data_8RMJ # _model_server_result.job_id ViGfT9kHP8UXjqBr18Ji5Q _model_server_result.datetime_utc '2024-10-11 20:30:59' _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 8rmj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":701}' # _entry.id 8RMJ # _exptl.entry_id 8RMJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 3 _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 120 _cell.entry_id 8RMJ _cell.length_a 181.489 _cell.length_b 181.489 _cell.length_c 168.379 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8RMJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall 'P 65 2 (x,y,z+1/12)' _symmetry.space_group_name_H-M 'P 65 2 2' # _pdbx_struct_assembly.method_details PISA _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 12_544 x,x-y-1,-z-1/6 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 90.7445 -157.174085 -28.063167 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 7 H N N ? 7 I N N ? 7 J N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 oligosaccharide 4 oligosaccharide 5 oligosaccharide 6 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 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 4 ? 3 4 3 MAN BMA C1 O1 . O6 HO6 . sing 5 ? 3 5 4 MAN MAN C1 O1 . O3 HO3 . sing 6 ? 3 6 4 MAN MAN C1 O1 . O6 HO6 . sing 7 ? 3 7 3 MAN BMA C1 O1 . O3 HO3 . sing 8 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 9 ? 4 3 2 BMA NAG C1 O1 . O4 HO4 . sing 10 ? 4 4 3 MAN BMA C1 O1 . O6 HO6 . sing 11 ? 4 5 4 MAN MAN C1 O1 . O6 HO6 . sing 12 ? 4 6 5 MAN MAN C1 O1 . O2 HO2 . sing 13 ? 4 7 4 MAN MAN C1 O1 . O3 HO3 . sing 14 ? 4 8 3 MAN BMA C1 O1 . O3 HO3 . sing 15 ? 4 9 8 MAN MAN C1 O1 . O2 HO2 . sing 16 ? 5 2 1 NAG NAG C1 O1 . O4 HO4 . sing 17 ? 5 3 2 BMA NAG C1 O1 . O4 HO4 . sing 18 ? 5 4 3 MAN BMA C1 O1 . O6 HO6 . sing 19 ? 6 1 2 GU4 YYJ C1 O1 . O2 HO2 . 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 B NAG 1 B 1 NAG A 1000 NAG 2 n B NAG 2 B 2 NAG A 1001 NAG 3 n C NAG 1 C 1 NAG A 1200 NAG 3 n C NAG 2 C 2 NAG A 1201 NAG 3 n C BMA 3 C 3 BMA A 1202 BMA 3 n C MAN 4 C 4 MAN A 1203 MAN 3 n C MAN 5 C 5 MAN A 1204 MAN 3 n C MAN 6 C 6 MAN A 1207 MAN 3 n C MAN 7 C 7 MAN A 1206 MAN 4 n D NAG 1 D 1 NAG A 1300 NAG 4 n D NAG 2 D 2 NAG A 1301 NAG 4 n D BMA 3 D 3 BMA A 1302 BMA 4 n D MAN 4 D 4 MAN A 1303 MAN 4 n D MAN 5 D 5 MAN A 1304 MAN 4 n D MAN 6 D 6 MAN A 1305 MAN 4 n D MAN 7 D 7 MAN A 1306 MAN 4 n D MAN 8 D 8 MAN A 1308 MAN 4 n D MAN 9 D 9 MAN A 1309 MAN 5 n E NAG 1 E 1 NAG A 1600 NAG 5 n E NAG 2 E 2 NAG A 1601 NAG 5 n E BMA 3 E 3 BMA A 1602 BMA 5 n E MAN 4 E 4 MAN A 1603 MAN 6 n F GU4 1 F 1 GU4 A 1800 SCR 6 n F YYJ 2 F 2 YYJ A 1800 SCR 6 n G GU4 1 G 1 GU4 A 1801 SCR 6 n G YYJ 2 G 2 YYJ A 1801 SCR # 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 16 A CYS 47 1_555 A SG CYS 17 A CYS 48 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf2 A SG CYS 38 A CYS 69 1_555 A SG CYS 76 A CYS 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf3 A SG CYS 93 A CYS 124 1_555 A SG CYS 104 A CYS 135 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf4 A SG CYS 124 A CYS 155 1_555 A SG CYS 159 A CYS 190 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf5 A SG CYS 255 A CYS 286 1_555 A SG CYS 255 A CYS 286 12_544 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf6 A SG CYS 267 A CYS 298 1_555 A SG CYS 375 A CYS 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf7 A SG CYS 291 A CYS 322 1_555 A SG CYS 334 A CYS 365 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf8 A SG CYS 502 A CYS 533 1_555 A SG CYS 518 A CYS 549 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf9 A SG CYS 509 A CYS 540 1_555 A SG CYS 546 A CYS 577 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf10 A SG CYS 512 A CYS 543 1_555 A SG CYS 527 A CYS 558 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf11 A SG CYS 567 A CYS 598 1_555 A SG CYS 632 A CYS 663 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? covale ? covale1 A ND2 ASN 70 A ASN 101 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale2 A ND2 ASN 139 A ASN 170 1_555 H C1 NAG . A NAG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale3 A ND2 ASN 166 A ASN 197 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale4 A ND2 ASN 205 A ASN 236 1_555 I C1 NAG . A NAG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale5 A ND2 ASN 290 A ASN 321 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale6 A ND2 ASN 377 A ASN 408 1_555 J C1 NAG . A NAG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale7 A ND2 ASN 540 A ASN 571 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale8 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale9 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? covale ? covale10 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale11 C O6 BMA . C BMA 3 1_555 C C1 MAN . C MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale12 C O3 BMA . C BMA 3 1_555 C C1 MAN . C MAN 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale13 C O3 MAN . C MAN 4 1_555 C C1 MAN . C MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale14 C O6 MAN . C MAN 4 1_555 C C1 MAN . C MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.472 ? covale ? covale15 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale16 D O4 NAG . D NAG 2 1_555 D C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale17 D O6 BMA . D BMA 3 1_555 D C1 MAN . D MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale18 D O3 BMA . D BMA 3 1_555 D C1 MAN . D MAN 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale19 D O6 MAN . D MAN 4 1_555 D C1 MAN . D MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale20 D O3 MAN . D MAN 4 1_555 D C1 MAN . D MAN 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale21 D O2 MAN . D MAN 5 1_555 D C1 MAN . D MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale22 D O2 MAN . D MAN 8 1_555 D C1 MAN . D MAN 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale23 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale24 E O4 NAG . E NAG 2 1_555 E C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale25 E O6 BMA . E BMA 3 1_555 E C1 MAN . E MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale26 F C1 GU4 . F GU4 1 1_555 F O2 YYJ . F YYJ 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.389 ? covale ? covale27 G C1 GU4 . G GU4 1 1_555 G O2 YYJ . G YYJ 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.385 ? # _chem_comp.formula 'C8 H15 N O6' _chem_comp.formula_weight 221.208 _chem_comp.id NAG _chem_comp.mon_nstd_flag . _chem_comp.name 2-acetamido-2-deoxy-beta-D-glucopyranose _chem_comp.type 'd-saccharide, beta linking' _chem_comp.pdbx_synonyms N-acetyl-beta-D-glucosamine;2-acetamido-2-deoxy-beta-D-glucose;2-acetamido-2-deoxy-D-glucose;2-acetamido-2-deoxy-glucose;N-ACETYL-D-GLUCOSAMINE # 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 NAG sing 323 n n C1 O1 NAG sing 324 n n C1 O5 NAG sing 325 n n C1 H1 NAG sing 326 n n C2 C3 NAG sing 327 n n C2 N2 NAG sing 328 n n C2 H2 NAG sing 329 n n C3 C4 NAG sing 330 n n C3 O3 NAG sing 331 n n C3 H3 NAG sing 332 n n C4 C5 NAG sing 333 n n C4 O4 NAG sing 334 n n C4 H4 NAG sing 335 n n C5 C6 NAG sing 336 n n C5 O5 NAG sing 337 n n C5 H5 NAG sing 338 n n C6 O6 NAG sing 339 n n C6 H61 NAG sing 340 n n C6 H62 NAG sing 341 n n C7 C8 NAG sing 342 n n C7 N2 NAG sing 343 n n C7 O7 NAG doub 344 n n C8 H81 NAG sing 345 n n C8 H82 NAG sing 346 n n C8 H83 NAG sing 347 n n N2 HN2 NAG sing 348 n n O1 HO1 NAG sing 349 n n O3 HO3 NAG sing 350 n n O4 HO4 NAG sing 351 n n O6 HO6 NAG sing 352 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 NAG DGlcpNAcb 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 NAG N-acetyl-b-D-glucopyranosamine 'COMMON NAME' GMML 1 NAG b-D-GlcpNAc 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 NAG GlcNAc 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 8RMJ _atom_sites.fract_transf_matrix[1][1] 0.00551 _atom_sites.fract_transf_matrix[1][2] 0.003181 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006362 _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] 0.005939 _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 H 7 NAG A 1 701 1100 NAG NAG . I 7 NAG A 1 702 1400 NAG NAG . J 7 NAG A 1 703 1500 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 NAG . . . H 7 17.757 -39.337 10.852 1 126.76 ? C1 NAG 701 A 1 HETATM 2 C C2 NAG . . . H 7 17.525 -37.959 11.469 1 133.01 ? C2 NAG 701 A 1 HETATM 3 C C3 NAG . . . H 7 16.146 -37.898 12.118 1 126.67 ? C3 NAG 701 A 1 HETATM 4 C C4 NAG . . . H 7 15.071 -38.301 11.117 1 118.36 ? C4 NAG 701 A 1 HETATM 5 C C5 NAG . . . H 7 15.4 -39.659 10.503 1 119.83 ? C5 NAG 701 A 1 HETATM 6 C C6 NAG . . . H 7 14.439 -40.061 9.409 1 134.85 ? C6 NAG 701 A 1 HETATM 7 C C7 NAG . . . H 7 19.703 -37.023 12.108 1 134.21 ? C7 NAG 701 A 1 HETATM 8 C C8 NAG . . . H 7 20.661 -36.77 13.233 1 137.71 ? C8 NAG 701 A 1 HETATM 9 N N2 NAG . . . H 7 18.562 -37.638 12.437 1 127.74 ? N2 NAG 701 A 1 HETATM 10 O O3 NAG . . . H 7 15.9 -36.578 12.589 1 132.23 ? O3 NAG 701 A 1 HETATM 11 O O4 NAG . . . H 7 13.805 -38.371 11.765 1 124.83 ? O4 NAG 701 A 1 HETATM 12 O O5 NAG . . . H 7 16.71 -39.628 9.914 1 126.28 ? O5 NAG 701 A 1 HETATM 13 O O6 NAG . . . H 7 14.76 -39.432 8.177 1 137.22 ? O6 NAG 701 A 1 HETATM 14 O O7 NAG . . . H 7 19.951 -36.688 10.954 1 132.21 ? O7 NAG 701 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 318 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 14 #