data_5U7Z # _model_server_result.job_id dxyu-q4X4VB0JNZmUmD5NA _model_server_result.datetime_utc '2024-11-25 16:13:12' _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 5u7z # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":405}' # _entry.id 5U7Z # _exptl.entry_id 5U7Z _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 5 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 120.72 _cell.angle_gamma 90 _cell.entry_id 5U7Z _cell.length_a 153.667 _cell.length_b 68.312 _cell.length_c 97.805 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5U7Z _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 2 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 tetrameric 4 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 PISA dimeric 2 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,B,E,G,H,I,J,K,L,M,N,O,Y,Z 1 1 C,D,F,P,Q,R,S,T,U,V,W,X,AA,BA 1 2 A,B,E,G,H,I,J,K,L,M,N,O,Y,Z 2 1 C,D,F,P,Q,R,S,T,U,V,W,X,AA,BA 3 1 # 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' 3_545 x+1/2,y-1/2,z 1 0 0 0 1 0 0 0 1 76.8335 -34.156 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 K N N ? 5 L N N ? 5 R N N ? 5 S N N ? 5 T N N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type 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 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 3 2 BMA 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 3 n E NAG 1 E 1 NAG E 1 NAG 3 n E NAG 2 E 2 NAG E 2 NAG 3 n E BMA 3 E 3 BMA F 1 BMA 3 n F NAG 1 F 1 NAG E 3 NAG 3 n F NAG 2 F 2 NAG E 4 NAG 3 n F BMA 3 F 3 BMA F 2 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 20 A CYS 31 1_555 B SG CYS 200 B CYS 340 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf2 B SG CYS 248 B CYS 388 1_555 B SG CYS 252 B CYS 392 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf3 C SG CYS 20 C CYS 31 1_555 D SG CYS 200 D CYS 340 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf4 D SG CYS 248 D CYS 388 1_555 D SG CYS 252 D CYS 392 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? covale ? covale1 B ND2 ASN 33 B ASN 173 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale2 B ND2 ASN 119 B ASN 259 1_555 K C1 NAG . B NAG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale3 B ND2 ASN 146 B ASN 286 1_555 L C1 NAG . B NAG 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale4 D ND2 ASN 33 D ASN 173 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale5 D ND2 ASN 119 D ASN 259 1_555 S C1 NAG . D NAG 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale6 D ND2 ASN 146 D ASN 286 1_555 R C1 NAG . D NAG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale7 D ND2 ASN 202 D ASN 342 1_555 T C1 NAG . D NAG 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale8 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale9 E O4 NAG . E NAG 2 1_555 E C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale10 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale11 F O4 NAG . F NAG 2 1_555 F C1 BMA . F BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? # _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 261 n n C1 O1 NAG sing 262 n n C1 O5 NAG sing 263 n n C1 H1 NAG sing 264 n n C2 C3 NAG sing 265 n n C2 N2 NAG sing 266 n n C2 H2 NAG sing 267 n n C3 C4 NAG sing 268 n n C3 O3 NAG sing 269 n n C3 H3 NAG sing 270 n n C4 C5 NAG sing 271 n n C4 O4 NAG sing 272 n n C4 H4 NAG sing 273 n n C5 C6 NAG sing 274 n n C5 O5 NAG sing 275 n n C5 H5 NAG sing 276 n n C6 O6 NAG sing 277 n n C6 H61 NAG sing 278 n n C6 H62 NAG sing 279 n n C7 C8 NAG sing 280 n n C7 N2 NAG sing 281 n n C7 O7 NAG doub 282 n n C8 H81 NAG sing 283 n n C8 H82 NAG sing 284 n n C8 H83 NAG sing 285 n n N2 HN2 NAG sing 286 n n O1 HO1 NAG sing 287 n n O3 HO3 NAG sing 288 n n O4 HO4 NAG sing 289 n n O6 HO6 NAG sing 290 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 5U7Z _atom_sites.fract_transf_matrix[1][1] 0.006508 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003867 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014639 _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] 0.011893 _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 SO4 A 1 201 3 SO4 SO4 . H 4 SO4 A 1 202 11 SO4 SO4 . I 4 SO4 A 1 203 12 SO4 SO4 . J 4 SO4 A 1 204 13 SO4 SO4 . K 5 NAG B 1 404 5 NAG NAG . L 5 NAG B 1 405 6 NAG NAG . M 4 SO4 B 1 406 2 SO4 SO4 . N 4 SO4 B 1 407 6 SO4 SO4 . O 4 SO4 B 1 408 9 SO4 SO4 . P 4 SO4 C 1 201 4 SO4 SO4 . Q 4 SO4 C 1 202 5 SO4 SO4 . R 5 NAG D 1 404 7 NAG NAG . S 5 NAG D 1 405 8 NAG NAG . T 5 NAG D 1 406 9 NAG NAG . U 4 SO4 D 1 407 1 SO4 SO4 . V 4 SO4 D 1 408 7 SO4 SO4 . W 4 SO4 D 1 409 8 SO4 SO4 . X 4 SO4 D 1 410 10 SO4 SO4 . Y 6 HOH A 1 301 18 HOH HOH . Y 6 HOH A 2 302 8 HOH HOH . Z 6 HOH B 1 501 1 HOH HOH . Z 6 HOH B 2 502 10 HOH HOH . Z 6 HOH B 3 503 25 HOH HOH . Z 6 HOH B 4 504 2 HOH HOH . Z 6 HOH B 5 505 27 HOH HOH . Z 6 HOH B 6 506 12 HOH HOH . Z 6 HOH B 7 507 20 HOH HOH . Z 6 HOH B 8 508 11 HOH HOH . Z 6 HOH B 9 509 24 HOH HOH . Z 6 HOH B 10 510 22 HOH HOH . Z 6 HOH B 11 511 3 HOH HOH . Z 6 HOH B 12 512 28 HOH HOH . Z 6 HOH B 13 513 4 HOH HOH . AA 6 HOH C 1 301 16 HOH HOH . AA 6 HOH C 2 302 7 HOH HOH . AA 6 HOH C 3 303 19 HOH HOH . AA 6 HOH C 4 304 23 HOH HOH . BA 6 HOH D 1 501 26 HOH HOH . BA 6 HOH D 2 502 17 HOH HOH . BA 6 HOH D 3 503 6 HOH HOH . BA 6 HOH D 4 504 21 HOH HOH . BA 6 HOH D 5 505 5 HOH HOH . BA 6 HOH D 6 506 9 HOH HOH . BA 6 HOH D 7 507 15 HOH HOH . BA 6 HOH D 8 508 14 HOH HOH . BA 6 HOH D 9 509 31 HOH HOH . BA 6 HOH D 10 510 13 HOH HOH . BA 6 HOH D 11 511 33 HOH HOH . BA 6 HOH D 12 512 29 HOH HOH . BA 6 HOH D 13 513 30 HOH HOH . BA 6 HOH D 14 514 32 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 . . . L 5 89.493 -24.878 169.252 1 66 ? C1 NAG 405 B 1 HETATM 2 C C2 NAG . . . L 5 88.742 -23.696 168.648 1 71.42 ? C2 NAG 405 B 1 HETATM 3 C C3 NAG . . . L 5 89.441 -23.22 167.384 1 71.68 ? C3 NAG 405 B 1 HETATM 4 C C4 NAG . . . L 5 90.894 -22.893 167.7 1 70.48 ? C4 NAG 405 B 1 HETATM 5 C C5 NAG . . . L 5 91.575 -24.086 168.372 1 72.34 ? C5 NAG 405 B 1 HETATM 6 C C6 NAG . . . L 5 92.99 -23.784 168.81 1 75 ? C6 NAG 405 B 1 HETATM 7 C C7 NAG . . . L 5 86.931 -25.129 167.776 1 78.09 ? C7 NAG 405 B 1 HETATM 8 C C8 NAG . . . L 5 85.448 -25.282 167.63 1 77.65 ? C8 NAG 405 B 1 HETATM 9 N N2 NAG . . . L 5 87.345 -24.016 168.392 1 75.71 ? N2 NAG 405 B 1 HETATM 10 O O3 NAG . . . L 5 88.779 -22.064 166.884 1 71.66 ? O3 NAG 405 B 1 HETATM 11 O O4 NAG . . . L 5 91.592 -22.555 166.507 1 69.99 ? O4 NAG 405 B 1 HETATM 12 O O5 NAG . . . L 5 90.846 -24.488 169.546 1 69.36 ? O5 NAG 405 B 1 HETATM 13 O O6 NAG . . . L 5 93.858 -23.652 167.692 1 76.38 ? O6 NAG 405 B 1 HETATM 14 O O7 NAG . . . L 5 87.715 -25.972 167.354 1 81.01 ? O7 NAG 405 B 1 HETATM 15 H H1 NAG . . . L 5 89.502 -25.615 168.612 1 79.2 ? H1 NAG 405 B 1 HETATM 16 H H2 NAG . . . L 5 88.771 -22.964 169.293 1 85.7 ? H2 NAG 405 B 1 HETATM 17 H H3 NAG . . . L 5 89.408 -23.927 166.712 1 86.01 ? H3 NAG 405 B 1 HETATM 18 H H4 NAG . . . L 5 90.921 -22.13 168.309 1 84.57 ? H4 NAG 405 B 1 HETATM 19 H H5 NAG . . . L 5 91.594 -24.832 167.743 1 86.8 ? H5 NAG 405 B 1 HETATM 20 H H61 NAG . . . L 5 93.31 -24.509 169.379 1 90 ? H61 NAG 405 B 1 HETATM 21 H H62 NAG . . . L 5 92.996 -22.951 169.319 1 90 ? H62 NAG 405 B 1 HETATM 22 H H81 NAG . . . L 5 85.25 -26.12 167.171 1 93.18 ? H81 NAG 405 B 1 HETATM 23 H H82 NAG . . . L 5 85.093 -24.535 167.111 1 93.18 ? H82 NAG 405 B 1 HETATM 24 H H83 NAG . . . L 5 85.033 -25.29 168.514 1 93.18 ? H83 NAG 405 B 1 HETATM 25 H HN2 NAG . . . L 5 86.711 -23.432 168.69 1 90.85 ? HN2 NAG 405 B 1 HETATM 26 H HO3 NAG . . . L 5 88.757 -21.439 167.515 1 85.99 ? HO3 NAG 405 B 1 HETATM 27 H HO4 NAG . . . L 5 91.817 -21.697 166.529 1 83.98 ? HO4 NAG 405 B 1 HETATM 28 H HO6 NAG . . . L 5 94.647 -23.35 167.964 1 91.65 ? HO6 NAG 405 B 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 271 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #