C3 C4 XIQ sing 600 n n C2 C1 XIQ doub 601 n n C2 O47 XIQ sing 602 n n C48 O47 XIQ sing 603 n n O4 C4 XIQ sing 604 n n C1 O5 XIQ sing 605 n n C4 C5 XIQ doub 606 n n C5 O5 XIQ sing 607 n n C5 C6 XIQ sing 608 n n C6 O50 XIQ sing 609 n n C1 OXT XIQ sing 610 n n C6 H4 XIQ sing 611 n n C6 H5 XIQ sing 612 n n C48 H8 XIQ sing 613 n n C48 H9 XIQ sing 614 n n C48 H10 XIQ sing 615 n n O4 H12 XIQ sing 616 n n O50 H13 XIQ sing 617 n n OXT HXT XIQ sing 618 n n # _atom_sites.entry_id 8WRY _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 K 4 2IL C 1 201 203 2IL 2IL . L 5 0IL C 1 202 204 0IL 0IL . M 4 2IL C 1 203 205 2IL 2IL . N 6 NAG C 1 204 201 NAG NAG . O 6 NAG C 1 205 202 NAG NAG . P 4 2IL D 1 201 203 2IL 2IL . Q 5 0IL D 1 202 204 0IL 0IL . R 4 2IL D 1 203 205 2IL 2IL . S 6 NAG D 1 204 201 NAG NAG . T 6 NAG D 1 205 202 NAG NAG . U 7 GP4 B 1 701 708 GP4 GP4 . V 8 XIQ B 1 702 707 XIQ XIQ . W 6 NAG B 1 703 701 NAG NAG . X 6 NAG B 1 704 702 NAG NAG . Y 6 NAG B 1 705 703 NAG NAG . Z 6 NAG B 1 706 704 NAG NAG . AA 6 NAG B 1 707 705 NAG NAG . BA 6 NAG B 1 708 706 NAG NAG . CA 8 XIQ A 1 701 707 XIQ XIQ . DA 7 GP4 A 1 702 708 GP4 GP4 . EA 6 NAG A 1 703 701 NAG NAG . FA 6 NAG A 1 704 702 NAG NAG . GA 6 NAG A 1 705 703 NAG NAG . HA 6 NAG A 1 706 704 NAG NAG . IA 6 NAG A 1 707 705 NAG NAG . JA 6 NAG A 1 708 706 NAG NAG . # 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 C3 XIQ . . . CA 8 150.466 180.706 178.16 1 112.17 ? C3 XIQ 701 A 1 HETATM 2 C C1 XIQ . . . CA 8 152.543 180.067 179.391 1 112.17 ? C1 XIQ 701 A 1 HETATM 3 C C4 XIQ . . . CA 8 150.074 181.536 179.373 1 112.17 ? C4 XIQ 701 A 1 HETATM 4 C C6 XIQ . . . CA 8 150.896 182.659 181.462 1 112.17 ? C6 XIQ 701 A 1 HETATM 5 C C5 XIQ . . . CA 8 151.298 181.923 180.19 1 112.17 ? C5 XIQ 701 A 1 HETATM 6 C C2 XIQ . . . CA 8 151.385 179.565 178.552 1 112.17 ? C2 XIQ 701 A 1 HETATM 7 C C48 XIQ . . . CA 8 150.973 177.272 178.876 1 112.17 ? C48 XIQ 701 A 1 HETATM 8 O O3 XIQ . . . CA 8 149.291 180.178 177.544 1 112.17 ? O3 XIQ 701 A 1 HETATM 9 O O47 XIQ . . . CA 8 150.653 178.596 179.287 1 112.17 ? O47 XIQ 701 A 1 HETATM 10 O O5 XIQ . . . CA 8 152.041 180.754 180.537 1 112.17 ? O5 XIQ 701 A 1 HETATM 11 O O50 XIQ . . . CA 8 150.545 184.004 181.144 1 112.17 ? O50 XIQ 701 A 1 HETATM 12 O OXT XIQ . . . CA 8 153.351 180.946 178.602 1 112.17 ? OXT XIQ 701 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 259 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 12 #