data_5ZSM # _model_server_result.job_id G_fDo08F88xN2jGzKIVk1w _model_server_result.datetime_utc '2024-11-28 10:02:59' _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 5zsm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":909}' # _entry.id 5ZSM # _exptl.entry_id 5ZSM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 4 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 13 _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 5ZSM _cell.length_a 99.655 _cell.length_b 139.173 _cell.length_c 150.794 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5ZSM _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 tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA _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 G N N ? 4 H N N ? 4 I N N ? 4 J N N ? 4 K N N ? 4 L N N ? 4 M N N ? 4 N N N ? 4 S N N ? 4 T N N ? 4 U N N ? 4 V N N ? 4 W N N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 3 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order 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 3 n E NAG 1 C 1 NAG B 838 NAG 3 n E NAG 2 C 2 NAG B 839 NAG 3 n F NAG 1 F 1 NAG A 838 NAG 3 n F NAG 2 F 2 NAG A 839 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 14 B CYS 36 1_555 A SG CYS 29 B CYS 51 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? disulf ? disulf2 A SG CYS 76 B CYS 98 1_555 A SG CYS 453 B CYS 475 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf3 A SG CYS 78 B CYS 100 1_555 A SG CYS 90 B CYS 112 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? disulf ? disulf4 A SG CYS 161 B CYS 183 1_555 A SG CYS 167 B CYS 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? disulf ? disulf5 A SG CYS 238 B CYS 260 1_555 A SG CYS 251 B CYS 273 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? disulf ? disulf6 A SG CYS 241 B CYS 263 1_555 A SG CYS 248 B CYS 270 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf7 A SG CYS 469 B CYS 491 1_555 A SG CYS 499 B CYS 521 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf8 A SG CYS 765 B CYS 787 1_555 A SG CYS 792 B CYS 814 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.948 ? disulf ? disulf9 A SG CYS 767 B CYS 789 1_555 A SG CYS 811 B CYS 833 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? disulf ? disulf10 B SG CYS 14 A CYS 36 1_555 B SG CYS 29 A CYS 51 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? disulf ? disulf11 B SG CYS 76 A CYS 98 1_555 B SG CYS 453 A CYS 475 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf12 B SG CYS 78 A CYS 100 1_555 B SG CYS 90 A CYS 112 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? disulf ? disulf13 B SG CYS 161 A CYS 183 1_555 B SG CYS 167 A CYS 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf14 B SG CYS 238 A CYS 260 1_555 B SG CYS 251 A CYS 273 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? disulf ? disulf15 B SG CYS 241 A CYS 263 1_555 B SG CYS 248 A CYS 270 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf16 B SG CYS 469 A CYS 491 1_555 B SG CYS 499 A CYS 521 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? disulf ? disulf17 B SG CYS 765 A CYS 787 1_555 B SG CYS 792 A CYS 814 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? disulf ? disulf18 B SG CYS 767 A CYS 789 1_555 B SG CYS 811 A CYS 833 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? covale ? covale1 A ND2 ASN 47 B ASN 69 1_555 M C1 NAG . B NAG 909 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale2 A ND2 ASN 193 B ASN 215 1_555 E C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale3 A ND2 ASN 339 B ASN 361 1_555 K C1 NAG . B NAG 907 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.418 ? covale ? covale4 A ND2 ASN 391 B ASN 413 1_555 I C1 NAG . B NAG 905 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale5 A ND2 ASN 501 B ASN 523 1_555 H C1 NAG . B NAG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.426 ? covale ? covale6 A ND2 ASN 512 B ASN 534 1_555 L C1 NAG . B NAG 908 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.412 ? covale ? covale7 A ND2 ASN 568 B ASN 590 1_555 G C1 NAG . B NAG 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale8 A ND2 ASN 657 B ASN 679 1_555 N C1 NAG . B NAG 910 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.476 ? covale ? covale9 A ND2 ASN 698 B ASN 720 1_555 J C1 NAG . B NAG 906 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale10 B ND2 ASN 47 A ASN 69 1_555 U C1 NAG . A NAG 905 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale11 B ND2 ASN 193 A ASN 215 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale12 B ND2 ASN 391 A ASN 413 1_555 V C1 NAG . A NAG 906 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? covale ? covale13 B ND2 ASN 501 A ASN 523 1_555 T C1 NAG . A NAG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.398 ? covale ? covale14 B ND2 ASN 512 A ASN 534 1_555 W C1 NAG . A NAG 907 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale15 B ND2 ASN 568 A ASN 590 1_555 S C1 NAG . A NAG 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale16 E O4 NAG . C NAG 1 1_555 E C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale17 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? # _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 351 n n C1 O1 NAG sing 352 n n C1 O5 NAG sing 353 n n C1 H1 NAG sing 354 n n C2 C3 NAG sing 355 n n C2 N2 NAG sing 356 n n C2 H2 NAG sing 357 n n C3 C4 NAG sing 358 n n C3 O3 NAG sing 359 n n C3 H3 NAG sing 360 n n C4 C5 NAG sing 361 n n C4 O4 NAG sing 362 n n C4 H4 NAG sing 363 n n C5 C6 NAG sing 364 n n C5 O5 NAG sing 365 n n C5 H5 NAG sing 366 n n C6 O6 NAG sing 367 n n C6 H61 NAG sing 368 n n C6 H62 NAG sing 369 n n C7 C8 NAG sing 370 n n C7 N2 NAG sing 371 n n C7 O7 NAG doub 372 n n C8 H81 NAG sing 373 n n C8 H82 NAG sing 374 n n C8 H83 NAG sing 375 n n N2 HN2 NAG sing 376 n n O1 HO1 NAG sing 377 n n O3 HO3 NAG sing 378 n n O4 HO4 NAG sing 379 n n O6 HO6 NAG sing 380 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 5ZSM _atom_sites.fract_transf_matrix[1][1] 0.010035 _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] 0.007185 _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] 0.006632 _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 NAG B 1 901 836 NAG NAG . H 4 NAG B 1 902 837 NAG NAG . I 4 NAG B 1 905 840 NAG NAG . J 4 NAG B 1 906 841 NAG NAG . K 4 NAG B 1 907 842 NAG NAG . L 4 NAG B 1 908 843 NAG NAG . M 4 NAG B 1 909 844 NAG NAG . N 4 NAG B 1 910 845 NAG NAG . O 5 SO4 B 1 911 2 SO4 SO4 . P 5 SO4 B 1 912 5 SO4 SO4 . Q 5 SO4 B 1 913 6 SO4 SO4 . R 6 9K9 B 1 914 2 9K9 sdf . S 4 NAG A 1 901 836 NAG NAG . T 4 NAG A 1 902 837 NAG NAG . U 4 NAG A 1 905 840 NAG NAG . V 4 NAG A 1 906 841 NAG NAG . W 4 NAG A 1 907 842 NAG NAG . X 5 SO4 A 1 908 1 SO4 SO4 . Y 5 SO4 A 1 909 3 SO4 SO4 . Z 5 SO4 A 1 910 4 SO4 SO4 . AA 5 SO4 A 1 911 7 SO4 SO4 . BA 5 SO4 A 1 912 8 SO4 SO4 . CA 5 SO4 A 1 913 9 SO4 SO4 . DA 6 9K9 A 1 914 1 9K9 sdf . EA 7 HOH B 1 1001 3 HOH HOH . EA 7 HOH B 2 1002 7 HOH HOH . EA 7 HOH B 3 1003 20 HOH HOH . EA 7 HOH B 4 1004 9 HOH HOH . EA 7 HOH B 5 1005 4 HOH HOH . EA 7 HOH B 6 1006 8 HOH HOH . EA 7 HOH B 7 1007 17 HOH HOH . EA 7 HOH B 8 1008 11 HOH HOH . EA 7 HOH B 9 1009 1 HOH HOH . EA 7 HOH B 10 1010 10 HOH HOH . EA 7 HOH B 11 1011 6 HOH HOH . EA 7 HOH B 12 1012 16 HOH HOH . EA 7 HOH B 13 1013 15 HOH HOH . EA 7 HOH B 14 1014 14 HOH HOH . EA 7 HOH B 15 1015 18 HOH HOH . EA 7 HOH B 16 1016 19 HOH HOH . EA 7 HOH B 17 1017 22 HOH HOH . EA 7 HOH B 18 1018 21 HOH HOH . FA 7 HOH A 1 1001 12 HOH HOH . FA 7 HOH A 2 1002 5 HOH HOH . FA 7 HOH A 3 1003 13 HOH HOH . FA 7 HOH A 4 1004 2 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 . . . M 4 36.808 12.265 -11.251 1 58.02 ? C1 NAG 909 B 1 HETATM 2 C C2 NAG . . . M 4 36.159 10.887 -11.489 1 63.91 ? C2 NAG 909 B 1 HETATM 3 C C3 NAG . . . M 4 37.224 9.808 -11.731 1 59.89 ? C3 NAG 909 B 1 HETATM 4 C C4 NAG . . . M 4 37.994 10.101 -13.015 1 59.03 ? C4 NAG 909 B 1 HETATM 5 C C5 NAG . . . M 4 38.587 11.501 -12.793 1 56.76 ? C5 NAG 909 B 1 HETATM 6 C C6 NAG . . . M 4 39.283 11.942 -14.059 1 56.43 ? C6 NAG 909 B 1 HETATM 7 C C7 NAG . . . M 4 33.94 10.911 -10.374 1 68.74 ? C7 NAG 909 B 1 HETATM 8 C C8 NAG . . . M 4 33.143 10.221 -9.292 1 65.2 ? C8 NAG 909 B 1 HETATM 9 N N2 NAG . . . M 4 35.202 10.461 -10.466 1 67.37 ? N2 NAG 909 B 1 HETATM 10 O O3 NAG . . . M 4 36.565 8.577 -11.923 1 57.94 ? O3 NAG 909 B 1 HETATM 11 O O4 NAG . . . M 4 38.912 9.025 -13.434 1 54.59 ? O4 NAG 909 B 1 HETATM 12 O O5 NAG . . . M 4 37.59 12.531 -12.44 1 57.12 ? O5 NAG 909 B 1 HETATM 13 O O6 NAG . . . M 4 38.355 12.584 -14.95 1 56.94 ? O6 NAG 909 B 1 HETATM 14 O O7 NAG . . . M 4 33.479 11.797 -11.103 1 61.8 ? O7 NAG 909 B 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 29 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 303 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #