data_8WO1 # _model_server_result.job_id YfBn7zky7QrBvCp_1hscVg _model_server_result.datetime_utc '2025-03-01 19:33:35' _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 8wo1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Y","auth_seq_id":204}' # _entry.id 8WO1 # _exptl.entry_id 8WO1 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 274.162 _entity.id 9 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(2~{R},3~{S},4~{R},5~{S})-2-(hydroxymethyl)-5-methoxy-4,6-bis(oxidanyl)oxan-3-yl] 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 8WO1 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8WO1 _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 _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 ? 9 T N N ? 9 Y N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 3 oligosaccharide 4 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 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . 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 E BMA 3 E 3 BMA E 3 BMA 3 n F NAG 1 F 1 NAG F 1 NAG 3 n F NAG 2 F 2 NAG F 2 NAG 3 n F BMA 3 F 3 BMA F 3 BMA 4 n G NAG 1 G 1 NAG G 1 NAG 4 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 H BMA 3 H 3 BMA H 3 BMA 3 n I NAG 1 I 1 NAG I 1 NAG 3 n I NAG 2 I 2 NAG I 2 NAG 3 n I BMA 3 I 3 BMA I 3 BMA 4 n J NAG 1 J 1 NAG J 1 NAG 4 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 3 A CYS 29 1_555 A SG CYS 14 A CYS 40 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf2 A SG CYS 364 A CYS 390 1_555 A SG CYS 365 A CYS 391 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf3 A SG CYS 557 A CYS 583 1_555 A SG CYS 583 A CYS 609 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf4 A SG CYS 559 A CYS 585 1_555 A SG CYS 601 A CYS 627 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf5 B SG CYS 3 B CYS 29 1_555 B SG CYS 14 B CYS 40 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf6 B SG CYS 364 B CYS 390 1_555 B SG CYS 365 B CYS 391 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf7 B SG CYS 557 B CYS 583 1_555 B SG CYS 583 B CYS 609 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf8 B SG CYS 559 B CYS 585 1_555 B SG CYS 601 B CYS 627 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf9 C SG CYS 7 C CYS 25 1_555 C SG CYS 33 C CYS 51 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf10 C SG CYS 19 C CYS 37 1_555 C SG CYS 130 C CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf11 C SG CYS 77 C CYS 95 1_555 C SG CYS 87 C CYS 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf12 D SG CYS 7 D CYS 25 1_555 D SG CYS 33 D CYS 51 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf13 D SG CYS 19 D CYS 37 1_555 D SG CYS 130 D CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf14 D SG CYS 77 D CYS 95 1_555 D SG CYS 87 D CYS 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? covale ? covale1 A ND2 ASN 179 A ASN 205 1_555 L C1 NAG . A NAG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.428 ? covale ? covale2 A ND2 ASN 471 A ASN 497 1_555 M C1 NAG . A NAG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale3 A ND2 ASN 500 A ASN 526 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale4 A ND2 ASN 549 A ASN 575 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale5 K N2 GP4 . A GP4 701 1_555 R C1 2IL . C 2IL 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.292 ? covale ? covale6 K C3 GP4 . A GP4 701 1_555 S O3E 0IL . C 0IL 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale7 K C1 GP4 . A GP4 701 1_555 T OXT X6N . C X6N 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale8 B ND2 ASN 179 B ASN 205 1_555 O C1 NAG . B NAG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.428 ? covale ? covale9 B ND2 ASN 471 B ASN 497 1_555 P C1 NAG . B NAG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale10 B ND2 ASN 500 B ASN 526 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale11 B ND2 ASN 549 B ASN 575 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale12 N N2 GP4 . B GP4 701 1_555 W C1 2IL . D 2IL 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.292 ? covale ? covale13 N C3 GP4 . B GP4 701 1_555 X O3E 0IL . D 0IL 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale14 N C1 GP4 . B GP4 701 1_555 Y OXT X6N . D X6N 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale15 C ND2 ASN 8 C ASN 26 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale16 C ND2 ASN 96 C ASN 114 1_555 Q C1 NAG . C NAG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale17 T C6 X6N . C X6N 204 1_555 U O52 A1L01 . C A1L01 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.423 ? covale ? covale18 D ND2 ASN 8 D ASN 26 1_555 J C1 NAG . J NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale19 D ND2 ASN 96 D ASN 114 1_555 V C1 NAG . D NAG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale20 Y C6 X6N . D X6N 204 1_555 Z O52 A1L01 . D A1L01 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.422 ? covale ? covale21 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.372 ? covale ? covale22 E O4 NAG . E NAG 2 1_555 E C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.373 ? covale ? covale23 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.379 ? covale ? covale24 F O4 NAG . F NAG 2 1_555 F C1 BMA . F BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.375 ? covale ? covale25 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.374 ? covale ? covale26 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.371 ? covale ? covale27 H O4 NAG . H NAG 2 1_555 H C1 BMA . H BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.372 ? covale ? covale28 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.379 ? covale ? covale29 I O4 NAG . I NAG 2 1_555 I C1 BMA . I BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.375 ? covale ? covale30 J O4 NAG . J NAG 1 1_555 J C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.374 ? # _chem_comp.formula 'C7 H15 O9 P' _chem_comp.formula_weight 274.162 _chem_comp.id X6N _chem_comp.mon_nstd_flag . _chem_comp.name '[(2~{R},3~{S},4~{R},5~{S})-2-(hydroxymethyl)-5-methoxy-4,6-bis(oxidanyl)oxan-3-yl] 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 O56 P51 X6N doub 695 n n O54 P51 X6N sing 696 n n O55 P51 X6N sing 697 n n P51 O4 X6N sing 698 n n O3 C3 X6N sing 699 n n C48 O47 X6N sing 700 n n O47 C2 X6N sing 701 n n O4 C4 X6N sing 702 n n C3 C4 X6N sing 703 n n C3 C2 X6N sing 704 n n C4 C5 X6N sing 705 n n C2 C1 X6N sing 706 n n C5 C6 X6N sing 707 n n C5 O5 X6N sing 708 n n C1 O5 X6N sing 709 n n C6 O52 X6N sing 710 n n C1 H1 X6N sing 711 n n C2 H3 X6N sing 712 n n C3 H4 X6N sing 713 n n C4 H5 X6N sing 714 n n C48 H6 X6N sing 715 n n C48 H7 X6N sing 716 n n C48 H8 X6N sing 717 n n C5 H9 X6N sing 718 n n C6 H10 X6N sing 719 n n C6 H11 X6N sing 720 n n O3 H12 X6N sing 721 n n O52 H13 X6N sing 722 n n O54 H14 X6N sing 723 n n O55 H15 X6N sing 724 n n C1 OXT X6N sing 725 n n OXT HXT X6N sing 726 n n # _atom_sites.entry_id 8WO1 _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 5 GP4 A 1 701 703 GP4 GP4 . L 6 NAG A 1 702 701 NAG NAG . M 6 NAG A 1 703 702 NAG NAG . N 5 GP4 B 1 701 703 GP4 GP4 . O 6 NAG B 1 702 701 NAG NAG . P 6 NAG B 1 703 702 NAG NAG . Q 6 NAG C 1 201 201 NAG NAG . R 7 2IL C 1 202 202 2IL 2IL . S 8 0IL C 1 203 203 0IL 0IL . T 9 X6N C 1 204 204 X6N X6N . U 10 A1L01 C 1 205 205 A1L01 A1L . V 6 NAG D 1 201 201 NAG NAG . W 7 2IL D 1 202 202 2IL 2IL . X 8 0IL D 1 203 203 0IL 0IL . Y 9 X6N D 1 204 204 X6N X6N . Z 10 A1L01 D 1 205 205 A1L01 A1L . # 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 X6N . . . Y 9 157.378 158.323 154.868 1 82.93 ? C1 X6N 204 D 1 HETATM 2 C C2 X6N . . . Y 9 157.376 158.361 153.347 1 82.93 ? C2 X6N 204 D 1 HETATM 3 C C3 X6N . . . Y 9 156.729 157.106 152.776 1 82.93 ? C3 X6N 204 D 1 HETATM 4 C C4 X6N . . . Y 9 157.337 155.852 153.389 1 82.93 ? C4 X6N 204 D 1 HETATM 5 C C48 X6N . . . Y 9 159.147 159.823 152.817 1 82.93 ? C48 X6N 204 D 1 HETATM 6 C C5 X6N . . . Y 9 157.359 155.948 154.907 1 82.93 ? C5 X6N 204 D 1 HETATM 7 C C6 X6N . . . Y 9 158.038 154.73 155.524 1 82.93 ? C6 X6N 204 D 1 HETATM 8 O O3 X6N . . . Y 9 156.91 157.08 151.356 1 82.93 ? O3 X6N 204 D 1 HETATM 9 O O4 X6N . . . Y 9 156.567 154.715 153.001 1 82.93 ? O4 X6N 204 D 1 HETATM 10 O O47 X6N . . . Y 9 158.714 158.465 152.873 1 82.93 ? O47 X6N 204 D 1 HETATM 11 O O5 X6N . . . Y 9 158.043 157.136 155.314 1 82.93 ? O5 X6N 204 D 1 HETATM 12 O O54 X6N . . . Y 9 156.283 154.831 150.308 1 82.93 ? O54 X6N 204 D 1 HETATM 13 O O55 X6N . . . Y 9 158.514 153.699 151.372 1 82.93 ? O55 X6N 204 D 1 HETATM 14 O O56 X6N . . . Y 9 156.096 152.418 151.56 1 82.93 ? O56 X6N 204 D 1 HETATM 15 P P51 X6N . . . Y 9 156.866 153.918 151.555 1 82.93 ? P51 X6N 204 D 1 HETATM 16 O OXT X6N . . . Y 9 156.028 158.333 155.341 1 82.93 ? OXT X6N 204 D 1 # _model_server_stats.io_time_ms 44 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 16 #