data_8P31 # _model_server_result.job_id xf7FjaZnsWYRmc8pRJYwDg _model_server_result.datetime_utc '2024-11-23 10:17:49' _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 8p31 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":902}' # _entry.id 8P31 # _exptl.entry_id 8P31 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 221.208 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-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 8P31 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8P31 _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_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 ? _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 ? 6 J N N ? 6 P 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 4 n F NAG 1 F 1 NAG F 1 NAG 4 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 G BMA 3 G 3 BMA G 3 BMA 4 n H NAG 1 H 1 NAG H 1 NAG 4 n H NAG 2 H 2 NAG H 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 140 A CYS 133 1_555 A SG CYS 148 A CYS 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 A SG CYS 351 A CYS 344 1_555 A SG CYS 368 A CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf3 A SG CYS 537 A CYS 530 1_555 A SG CYS 549 A CYS 542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf4 B SG CYS 140 B CYS 133 1_555 B SG CYS 148 B CYS 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf5 B SG CYS 351 B CYS 344 1_555 B SG CYS 368 B CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf6 B SG CYS 537 B CYS 530 1_555 B SG CYS 549 B CYS 542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf7 C SG CYS 126 C CYS 126 1_555 C SG CYS 139 C CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf8 C SG CYS 309 C CYS 309 1_555 C SG CYS 358 C CYS 358 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf9 D SG CYS 126 D CYS 126 1_555 D SG CYS 139 D CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf10 D SG CYS 309 D CYS 309 1_555 D SG CYS 358 D CYS 358 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? covale ? covale1 A ND2 ASN 97 A ASN 90 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale2 A ND2 ASN 110 A ASN 103 1_555 K C1 NAG . A NAG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale3 A ND2 ASN 329 A ASN 322 1_555 L C1 NAG . A NAG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale4 A ND2 ASN 439 A ASN 432 1_555 M C1 NAG . A NAG 905 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale5 A ND2 ASN 553 A ASN 546 1_555 N C1 NAG . A NAG 906 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale6 A ND2 ASN 697 A ASN 690 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale7 A OG1 THR 737 A THR 730 1_555 J C1 NDG . A NDG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.374 ? covale ? covale8 B ND2 ASN 97 B ASN 90 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale9 B ND2 ASN 110 B ASN 103 1_555 Q C1 NAG . B NAG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale10 B ND2 ASN 329 B ASN 322 1_555 R C1 NAG . B NAG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale11 B ND2 ASN 439 B ASN 432 1_555 S C1 NAG . B NAG 905 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale12 B ND2 ASN 553 B ASN 546 1_555 T C1 NAG . B NAG 906 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale13 B ND2 ASN 697 B ASN 690 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale14 B OG1 THR 737 B THR 730 1_555 P C1 NDG . B NDG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.374 ? covale ? covale15 C ND2 ASN 131 C ASN 131 1_555 U C1 NAG . C NAG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale16 C ND2 ASN 357 C ASN 357 1_555 V C1 NAG . C NAG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale17 D ND2 ASN 131 D ASN 131 1_555 X C1 NAG . D NAG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale18 D ND2 ASN 357 D ASN 357 1_555 Y C1 NAG . D NAG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale19 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale20 E O4 NAG . E NAG 2 1_555 E C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale21 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale22 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale23 G O4 NAG . G NAG 2 1_555 G C1 BMA . G BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale24 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? metalc ? metalc1 A NE2 HIS 381 A HIS 374 1_555 I ZN ZN . A ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? metalc ? metalc2 A NE2 HIS 385 A HIS 378 1_555 I ZN ZN . A ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? metalc ? metalc3 A OE1 GLU 409 A GLU 402 1_555 I ZN ZN . A ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.668 ? metalc ? metalc4 A OE2 GLU 409 A GLU 402 1_555 I ZN ZN . A ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.245 ? metalc ? metalc5 B NE2 HIS 381 B HIS 374 1_555 O ZN ZN . B ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? metalc ? metalc6 B NE2 HIS 385 B HIS 378 1_555 O ZN ZN . B ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? metalc ? metalc7 B OE1 GLU 409 B GLU 402 1_555 O ZN ZN . B ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.668 ? metalc ? metalc8 B OE2 GLU 409 B GLU 402 1_555 O ZN ZN . B ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.243 ? # _chem_comp.formula 'C8 H15 N O6' _chem_comp.formula_weight 221.208 _chem_comp.id NDG _chem_comp.mon_nstd_flag . _chem_comp.name 2-acetamido-2-deoxy-alpha-D-glucopyranose _chem_comp.type 'd-saccharide, alpha linking' _chem_comp.pdbx_synonyms N-acetyl-alpha-D-glucosamine;2-acetamido-2-deoxy-alpha-D-glucose;2-acetamido-2-deoxy-D-glucose;2-acetamido-2-deoxy-glucose;2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE # 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 NDG sing 289 n n C1 O5 NDG sing 290 n n C1 O1 NDG sing 291 n n C1 H1 NDG sing 292 n n C2 C3 NDG sing 293 n n C2 N2 NDG sing 294 n n C2 H2 NDG sing 295 n n C3 C4 NDG sing 296 n n C3 O3 NDG sing 297 n n C3 H3 NDG sing 298 n n C4 C5 NDG sing 299 n n C4 O4 NDG sing 300 n n C4 H4 NDG sing 301 n n C5 C6 NDG sing 302 n n C5 O5 NDG sing 303 n n C5 H5 NDG sing 304 n n C6 O6 NDG sing 305 n n C6 H61 NDG sing 306 n n C6 H62 NDG sing 307 n n C7 C8 NDG sing 308 n n C7 O7 NDG doub 309 n n C7 N2 NDG sing 310 n n C8 H81 NDG sing 311 n n C8 H82 NDG sing 312 n n C8 H83 NDG sing 313 n n O3 HO3 NDG sing 314 n n O4 HO4 NDG sing 315 n n O6 HO6 NDG sing 316 n n N2 HN2 NDG sing 317 n n O1 HO1 NDG sing 318 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 NDG DGlcpNAca 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 NDG N-acetyl-a-D-glucopyranosamine 'COMMON NAME' GMML 1 NDG a-D-GlcpNAc 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 NDG GlcNAc 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 8P31 _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 I 5 ZN A 1 901 914 ZN ZN . J 6 NDG A 1 902 940 NDG NDG . K 7 NAG A 1 903 945 NAG NAG . L 7 NAG A 1 904 946 NAG NAG . M 7 NAG A 1 905 947 NAG NAG . N 7 NAG A 1 906 948 NAG NAG . O 5 ZN B 1 901 914 ZN ZN . P 6 NDG B 1 902 940 NDG NDG . Q 7 NAG B 1 903 945 NAG NAG . R 7 NAG B 1 904 946 NAG NAG . S 7 NAG B 1 905 947 NAG NAG . T 7 NAG B 1 906 948 NAG NAG . U 7 NAG C 1 701 583 NAG NAG . V 7 NAG C 1 702 584 NAG NAG . W 8 YCP C 1 703 585 YCP PIC . X 7 NAG D 1 701 583 NAG NAG . Y 7 NAG D 1 702 584 NAG NAG . Z 8 YCP D 1 703 585 YCP PIC . # 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 NDG . . . J 6 152.844 177.031 188.735 1 134.65 ? C1 NDG 902 A 1 HETATM 2 C C2 NDG . . . J 6 154.179 176.261 188.6 1 134.65 ? C2 NDG 902 A 1 HETATM 3 C C3 NDG . . . J 6 154.864 176.168 189.963 1 134.65 ? C3 NDG 902 A 1 HETATM 4 C C4 NDG . . . J 6 155.066 177.567 190.525 1 134.65 ? C4 NDG 902 A 1 HETATM 5 C C5 NDG . . . J 6 153.693 178.246 190.643 1 134.65 ? C5 NDG 902 A 1 HETATM 6 C C6 NDG . . . J 6 153.774 179.697 191.124 1 134.65 ? C6 NDG 902 A 1 HETATM 7 C C7 NDG . . . J 6 154.787 174.442 187.02 1 134.65 ? C7 NDG 902 A 1 HETATM 8 C C8 NDG . . . J 6 155.793 175.426 186.434 1 134.65 ? C8 NDG 902 A 1 HETATM 9 O O5 NDG . . . J 6 153.06 178.297 189.36 1 134.65 ? O5 NDG 902 A 1 HETATM 10 O O3 NDG . . . J 6 156.102 175.486 189.8 1 134.65 ? O3 NDG 902 A 1 HETATM 11 O O4 NDG . . . J 6 155.72 177.411 191.776 1 134.65 ? O4 NDG 902 A 1 HETATM 12 O O6 NDG . . . J 6 152.592 180.432 190.781 1 134.65 ? O6 NDG 902 A 1 HETATM 13 O O7 NDG . . . J 6 154.663 173.303 186.584 1 134.65 ? O7 NDG 902 A 1 HETATM 14 N N2 NDG . . . J 6 154.043 174.915 188.065 1 134.65 ? N2 NDG 902 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 45 _model_server_stats.query_time_ms 222 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 14 #