data_8SJ9 # _model_server_result.job_id 5IT30HwrW3c_5KLrbzne1w _model_server_result.datetime_utc '2025-09-09 12:06:42' _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 8sj9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":602}' # _entry.id 8SJ9 # _exptl.entry_id 8SJ9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 10 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 109.68 _cell.angle_gamma 90 _cell.entry_id 8SJ9 _cell.length_a 68.504 _cell.length_b 218.725 _cell.length_c 68.572 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8SJ9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall 'P 2yb' _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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 ? 4 I N N ? 4 J N N ? 4 K N N ? 4 N N N ? 4 O N N ? 4 P N N ? 4 Q N N ? 4 S N N ? 4 T N N ? 4 U N 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 D NAG 1 D 1 NAG A 494 NAG 2 n D NAG 2 D 2 NAG A 495 NAG 2 n D BMA 3 D 3 BMA A 496 BMA 3 n E NAG 1 E 1 NAG B 492 NAG 3 n E NAG 2 E 2 NAG B 493 NAG 2 n F NAG 1 F 1 NAG C 492 NAG 2 n F NAG 2 F 2 NAG C 493 NAG 2 n F BMA 3 F 3 BMA C 494 BMA 2 n G NAG 1 G 1 NAG C 503 NAG 2 n G NAG 2 G 2 NAG C 504 NAG 2 n G BMA 3 G 3 BMA C 505 BMA 3 n H NAG 1 H 1 NAG C 506 NAG 3 n H NAG 2 H 2 NAG C 507 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 9 A CYS 4 1_555 A SG CYS 468 A CYS 463 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 A SG CYS 47 A CYS 42 1_555 A SG CYS 279 A CYS 274 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf3 A SG CYS 60 A CYS 55 1_555 A SG CYS 72 A CYS 67 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf4 A SG CYS 95 A CYS 90 1_555 A SG CYS 140 A CYS 135 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf5 A SG CYS 283 A CYS 278 1_555 A SG CYS 307 A CYS 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf6 A SG CYS 475 A CYS 470 1_555 A SG CYS 479 A CYS 474 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf7 B SG CYS 9 B CYS 4 1_555 B SG CYS 468 B CYS 463 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf8 B SG CYS 47 B CYS 42 1_555 B SG CYS 279 B CYS 274 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf9 B SG CYS 60 B CYS 55 1_555 B SG CYS 72 B CYS 67 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf10 B SG CYS 95 B CYS 90 1_555 B SG CYS 140 B CYS 135 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf11 B SG CYS 283 B CYS 278 1_555 B SG CYS 307 B CYS 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf12 B SG CYS 475 B CYS 470 1_555 B SG CYS 479 B CYS 474 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf13 C SG CYS 9 C CYS 4 1_555 C SG CYS 468 C CYS 463 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf14 C SG CYS 47 C CYS 42 1_555 C SG CYS 279 C CYS 274 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf15 C SG CYS 60 C CYS 55 1_555 C SG CYS 72 C CYS 67 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf16 C SG CYS 95 C CYS 90 1_555 C SG CYS 140 C CYS 135 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf17 C SG CYS 283 C CYS 278 1_555 C SG CYS 307 C CYS 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf18 C SG CYS 475 C CYS 470 1_555 C SG CYS 479 C CYS 474 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? covale ? covale1 A ND2 ASN 16 A ASN 11 1_555 I C1 NAG . A NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale2 A ND2 ASN 28 A ASN 23 1_555 K C1 NAG . A NAG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale3 A ND2 ASN 92 A ASN 87 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale4 A ND2 ASN 164 A ASN 159 1_555 J C1 NAG . A NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale5 B ND2 ASN 28 B ASN 23 1_555 O C1 NAG . B NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale6 B ND2 ASN 59 B ASN 54 1_555 N C1 NAG . B NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale7 B ND2 ASN 92 B ASN 87 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale8 B ND2 ASN 130 B ASN 125 1_555 Q C1 NAG . B NAG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale9 B ND2 ASN 164 B ASN 159 1_555 P C1 NAG . B NAG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale10 C ND2 ASN 16 C ASN 11 1_555 U C1 NAG . C NAG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale11 C ND2 ASN 28 C ASN 23 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale12 C ND2 ASN 59 C ASN 54 1_555 S C1 NAG . C NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale13 C ND2 ASN 92 C ASN 87 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale14 C ND2 ASN 164 C ASN 159 1_555 T C1 NAG . C NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale15 C ND2 ASN 291 C ASN 286 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale16 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale17 D O4 NAG . D NAG 2 1_555 D C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale18 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale19 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale20 F O4 NAG . F NAG 2 1_555 F C1 BMA . F BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale21 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.46 ? covale ? covale22 G O4 NAG . G NAG 2 1_555 G C1 BMA . G BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale23 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? # _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 281 n n C1 O1 NAG sing 282 n n C1 O5 NAG sing 283 n n C1 H1 NAG sing 284 n n C2 C3 NAG sing 285 n n C2 N2 NAG sing 286 n n C2 H2 NAG sing 287 n n C3 C4 NAG sing 288 n n C3 O3 NAG sing 289 n n C3 H3 NAG sing 290 n n C4 C5 NAG sing 291 n n C4 O4 NAG sing 292 n n C4 H4 NAG sing 293 n n C5 C6 NAG sing 294 n n C5 O5 NAG sing 295 n n C5 H5 NAG sing 296 n n C6 O6 NAG sing 297 n n C6 H61 NAG sing 298 n n C6 H62 NAG sing 299 n n C7 C8 NAG sing 300 n n C7 N2 NAG sing 301 n n C7 O7 NAG doub 302 n n C8 H81 NAG sing 303 n n C8 H82 NAG sing 304 n n C8 H83 NAG sing 305 n n N2 HN2 NAG sing 306 n n O1 HO1 NAG sing 307 n n O3 HO3 NAG sing 308 n n O4 HO4 NAG sing 309 n n O6 HO6 NAG sing 310 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 8SJ9 _atom_sites.fract_transf_matrix[1][1] 0.014598 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.005221 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.004572 _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] 0.015488 _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 NAG A 1 601 492 NAG NAG . J 4 NAG A 1 602 498 NAG NAG . K 4 NAG A 1 603 499 NAG NAG . L 5 EDO A 1 604 500 EDO EDO . M 6 GOL A 1 605 497 GOL GOL . N 4 NAG B 1 601 496 NAG NAG . O 4 NAG B 1 602 498 NAG NAG . P 4 NAG B 1 603 499 NAG NAG . Q 4 NAG B 1 604 500 NAG NAG . R 5 EDO B 1 605 1 EDO EDO . S 4 NAG C 1 601 495 NAG NAG . T 4 NAG C 1 602 499 NAG NAG . U 4 NAG C 1 603 500 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 . . . J 4 -20.707 -94.157 -46.764 1 169.96 ? C1 NAG 602 A 1 HETATM 2 C C2 NAG . . . J 4 -20.754 -95.641 -46.401 1 175.25 ? C2 NAG 602 A 1 HETATM 3 C C3 NAG . . . J 4 -22.16 -96.193 -46.618 1 178.52 ? C3 NAG 602 A 1 HETATM 4 C C4 NAG . . . J 4 -23.185 -95.349 -45.872 1 181.8 ? C4 NAG 602 A 1 HETATM 5 C C5 NAG . . . J 4 -23.037 -93.878 -46.252 1 173.35 ? C5 NAG 602 A 1 HETATM 6 C C6 NAG . . . J 4 -23.944 -92.966 -45.459 1 172.15 ? C6 NAG 602 A 1 HETATM 7 C C7 NAG . . . J 4 -18.534 -96.633 -46.755 1 146.7 ? C7 NAG 602 A 1 HETATM 8 C C8 NAG . . . J 4 -17.67 -97.433 -47.682 1 155.26 ? C8 NAG 602 A 1 HETATM 9 N N2 NAG . . . J 4 -19.783 -96.399 -47.174 1 163.72 ? N2 NAG 602 A 1 HETATM 10 O O3 NAG . . . J 4 -22.216 -97.541 -46.166 1 184.52 ? O3 NAG 602 A 1 HETATM 11 O O4 NAG . . . J 4 -24.501 -95.786 -46.192 1 184.45 ? O4 NAG 602 A 1 HETATM 12 O O5 NAG . . . J 4 -21.692 -93.444 -46.003 1 174.43 ? O5 NAG 602 A 1 HETATM 13 O O6 NAG . . . J 4 -23.809 -93.184 -44.061 1 180.9 ? O6 NAG 602 A 1 HETATM 14 O O7 NAG . . . J 4 -18.12 -96.215 -45.679 1 128.54 ? O7 NAG 602 A 1 # _model_server_stats.io_time_ms 64 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 334 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #