data_4XJR # _model_server_result.job_id SmJ2Ey5lr0f2Q5RxPbZevg _model_server_result.datetime_utc '2024-11-18 06:52:33' _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 4xjr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":605}' # _entry.id 4XJR # _exptl.entry_id 4XJR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 6 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-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 4XJR _cell.length_a 81.85 _cell.length_b 98.303 _cell.length_c 103.261 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4XJR _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _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,K,L,M,N _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 ? 6 G N N ? 6 J 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 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 3 3 2 BMA NAG C1 O1 . O3 HO3 . 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 D 1 NAG 2 n C NAG 2 C 2 NAG D 2 NAG 3 n D NAG 1 D 1 NAG D 4 NAG 3 n D NAG 2 D 2 NAG D 5 NAG 3 n D BMA 3 D 3 BMA D 6 BMA # 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 35 A CYS 159 1_555 A SG CYS 447 A CYS 571 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 A SG CYS 66 A CYS 190 1_555 A SG CYS 90 A CYS 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? disulf ? disulf3 A SG CYS 132 A CYS 256 1_555 A SG CYS 145 A CYS 269 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf4 A SG CYS 226 A CYS 350 1_555 A SG CYS 239 A CYS 363 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf5 A SG CYS 231 A CYS 355 1_555 A SG CYS 345 A CYS 469 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf6 A SG CYS 339 A CYS 463 1_555 A SG CYS 349 A CYS 473 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? disulf ? disulf7 A SG CYS 411 A CYS 535 1_555 A SG CYS 420 A CYS 544 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? disulf ? disulf8 B SG CYS 35 B CYS 159 1_555 B SG CYS 447 B CYS 571 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? disulf ? disulf9 B SG CYS 66 B CYS 190 1_555 B SG CYS 90 B CYS 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf10 B SG CYS 132 B CYS 256 1_555 B SG CYS 145 B CYS 269 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf11 B SG CYS 226 B CYS 350 1_555 B SG CYS 239 B CYS 363 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf12 B SG CYS 231 B CYS 355 1_555 B SG CYS 345 B CYS 469 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? disulf ? disulf13 B SG CYS 339 B CYS 463 1_555 B SG CYS 349 B CYS 473 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf14 B SG CYS 411 B CYS 535 1_555 B SG CYS 420 B CYS 544 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? covale ? covale1 A ND2 ASN 227 A ASN 351 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale2 A ND2 ASN 399 A ASN 523 1_555 G C1 NAG . A NAG 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale3 A OH TYR 406 A TYR 530 1_555 H C2 OEL . A OEL 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.387 ? covale ? covale4 B ND2 ASN 227 B ASN 351 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale5 B ND2 ASN 399 B ASN 523 1_555 J C1 NAG . B NAG 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale6 B OH TYR 406 B TYR 530 1_555 K C2 OEL . B OEL 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.385 ? covale ? covale7 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale8 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale9 D O3 NAG . D NAG 2 1_555 D C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.465 ? metalc ? metalc1 A O ASP 155 A ASP 279 1_555 E CA CA . A CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.405 ? metalc ? metalc2 A OD1 ASP 155 A ASP 279 1_555 E CA CA . A CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.473 ? metalc ? metalc3 A O SER 158 A SER 282 1_555 E CA CA . A CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.322 ? metalc ? metalc4 A OG SER 158 A SER 282 1_555 E CA CA . A CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.496 ? metalc ? metalc5 A O GLY 160 A GLY 284 1_555 E CA CA . A CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? metalc ? metalc6 A O ALA 192 A ALA 316 1_555 E CA CA . A CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? metalc ? metalc7 B O ASP 155 B ASP 279 1_555 I CA CA . B CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.412 ? metalc ? metalc8 B OD1 ASP 155 B ASP 279 1_555 I CA CA . B CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.204 ? metalc ? metalc9 B O SER 158 B SER 282 1_555 I CA CA . B CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.254 ? metalc ? metalc10 B OG SER 158 B SER 282 1_555 I CA CA . B CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.774 ? metalc ? metalc11 B O GLY 160 B GLY 284 1_555 I CA CA . B CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.426 ? metalc ? metalc12 B O ALA 192 B ALA 316 1_555 I CA CA . B CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.413 ? # _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 270 n n C1 O1 NAG sing 271 n n C1 O5 NAG sing 272 n n C1 H1 NAG sing 273 n n C2 C3 NAG sing 274 n n C2 N2 NAG sing 275 n n C2 H2 NAG sing 276 n n C3 C4 NAG sing 277 n n C3 O3 NAG sing 278 n n C3 H3 NAG sing 279 n n C4 C5 NAG sing 280 n n C4 O4 NAG sing 281 n n C4 H4 NAG sing 282 n n C5 C6 NAG sing 283 n n C5 O5 NAG sing 284 n n C5 H5 NAG sing 285 n n C6 O6 NAG sing 286 n n C6 H61 NAG sing 287 n n C6 H62 NAG sing 288 n n C7 C8 NAG sing 289 n n C7 N2 NAG sing 290 n n C7 O7 NAG doub 291 n n C8 H81 NAG sing 292 n n C8 H82 NAG sing 293 n n C8 H83 NAG sing 294 n n N2 HN2 NAG sing 295 n n O1 HO1 NAG sing 296 n n O3 HO3 NAG sing 297 n n O4 HO4 NAG sing 298 n n O6 HO6 NAG sing 299 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 4XJR _atom_sites.fract_transf_matrix[1][1] 0.012217 _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] 0.010173 _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] 0.009684 _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 E 4 CA A 1 601 1 CA CA . F 5 SO4 A 1 602 3 SO4 SO4 . G 6 NAG A 1 605 3 NAG NAG . H 7 OEL A 1 606 9 OEL OEL . I 4 CA B 1 601 2 CA CA . J 6 NAG B 1 605 8 NAG NAG . K 7 OEL B 1 606 10 OEL OEL . L 8 EDO B 1 607 1 EDO EDO . M 9 HOH A 1 701 2 HOH HOH . M 9 HOH A 2 702 6 HOH HOH . M 9 HOH A 3 703 8 HOH HOH . N 9 HOH B 1 701 9 HOH HOH . N 9 HOH B 2 702 3 HOH HOH . # 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 6 38.645 -38.147 -29.498 1 63.05 ? C1 NAG 605 B 1 HETATM 2 C C2 NAG . . . J 6 39.933 -38.241 -30.311 1 65.73 ? C2 NAG 605 B 1 HETATM 3 C C3 NAG . . . J 6 40.03 -37.065 -31.276 1 65.69 ? C3 NAG 605 B 1 HETATM 4 C C4 NAG . . . J 6 38.779 -37.028 -32.159 1 64.81 ? C4 NAG 605 B 1 HETATM 5 C C5 NAG . . . J 6 37.525 -36.934 -31.288 1 64.21 ? C5 NAG 605 B 1 HETATM 6 C C6 NAG . . . J 6 36.224 -36.956 -32.095 1 63.65 ? C6 NAG 605 B 1 HETATM 7 C C7 NAG . . . J 6 41.68 -39.428 -29.075 1 63.79 ? C7 NAG 605 B 1 HETATM 8 C C8 NAG . . . J 6 42.802 -39.298 -28.092 1 64.16 ? C8 NAG 605 B 1 HETATM 9 N N2 NAG . . . J 6 41.06 -38.289 -29.391 1 63.15 ? N2 NAG 605 B 1 HETATM 10 O O3 NAG . . . J 6 41.217 -37.212 -32.064 1 64.39 ? O3 NAG 605 B 1 HETATM 11 O O4 NAG . . . J 6 38.83 -35.926 -33.067 1 65.14 ? O4 NAG 605 B 1 HETATM 12 O O5 NAG . . . J 6 37.516 -38.039 -30.384 1 65.15 ? O5 NAG 605 B 1 HETATM 13 O O6 NAG . . . J 6 36.09 -38.177 -32.839 1 62.97 ? O6 NAG 605 B 1 HETATM 14 O O7 NAG . . . J 6 41.376 -40.516 -29.544 1 63.16 ? O7 NAG 605 B 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 317 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #