data_8WRY # _model_server_result.job_id GmjBp2QmtzxWD82mPZVAmA _model_server_result.datetime_utc '2025-03-01 19:25:14' _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":"DA","auth_seq_id":702}' # _entry.id 8WRY # _exptl.entry_id 8WRY _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 259.151 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-amino-2-deoxy-4-O-phosphono-alpha-D-glucopyranose _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 ? 7 U N N ? 7 DA 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 'C6 H14 N O8 P' _chem_comp.formula_weight 259.151 _chem_comp.id GP4 _chem_comp.mon_nstd_flag . _chem_comp.name 2-amino-2-deoxy-4-O-phosphono-alpha-D-glucopyranose _chem_comp.type 'd-saccharide, alpha linking' _chem_comp.pdbx_synonyms 'GLUCOSAMINE 4-PHOSPHATE;N-acetyl-4-O-phosphono-alpha-D-glucosamine;2-amino-2-deoxy-4-O-phosphono-alpha-D-glucose;2-amino-2-deoxy-4-O-phosphono-D-glucose;2-amino-2-deoxy-4-O-phosphono-glucose' # 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 GP4 sing 293 n n C1 O5 GP4 sing 294 n n C1 O1 GP4 sing 295 n n C1 H1 GP4 sing 296 n n C2 C3 GP4 sing 297 n n C2 N2 GP4 sing 298 n n C2 H2 GP4 sing 299 n n C3 C4 GP4 sing 300 n n C3 O3 GP4 sing 301 n n C3 H3 GP4 sing 302 n n C4 C5 GP4 sing 303 n n C4 O4 GP4 sing 304 n n C4 H4 GP4 sing 305 n n C5 C6 GP4 sing 306 n n C5 O5 GP4 sing 307 n n C5 H5 GP4 sing 308 n n C6 O6 GP4 sing 309 n n C6 H61 GP4 sing 310 n n C6 H62 GP4 sing 311 n n N2 HN2 GP4 sing 312 n n N2 HN22 GP4 sing 313 n n O3 HO3 GP4 sing 314 n n O4 P4A GP4 sing 315 n n O6 HO6 GP4 sing 316 n n O7A P4A GP4 sing 317 n n O7A HOP1 GP4 sing 318 n n P4A O8A GP4 doub 319 n n P4A O9A GP4 sing 320 n n O9A HOP2 GP4 sing 321 n n O1 HO1 GP4 sing 322 n n # _pdbx_chem_comp_identifier.comp_id GP4 _pdbx_chem_comp_identifier.identifier a-D-GlcpN4PO3 _pdbx_chem_comp_identifier.type 'IUPAC CARBOHYDRATE SYMBOL' _pdbx_chem_comp_identifier.program PDB-CARE _pdbx_chem_comp_identifier.program_version 1 # _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 C1 GP4 . . . DA 7 184.39 157.926 179.363 1 112.17 ? C1 GP4 702 A 1 HETATM 2 C C2 GP4 . . . DA 7 183.628 156.926 178.5 1 112.17 ? C2 GP4 702 A 1 HETATM 3 C C3 GP4 . . . DA 7 183.039 157.584 177.255 1 112.17 ? C3 GP4 702 A 1 HETATM 4 C C4 GP4 . . . DA 7 182.334 158.886 177.594 1 112.17 ? C4 GP4 702 A 1 HETATM 5 C C5 GP4 . . . DA 7 183.211 159.767 178.454 1 112.17 ? C5 GP4 702 A 1 HETATM 6 C C6 GP4 . . . DA 7 182.486 161.047 178.836 1 112.17 ? C6 GP4 702 A 1 HETATM 7 N N2 GP4 . . . DA 7 184.574 155.815 178.074 1 112.17 ? N2 GP4 702 A 1 HETATM 8 O O4 GP4 . . . DA 7 182.012 159.576 176.388 1 112.17 ? O4 GP4 702 A 1 HETATM 9 O O6 GP4 . . . DA 7 181.918 160.9 180.141 1 112.17 ? O6 GP4 702 A 1 HETATM 10 O O5 GP4 . . . DA 7 183.573 159.065 179.636 1 112.17 ? O5 GP4 702 A 1 HETATM 11 O O7A GP4 . . . DA 7 180.245 161.702 176.641 1 112.17 ? O7A GP4 702 A 1 HETATM 12 P P4A GP4 . . . DA 7 180.443 160.1 176.079 1 112.17 ? P4A GP4 702 A 1 HETATM 13 O O8A GP4 . . . DA 7 179.352 159.083 176.868 1 112.17 ? O8A GP4 702 A 1 HETATM 14 O O9A GP4 . . . DA 7 180.151 160.072 174.427 1 112.17 ? O9A GP4 702 A 1 # _model_server_stats.io_time_ms 40 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 300 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #