data_8WQT # _model_server_result.job_id -QEZKoFYe4RCMUeYcvAAqA _model_server_result.datetime_utc '2025-03-01 19:34:54' _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 8wqt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"BA","auth_seq_id":701}' # _entry.id 8WQT # _exptl.entry_id 8WQT _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 274.162 _entity.id 8 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(2~{R},3~{S},4~{S},5~{S})-5-methoxy-3,4,6-tris(oxidanyl)oxan-2-yl]methyl dihydrogen phosphate' _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 8WQT _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8WQT _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 U N N ? 8 BA 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 F 1 NAG F 1 NAG 3 n E NAG 2 F 2 NAG F 2 NAG 3 n F NAG 1 G 1 NAG G 1 NAG 3 n F NAG 2 G 2 NAG G 2 NAG 3 n G NAG 1 H 1 NAG H 1 NAG 3 n G NAG 2 H 2 NAG H 2 NAG 3 n H NAG 1 I 1 NAG I 1 NAG 3 n H NAG 2 I 2 NAG I 2 NAG 3 n I NAG 1 J 1 NAG J 1 NAG 3 n I NAG 2 J 2 NAG J 2 NAG 3 n J NAG 1 E 1 NAG E 1 NAG 3 n J NAG 2 E 2 NAG E 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 C CYS 25 1_555 A SG CYS 33 C CYS 51 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf2 A SG CYS 19 C CYS 37 1_555 A SG CYS 130 C CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf3 A SG CYS 77 C CYS 95 1_555 A SG CYS 87 C CYS 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf4 B SG CYS 7 D CYS 25 1_555 B SG CYS 33 D CYS 51 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf5 B SG CYS 19 D CYS 37 1_555 B SG CYS 130 D CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf6 B SG CYS 77 D CYS 95 1_555 B SG CYS 87 D CYS 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf7 C SG CYS 3 A CYS 28 1_555 C SG CYS 14 A CYS 39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf8 C SG CYS 255 A CYS 280 1_555 C SG CYS 279 A CYS 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf9 C SG CYS 363 A CYS 388 1_555 C SG CYS 364 A CYS 389 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? disulf ? disulf10 C SG CYS 555 A CYS 580 1_555 C SG CYS 581 A CYS 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf11 D SG CYS 3 B CYS 28 1_555 D SG CYS 14 B CYS 39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf12 D SG CYS 255 B CYS 280 1_555 D SG CYS 279 B CYS 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf13 D SG CYS 363 B CYS 388 1_555 D SG CYS 364 B CYS 389 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? disulf ? disulf14 D SG CYS 555 B CYS 580 1_555 D SG CYS 581 B CYS 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? covale ? covale1 A ND2 ASN 96 C ASN 114 1_555 M C1 NAG . C NAG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale2 A ND2 ASN 132 C ASN 150 1_555 N C1 NAG . C NAG 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale3 K C1 2IL . C 2IL 201 1_555 CA N2 GP4 . B GP4 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.472 ? covale ? covale4 L C1 2IL . C 2IL 202 1_555 U O4 X6Z . A X6Z 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.371 ? covale ? covale5 B ND2 ASN 96 D ASN 114 1_555 Q C1 NAG . D NAG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale6 B ND2 ASN 132 D ASN 150 1_555 R C1 NAG . D NAG 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale7 O C1 2IL . D 2IL 201 1_555 S N2 GP4 . A GP4 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.473 ? covale ? covale8 P C1 2IL . D 2IL 202 1_555 BA O4 X6Z . B X6Z 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.371 ? covale ? covale9 C ND2 ASN 9 A ASN 34 1_555 X C1 NAG . A NAG 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale10 C ND2 ASN 50 A ASN 75 1_555 W C1 NAG . A NAG 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale11 C ND2 ASN 147 A ASN 172 1_555 V C1 NAG . A NAG 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale12 C ND2 ASN 179 A ASN 204 1_555 G C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale13 C ND2 ASN 212 A ASN 237 1_555 Z C1 NAG . A NAG 708 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale14 C ND2 ASN 282 A ASN 307 1_555 AA C1 NAG . A NAG 709 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale15 C ND2 ASN 467 A ASN 492 1_555 Y C1 NAG . A NAG 707 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale16 C ND2 ASN 499 A ASN 524 1_555 H C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.467 ? covale ? covale17 C ND2 ASN 547 A ASN 572 1_555 I C1 NAG . J NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? covale ? covale18 S C3 GP4 . A GP4 701 1_555 T O3E 0IL . A 0IL 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.42 ? covale ? covale19 S C1 GP4 . A GP4 701 1_555 BA OXT X6Z . B X6Z 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.423 ? covale ? covale20 U OXT X6Z . A X6Z 703 1_555 CA C1 GP4 . B GP4 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.423 ? covale ? covale21 D ND2 ASN 9 B ASN 34 1_555 GA C1 NAG . B NAG 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale22 D ND2 ASN 50 B ASN 75 1_555 FA C1 NAG . B NAG 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale23 D ND2 ASN 147 B ASN 172 1_555 EA C1 NAG . B NAG 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale24 D ND2 ASN 179 B ASN 204 1_555 J C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.564 ? covale ? covale25 D ND2 ASN 212 B ASN 237 1_555 IA C1 NAG . B NAG 708 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale26 D ND2 ASN 282 B ASN 307 1_555 JA C1 NAG . B NAG 709 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale27 D ND2 ASN 467 B ASN 492 1_555 HA C1 NAG . B NAG 707 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale28 CA C3 GP4 . B GP4 702 1_555 DA O3E 0IL . B 0IL 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.42 ? covale ? covale29 E O4 NAG . F NAG 1 1_555 E C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? covale ? covale30 F O4 NAG . G NAG 1 1_555 F C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale31 G O4 NAG . H NAG 1 1_555 G C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.46 ? covale ? covale32 H O4 NAG . I NAG 1 1_555 H C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? covale ? covale33 I O4 NAG . J NAG 1 1_555 I C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale34 J O4 NAG . E NAG 1 1_555 J C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? # _chem_comp.formula 'C7 H15 O9 P' _chem_comp.formula_weight 274.162 _chem_comp.id X6Z _chem_comp.mon_nstd_flag . _chem_comp.name '[(2~{R},3~{S},4~{S},5~{S})-5-methoxy-3,4,6-tris(oxidanyl)oxan-2-yl]methyl dihydrogen phosphate' _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 O60 P51 X6Z doub 598 n n O58 P51 X6Z sing 599 n n O62 P51 X6Z sing 600 n n P51 O50 X6Z sing 601 n n O50 C6 X6Z sing 602 n n C6 C5 X6Z sing 603 n n C5 O5 X6Z sing 604 n n C5 C4 X6Z sing 605 n n O5 C1 X6Z sing 606 n n C4 O4 X6Z sing 607 n n C4 C3 X6Z sing 608 n n C1 C2 X6Z sing 609 n n C48 O47 X6Z sing 610 n n O47 C2 X6Z sing 611 n n C2 C3 X6Z sing 612 n n C3 O3 X6Z sing 613 n n C1 H1 X6Z sing 614 n n C2 H3 X6Z sing 615 n n C3 H4 X6Z sing 616 n n C4 H5 X6Z sing 617 n n C5 H6 X6Z sing 618 n n C6 H7 X6Z sing 619 n n C6 H8 X6Z sing 620 n n C48 H9 X6Z sing 621 n n C48 H10 X6Z sing 622 n n C48 H11 X6Z sing 623 n n O3 H12 X6Z sing 624 n n O4 H13 X6Z sing 625 n n O58 H14 X6Z sing 626 n n O62 H15 X6Z sing 627 n n C1 OXT X6Z sing 628 n n OXT HXT X6Z sing 629 n n # _atom_sites.entry_id 8WQT _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 1 201 201 2IL 2IL . L 4 2IL C 1 202 202 2IL 2IL . M 5 NAG C 1 203 203 NAG NAG . N 5 NAG C 1 204 204 NAG NAG . O 4 2IL D 1 201 201 2IL 2IL . P 4 2IL D 1 202 202 2IL 2IL . Q 5 NAG D 1 203 203 NAG NAG . R 5 NAG D 1 204 204 NAG NAG . S 6 GP4 A 1 701 701 GP4 GP4 . T 7 0IL A 1 702 702 0IL 0IL . U 8 X6Z A 1 703 703 X6Z X6Z . V 5 NAG A 1 704 704 NAG NAG . W 5 NAG A 1 705 705 NAG NAG . X 5 NAG A 1 706 706 NAG NAG . Y 5 NAG A 1 707 707 NAG NAG . Z 5 NAG A 1 708 708 NAG NAG . AA 5 NAG A 1 709 709 NAG NAG . BA 8 X6Z B 1 701 701 X6Z X6Z . CA 6 GP4 B 1 702 702 GP4 GP4 . DA 7 0IL B 1 703 703 0IL 0IL . EA 5 NAG B 1 704 704 NAG NAG . FA 5 NAG B 1 705 705 NAG NAG . GA 5 NAG B 1 706 706 NAG NAG . HA 5 NAG B 1 707 707 NAG NAG . IA 5 NAG B 1 708 708 NAG NAG . JA 5 NAG B 1 709 709 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 O O47 X6Z . . . BA 8 150.985 161.76 159.234 1 103.42 ? O47 X6Z 701 B 1 HETATM 2 O O50 X6Z . . . BA 8 151.352 158.468 155.716 1 103.42 ? O50 X6Z 701 B 1 HETATM 3 C C1 X6Z . . . BA 8 152.785 160.142 159.124 1 103.42 ? C1 X6Z 701 B 1 HETATM 4 C C2 X6Z . . . BA 8 151.509 160.605 159.868 1 103.42 ? C2 X6Z 701 B 1 HETATM 5 C C3 X6Z . . . BA 8 150.439 159.52 159.916 1 103.42 ? C3 X6Z 701 B 1 HETATM 6 C C4 X6Z . . . BA 8 150.275 158.905 158.56 1 103.42 ? C4 X6Z 701 B 1 HETATM 7 C C5 X6Z . . . BA 8 151.585 158.356 158.102 1 103.42 ? C5 X6Z 701 B 1 HETATM 8 C C6 X6Z . . . BA 8 151.435 157.571 156.811 1 103.42 ? C6 X6Z 701 B 1 HETATM 9 C C48 X6Z . . . BA 8 151.278 162.928 159.991 1 103.42 ? C48 X6Z 701 B 1 HETATM 10 O O3 X6Z . . . BA 8 149.202 160.089 160.336 1 103.42 ? O3 X6Z 701 B 1 HETATM 11 O O4 X6Z . . . BA 8 149.268 157.883 158.578 1 103.42 ? O4 X6Z 701 B 1 HETATM 12 O O5 X6Z . . . BA 8 152.466 159.448 157.896 1 103.42 ? O5 X6Z 701 B 1 HETATM 13 O O58 X6Z . . . BA 8 150.039 159.201 153.307 1 103.42 ? O58 X6Z 701 B 1 HETATM 14 O O60 X6Z . . . BA 8 151.793 157.017 153.303 1 103.42 ? O60 X6Z 701 B 1 HETATM 15 O O62 X6Z . . . BA 8 149.359 156.832 154.562 1 103.42 ? O62 X6Z 701 B 1 HETATM 16 P P51 X6Z . . . BA 8 150.615 157.867 154.201 1 103.42 ? P51 X6Z 701 B 1 HETATM 17 O OXT X6Z . . . BA 8 153.56 159.305 159.967 1 103.42 ? OXT X6Z 701 B 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 292 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 17 #