data_3MDJ # _model_server_result.job_id 9_HZQ8MrIToZlg3UkijgXg _model_server_result.datetime_utc '2024-12-24 17:42:58' _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 3mdj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":6000}' # _entry.id 3MDJ # _exptl.entry_id 3MDJ _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 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 103.59 _cell.angle_gamma 90 _cell.entry_id 3MDJ _cell.length_a 71.029 _cell.length_b 234.635 _cell.length_c 95.86 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3MDJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 PISA monomeric 1 author_and_software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,G,H,I,J 1 1 B,E,K,L,M 2 1 C,F,N,O 3 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 I N N ? 6 J N N ? 6 M 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 ? 2 4 3 MAN BMA C1 O1 . O3 HO3 . sing 4 ? 2 5 3 MAN BMA C1 O1 . O6 HO6 . sing 5 ? 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 5001 NAG 2 n D NAG 2 D 2 NAG A 5002 NAG 2 n D BMA 3 D 3 BMA A 5003 BMA 2 n D MAN 4 D 4 MAN A 5004 MAN 2 n D MAN 5 D 5 MAN A 5005 MAN 3 n E NAG 1 E 1 NAG B 5001 NAG 3 n E NAG 2 E 2 NAG B 5002 NAG 2 n F NAG 1 F 1 NAG C 5001 NAG 2 n F NAG 2 F 2 NAG C 5002 NAG 2 n F BMA 3 F 3 BMA C 5003 BMA 2 n F MAN 4 F 4 MAN C 5004 MAN 2 n F MAN 5 F 5 MAN C 5005 MAN # 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 368 A CYS 404 1_555 A SG CYS 407 A CYS 443 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 A SG CYS 700 A CYS 736 1_555 A SG CYS 707 A CYS 743 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf3 B SG CYS 368 B CYS 404 1_555 B SG CYS 407 B CYS 443 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf4 B SG CYS 700 B CYS 736 1_555 B SG CYS 707 B CYS 743 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.964 ? disulf ? disulf5 C SG CYS 368 C CYS 404 1_555 C SG CYS 407 C CYS 443 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf6 C SG CYS 700 C CYS 736 1_555 C SG CYS 707 C CYS 743 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? covale ? covale1 A ND2 ASN 34 A ASN 70 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.478 ? covale ? covale2 A ND2 ASN 118 A ASN 154 1_555 I C1 NAG . A NAG 6000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.482 ? covale ? covale3 A ND2 ASN 724 A ASN 760 1_555 J C1 NAG . A NAG 6001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.479 ? covale ? covale4 B ND2 ASN 34 B ASN 70 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.498 ? covale ? covale5 B ND2 ASN 118 B ASN 154 1_555 M C1 NAG . B NAG 6000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.487 ? covale ? covale6 C ND2 ASN 34 C ASN 70 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.492 ? covale ? covale7 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.471 ? covale ? covale8 D O4 NAG . D NAG 2 1_555 D C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.418 ? covale ? covale9 D O3 BMA . D BMA 3 1_555 D C1 MAN . D MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.374 ? covale ? covale10 D O6 BMA . D BMA 3 1_555 D C1 MAN . D MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.485 ? covale ? covale11 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale12 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.477 ? covale ? covale13 F O4 NAG . F NAG 2 1_555 F C1 BMA . F BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.421 ? covale ? covale14 F O3 BMA . F BMA 3 1_555 F C1 MAN . F MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.381 ? covale ? covale15 F O6 BMA . F BMA 3 1_555 F C1 MAN . F MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.479 ? metalc ? metalc1 A NE2 HIS 317 A HIS 353 1_555 G ZN ZN . A ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? metalc ? metalc2 A NE2 HIS 321 A HIS 357 1_555 G ZN ZN . A ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.185 ? metalc ? metalc3 A OE1 GLU 340 A GLU 376 1_555 G ZN ZN . A ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.143 ? metalc ? metalc4 A OE2 GLU 340 A GLU 376 1_555 G ZN ZN . A ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.473 ? metalc ? metalc5 G ZN ZN . A ZN 1000 1_555 H O2 BES . A BES 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.191 ? metalc ? metalc6 B NE2 HIS 317 B HIS 353 1_555 K ZN ZN . B ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.203 ? metalc ? metalc7 B NE2 HIS 321 B HIS 357 1_555 K ZN ZN . B ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc8 B OE1 GLU 340 B GLU 376 1_555 K ZN ZN . B ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.238 ? metalc ? metalc9 B OE2 GLU 340 B GLU 376 1_555 K ZN ZN . B ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.502 ? metalc ? metalc10 K ZN ZN . B ZN 1000 1_555 L O2 BES . B BES 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? metalc ? metalc11 C NE2 HIS 317 C HIS 353 1_555 N ZN ZN . C ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.147 ? metalc ? metalc12 C NE2 HIS 321 C HIS 357 1_555 N ZN ZN . C ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.268 ? metalc ? metalc13 C OE1 GLU 340 C GLU 376 1_555 N ZN ZN . C ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? metalc ? metalc14 C OE2 GLU 340 C GLU 376 1_555 N ZN ZN . C ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.537 ? metalc ? metalc15 N ZN ZN . C ZN 1000 1_555 O O2 BES . C BES 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.402 ? # _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 329 n n C1 O1 NAG sing 330 n n C1 O5 NAG sing 331 n n C1 H1 NAG sing 332 n n C2 C3 NAG sing 333 n n C2 N2 NAG sing 334 n n C2 H2 NAG sing 335 n n C3 C4 NAG sing 336 n n C3 O3 NAG sing 337 n n C3 H3 NAG sing 338 n n C4 C5 NAG sing 339 n n C4 O4 NAG sing 340 n n C4 H4 NAG sing 341 n n C5 C6 NAG sing 342 n n C5 O5 NAG sing 343 n n C5 H5 NAG sing 344 n n C6 O6 NAG sing 345 n n C6 H61 NAG sing 346 n n C6 H62 NAG sing 347 n n C7 C8 NAG sing 348 n n C7 N2 NAG sing 349 n n C7 O7 NAG doub 350 n n C8 H81 NAG sing 351 n n C8 H82 NAG sing 352 n n C8 H83 NAG sing 353 n n N2 HN2 NAG sing 354 n n O1 HO1 NAG sing 355 n n O3 HO3 NAG sing 356 n n O4 HO4 NAG sing 357 n n O6 HO6 NAG sing 358 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 3MDJ _atom_sites.fract_transf_matrix[1][1] 0.014079 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003403 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.004262 _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] 0.010732 _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 G 4 ZN A 1 1000 1000 ZN ZN . H 5 BES A 1 1001 1001 BES BES . I 6 NAG A 1 6000 6000 NAG NAG . J 6 NAG A 1 6001 6001 NAG NAG . K 4 ZN B 1 1000 1000 ZN ZN . L 5 BES B 1 1001 1001 BES BES . M 6 NAG B 1 6000 6000 NAG NAG . N 4 ZN C 1 1000 1000 ZN ZN . O 5 BES C 1 1001 1001 BES BES . # 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 . . . M 6 27.955 52.088 -79.001 1 103.21 ? C1 NAG 6000 B 1 HETATM 2 C C2 NAG . . . M 6 28.307 51.613 -80.419 1 110.06 ? C2 NAG 6000 B 1 HETATM 3 C C3 NAG . . . M 6 27.097 50.981 -81.111 1 135.34 ? C3 NAG 6000 B 1 HETATM 4 C C4 NAG . . . M 6 26.563 49.839 -80.26 1 146.68 ? C4 NAG 6000 B 1 HETATM 5 C C5 NAG . . . M 6 26.169 50.418 -78.91 1 153.52 ? C5 NAG 6000 B 1 HETATM 6 C C6 NAG . . . M 6 25.632 49.401 -77.903 1 144.56 ? C6 NAG 6000 B 1 HETATM 7 C C7 NAG . . . M 6 29.974 52.702 -81.887 1 128.35 ? C7 NAG 6000 B 1 HETATM 8 C C8 NAG . . . M 6 30.819 51.473 -81.607 1 119.93 ? C8 NAG 6000 B 1 HETATM 9 N N2 NAG . . . M 6 28.77 52.708 -81.283 1 144.52 ? N2 NAG 6000 B 1 HETATM 10 O O3 NAG . . . M 6 27.465 50.492 -82.395 1 146.06 ? O3 NAG 6000 B 1 HETATM 11 O O4 NAG . . . M 6 25.432 49.25 -80.932 1 117.99 ? O4 NAG 6000 B 1 HETATM 12 O O5 NAG . . . M 6 27.325 51.01 -78.263 1 128.48 ? O5 NAG 6000 B 1 HETATM 13 O O6 NAG . . . M 6 25.318 50.093 -76.693 1 98.11 ? O6 NAG 6000 B 1 HETATM 14 O O7 NAG . . . M 6 30.361 53.605 -82.637 1 59.6 ? O7 NAG 6000 B 1 # _model_server_stats.io_time_ms 91 _model_server_stats.parse_time_ms 290 _model_server_stats.create_model_time_ms 222 _model_server_stats.query_time_ms 365 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 14 #