data_8Y8J # _model_server_result.job_id MmNLi-2vVq9kAuHbZxRsNw _model_server_result.datetime_utc '2024-11-22 13:24:10' _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 8y8j # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":1301}' # _entry.id 8Y8J # _exptl.entry_id 8Y8J _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 365.333 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'methyl 9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid' _entity.pdbx_number_of_molecules 1 _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 8Y8J _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8Y8J _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id I _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 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 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 3 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 2 n C NAG 1 C 1 NAG A 304 NAG 2 n C NAG 2 C 2 NAG A 305 NAG 2 n C BMA 3 C 3 BMA A 306 BMA 3 n D NAG 1 D 1 NAG A 312 NAG 3 n D NAG 2 D 2 NAG A 313 NAG 3 n E NAG 1 E 1 NAG A 315 NAG 3 n E NAG 2 E 2 NAG A 316 NAG 3 n F NAG 1 F 1 NAG A 319 NAG 3 n F NAG 2 F 2 NAG A 320 NAG 3 n G NAG 1 G 1 NAG B 672 NAG 3 n G NAG 2 G 2 NAG B 673 NAG 3 n H NAG 1 H 1 NAG B 674 NAG 3 n H NAG 2 H 2 NAG B 675 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 A CYS 20 1_555 A SG CYS 143 A CYS 156 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf2 A SG CYS 138 A CYS 151 1_555 A SG CYS 170 A CYS 183 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf3 A SG CYS 150 A CYS 163 1_555 A SG CYS 229 A CYS 242 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf4 B SG CYS 314 B CYS 327 1_555 B SG CYS 339 B CYS 352 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf5 B SG CYS 357 B CYS 370 1_555 B SG CYS 410 B CYS 423 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf6 B SG CYS 369 B CYS 382 1_555 B SG CYS 590 B CYS 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf7 B SG CYS 453 B CYS 466 1_555 B SG CYS 533 B CYS 546 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf8 B SG CYS 461 B CYS 474 1_555 B SG CYS 482 B CYS 495 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf9 B SG CYS 463 B CYS 476 1_555 B SG CYS 552 B CYS 565 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf10 B SG CYS 472 B CYS 485 1_555 B SG CYS 503 B CYS 516 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf11 B SG CYS 491 B CYS 504 1_555 B SG CYS 505 B CYS 518 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf12 B SG CYS 507 B CYS 520 1_555 B SG CYS 520 B CYS 533 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf13 B SG CYS 543 B CYS 556 1_555 B SG CYS 554 B CYS 567 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? covale ? covale1 A ND2 ASN 6 A ASN 19 1_555 J C1 NAG . A NAG 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale2 A ND2 ASN 119 A ASN 132 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale3 A ND2 ASN 158 A ASN 171 1_555 K C1 NAG . A NAG 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale4 A ND2 ASN 175 A ASN 188 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale5 A ND2 ASN 179 A ASN 192 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale6 A ND2 ASN 238 A ASN 251 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale7 B ND2 ASN 342 B ASN 355 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale8 B ND2 ASN 420 B ASN 433 1_555 M C1 NAG . B NAG 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale9 B ND2 ASN 441 B ASN 454 1_555 L C1 NAG . B NAG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale10 B ND2 ASN 651 B ASN 664 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale11 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale12 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale13 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale14 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale15 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale16 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale17 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? # _chem_comp.formula 'C14 H23 N O10' _chem_comp.formula_weight 365.333 _chem_comp.id MJJ _chem_comp.mon_nstd_flag n _chem_comp.name 'methyl 9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid' _chem_comp.type d-saccharide _chem_comp.pdbx_synonyms 'methyl 9-O-acetyl-5-(acetylamino)-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid;methyl 9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulosidonic acid;methyl 9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-D-galacto-non-2-ulosidonic acid;methyl 9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-galacto-non-2-ulosidonic acid' # 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 O4 C4 MJJ sing 259 n n C3 C4 MJJ sing 260 n n C3 C2 MJJ sing 261 n n O2 C2 MJJ sing 262 n n O2 CM2 MJJ sing 263 n n C4 C5 MJJ sing 264 n n O10 C10 MJJ doub 265 n n C2 O6 MJJ sing 266 n n C2 C1 MJJ sing 267 n n C5 N5 MJJ sing 268 n n C5 C6 MJJ sing 269 n n C10 N5 MJJ sing 270 n n C10 C11 MJJ sing 271 n n O1A C1 MJJ doub 272 n n O6 C6 MJJ sing 273 n n C1 O1B MJJ sing 274 n n C6 C7 MJJ sing 275 n n O7 C7 MJJ sing 276 n n C7 C8 MJJ sing 277 n n C8 O8 MJJ sing 278 n n C8 C9 MJJ sing 279 n n C9 O9 MJJ sing 280 n n O9 CA9 MJJ sing 281 n n CA9 OA9 MJJ doub 282 n n CA9 CM9 MJJ sing 283 n n O4 HO4 MJJ sing 284 n n C4 H4 MJJ sing 285 n n C5 H5 MJJ sing 286 n n N5 HN5 MJJ sing 287 n n C11 H111 MJJ sing 288 n n C11 H113 MJJ sing 289 n n C11 H112 MJJ sing 290 n n C3 H32 MJJ sing 291 n n C3 H31 MJJ sing 292 n n CM2 H10 MJJ sing 293 n n CM2 H11 MJJ sing 294 n n CM2 H12 MJJ sing 295 n n O1B HO1B MJJ sing 296 n n C6 H6 MJJ sing 297 n n C7 H7 MJJ sing 298 n n O7 HO7 MJJ sing 299 n n C8 H8 MJJ sing 300 n n O8 HO8 MJJ sing 301 n n C9 H92 MJJ sing 302 n n C9 H91 MJJ sing 303 n n CM9 H21 MJJ sing 304 n n CM9 H22 MJJ sing 305 n n CM9 H23 MJJ sing 306 n n # _atom_sites.entry_id 8Y8J _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 4 MJJ A 1 1301 301 MJJ MJJ . J 5 NAG A 1 1302 308 NAG NAG . K 5 NAG A 1 1303 318 NAG NAG . L 5 NAG B 1 1301 676 NAG NAG . M 5 NAG B 1 1302 677 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 O4 MJJ . . . I 4 195.738 214.9 195.107 1 92.85 ? O4 MJJ 1301 A 1 HETATM 2 C C4 MJJ . . . I 4 196.011 213.526 194.678 1 92.85 ? C4 MJJ 1301 A 1 HETATM 3 C C5 MJJ . . . I 4 195.47 212.579 195.719 1 92.85 ? C5 MJJ 1301 A 1 HETATM 4 N N5 MJJ . . . I 4 195.547 211.196 195.184 1 92.85 ? N5 MJJ 1301 A 1 HETATM 5 C C10 MJJ . . . I 4 194.396 210.631 194.503 1 92.85 ? C10 MJJ 1301 A 1 HETATM 6 O O10 MJJ . . . I 4 193.408 211.274 194.381 1 92.85 ? O10 MJJ 1301 A 1 HETATM 7 C C11 MJJ . . . I 4 194.456 209.211 193.947 1 92.85 ? C11 MJJ 1301 A 1 HETATM 8 C C3 MJJ . . . I 4 197.45 213.381 194.452 1 92.85 ? C3 MJJ 1301 A 1 HETATM 9 C C2 MJJ . . . I 4 198.182 213.199 195.777 1 92.85 ? C2 MJJ 1301 A 1 HETATM 10 O O2 MJJ . . . I 4 198.348 214.606 195.859 1 92.85 ? O2 MJJ 1301 A 1 HETATM 11 C CM2 MJJ . . . I 4 199.052 215.347 194.882 1 92.85 ? CM2 MJJ 1301 A 1 HETATM 12 C C1 MJJ . . . I 4 199.669 213.031 195.821 1 92.85 ? C1 MJJ 1301 A 1 HETATM 13 O O1A MJJ . . . I 4 200.313 213.362 196.854 1 92.85 ? O1A MJJ 1301 A 1 HETATM 14 O O1B MJJ . . . I 4 200.279 212.525 194.841 1 92.85 ? O1B MJJ 1301 A 1 HETATM 15 O O6 MJJ . . . I 4 197.43 213.388 197.065 1 92.85 ? O6 MJJ 1301 A 1 HETATM 16 C C6 MJJ . . . I 4 196.185 212.63 197.071 1 92.85 ? C6 MJJ 1301 A 1 HETATM 17 C C7 MJJ . . . I 4 195.25 213.238 198.096 1 92.85 ? C7 MJJ 1301 A 1 HETATM 18 O O7 MJJ . . . I 4 194.595 214.349 197.538 1 92.85 ? O7 MJJ 1301 A 1 HETATM 19 C C8 MJJ . . . I 4 196.053 213.683 199.321 1 92.85 ? C8 MJJ 1301 A 1 HETATM 20 O O8 MJJ . . . I 4 197.164 212.849 199.481 1 92.85 ? O8 MJJ 1301 A 1 HETATM 21 C C9 MJJ . . . I 4 195.173 213.602 200.564 1 92.85 ? C9 MJJ 1301 A 1 HETATM 22 O O9 MJJ . . . I 4 194.297 212.519 200.445 1 92.85 ? O9 MJJ 1301 A 1 HETATM 23 C CA9 MJJ . . . I 4 193.568 212.243 201.607 1 92.85 ? CA9 MJJ 1301 A 1 HETATM 24 O OA9 MJJ . . . I 4 193.802 212.83 202.61 1 92.85 ? OA9 MJJ 1301 A 1 HETATM 25 C CM9 MJJ . . . I 4 192.47 211.183 201.581 1 92.85 ? CM9 MJJ 1301 A 1 # _model_server_stats.io_time_ms 110 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 301 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 25 #