data_6LVZ # _model_server_result.job_id N-5hQdW77Jp0WYoLsa2kMw _model_server_result.datetime_utc '2024-11-15 09:44:40' _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 6lvz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":1003}' # _entry.id 6LVZ # _exptl.entry_id 6LVZ _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 11 _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 6LVZ _cell.length_a 98.548 _cell.length_b 139.079 _cell.length_c 149.2 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6LVZ _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,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA _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 F N N ? 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 U N N ? 4 V N N ? 4 W 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 C NAG 1 C 1 NAG B 838 NAG 2 n C NAG 2 C 2 NAG B 839 NAG 2 n C BMA 3 C 3 BMA B 840 BMA 2 n D NAG 1 D 1 NAG A 836 NAG 2 n D NAG 2 D 2 NAG A 837 NAG 2 n D BMA 3 D 3 BMA A 841 BMA 3 n E NAG 1 E 1 NAG A 839 NAG 3 n E NAG 2 E 2 NAG A 840 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? disulf ? disulf2 A SG CYS 76 B CYS 98 1_555 A SG CYS 453 B CYS 475 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf3 A SG CYS 78 B CYS 100 1_555 A SG CYS 90 B CYS 112 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? disulf ? disulf4 A SG CYS 161 B CYS 183 1_555 A SG CYS 167 B CYS 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? disulf ? disulf5 A SG CYS 238 B CYS 260 1_555 A SG CYS 251 B CYS 273 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? disulf ? disulf6 A SG CYS 241 B CYS 263 1_555 A SG CYS 248 B CYS 270 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf7 A SG CYS 469 B CYS 491 1_555 A SG CYS 499 B CYS 521 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf8 A SG CYS 765 B CYS 787 1_555 A SG CYS 792 B CYS 814 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf9 A SG CYS 767 B CYS 789 1_555 A SG CYS 811 B CYS 833 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf10 B SG CYS 14 A CYS 36 1_555 B SG CYS 29 A CYS 51 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? disulf ? disulf11 B SG CYS 76 A CYS 98 1_555 B SG CYS 453 A CYS 475 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf12 B SG CYS 78 A CYS 100 1_555 B SG CYS 90 A CYS 112 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? disulf ? disulf13 B SG CYS 161 A CYS 183 1_555 B SG CYS 167 A CYS 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? disulf ? disulf14 B SG CYS 238 A CYS 260 1_555 B SG CYS 251 A CYS 273 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf15 B SG CYS 241 A CYS 263 1_555 B SG CYS 248 A CYS 270 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf16 B SG CYS 469 A CYS 491 1_555 B SG CYS 499 A CYS 521 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? disulf ? disulf17 B SG CYS 765 A CYS 787 1_555 B SG CYS 792 A CYS 814 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf18 B SG CYS 767 A CYS 789 1_555 B SG CYS 811 A CYS 833 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? covale ? covale1 A ND2 ASN 47 B ASN 69 1_555 J C1 NAG . B NAG 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale2 A ND2 ASN 193 B ASN 215 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale3 A ND2 ASN 339 B ASN 361 1_555 M C1 NAG . B NAG 1008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale4 A ND2 ASN 391 B ASN 413 1_555 G C1 NAG . B NAG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale5 A ND2 ASN 501 B ASN 523 1_555 F C1 NAG . B NAG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale6 A ND2 ASN 512 B ASN 534 1_555 H C1 NAG . B NAG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale7 A ND2 ASN 568 B ASN 590 1_555 I C1 NAG . B NAG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.42 ? covale ? covale8 A ND2 ASN 657 B ASN 679 1_555 L C1 NAG . B NAG 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale9 A ND2 ASN 698 B ASN 720 1_555 K C1 NAG . B NAG 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale10 B ND2 ASN 47 A ASN 69 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.421 ? covale ? covale11 B ND2 ASN 193 A ASN 215 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.42 ? covale ? covale12 B ND2 ASN 339 A ASN 361 1_555 W C1 NAG . A NAG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.427 ? covale ? covale13 B ND2 ASN 501 A ASN 523 1_555 U C1 NAG . A NAG 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.427 ? covale ? covale14 B ND2 ASN 568 A ASN 590 1_555 V C1 NAG . A NAG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale15 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.422 ? covale ? covale16 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale17 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale18 D O4 NAG . D NAG 2 1_555 D C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale19 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.46 ? # _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 302 n n C1 O1 NAG sing 303 n n C1 O5 NAG sing 304 n n C1 H1 NAG sing 305 n n C2 C3 NAG sing 306 n n C2 N2 NAG sing 307 n n C2 H2 NAG sing 308 n n C3 C4 NAG sing 309 n n C3 O3 NAG sing 310 n n C3 H3 NAG sing 311 n n C4 C5 NAG sing 312 n n C4 O4 NAG sing 313 n n C4 H4 NAG sing 314 n n C5 C6 NAG sing 315 n n C5 O5 NAG sing 316 n n C5 H5 NAG sing 317 n n C6 O6 NAG sing 318 n n C6 H61 NAG sing 319 n n C6 H62 NAG sing 320 n n C7 C8 NAG sing 321 n n C7 N2 NAG sing 322 n n C7 O7 NAG doub 323 n n C8 H81 NAG sing 324 n n C8 H82 NAG sing 325 n n C8 H83 NAG sing 326 n n N2 HN2 NAG sing 327 n n O1 HO1 NAG sing 328 n n O3 HO3 NAG sing 329 n n O4 HO4 NAG sing 330 n n O6 HO6 NAG sing 331 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 6LVZ _atom_sites.fract_transf_matrix[1][1] 0.010147 _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] 0.00719 _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] 0.006702 _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 F 4 NAG B 1 1001 836 NAG NAG . G 4 NAG B 1 1002 837 NAG NAG . H 4 NAG B 1 1003 841 NAG NAG . I 4 NAG B 1 1004 842 NAG NAG . J 4 NAG B 1 1005 843 NAG NAG . K 4 NAG B 1 1006 844 NAG NAG . L 4 NAG B 1 1007 845 NAG NAG . M 4 NAG B 1 1008 846 NAG NAG . N 5 SO4 B 1 1009 1 SO4 SO4 . O 5 SO4 B 1 1010 3 SO4 SO4 . P 5 SO4 B 1 1011 5 SO4 SO4 . Q 5 SO4 B 1 1012 6 SO4 SO4 . R 5 SO4 B 1 1013 7 SO4 SO4 . S 6 EWX B 1 1014 1 EWX sdf . T 6 EWX B 1 1015 2 EWX sdf . U 4 NAG A 1 901 838 NAG NAG . V 4 NAG A 1 902 842 NAG NAG . W 4 NAG A 1 903 843 NAG NAG . X 5 SO4 A 1 904 2 SO4 SO4 . Y 5 SO4 A 1 905 4 SO4 SO4 . Z 5 SO4 A 1 906 8 SO4 SO4 . AA 5 SO4 A 1 907 9 SO4 SO4 . BA 7 HOH B 1 1101 5 HOH HOH . BA 7 HOH B 2 1102 2 HOH HOH . BA 7 HOH B 3 1103 7 HOH HOH . BA 7 HOH B 4 1104 3 HOH HOH . BA 7 HOH B 5 1105 8 HOH HOH . BA 7 HOH B 6 1106 11 HOH HOH . CA 7 HOH A 1 1101 4 HOH HOH . CA 7 HOH A 2 1102 9 HOH HOH . CA 7 HOH A 3 1103 13 HOH HOH . CA 7 HOH A 4 1104 6 HOH HOH . CA 7 HOH A 5 1105 1 HOH HOH . CA 7 HOH A 6 1106 12 HOH HOH . CA 7 HOH A 7 1107 10 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 . . . H 4 2.989 -37.075 12.737 1 89.8 ? C1 NAG 1003 B 1 HETATM 2 C C2 NAG . . . H 4 3.609 -38.403 12.296 1 85.98 ? C2 NAG 1003 B 1 HETATM 3 C C3 NAG . . . H 4 2.848 -39.549 12.948 1 93.5 ? C3 NAG 1003 B 1 HETATM 4 C C4 NAG . . . H 4 2.97 -39.399 14.47 1 98.65 ? C4 NAG 1003 B 1 HETATM 5 C C5 NAG . . . H 4 2.373 -38.025 14.847 1 102.57 ? C5 NAG 1003 B 1 HETATM 6 C C6 NAG . . . H 4 2.366 -37.745 16.354 1 99.91 ? C6 NAG 1003 B 1 HETATM 7 C C7 NAG . . . H 4 4.559 -38.786 10.127 1 80.12 ? C7 NAG 1003 B 1 HETATM 8 C C8 NAG . . . H 4 4.355 -38.946 8.649 1 78.78 ? C8 NAG 1003 B 1 HETATM 9 N N2 NAG . . . H 4 3.502 -38.548 10.87 1 83.81 ? N2 NAG 1003 B 1 HETATM 10 O O3 NAG . . . H 4 3.325 -40.799 12.444 1 92.28 ? O3 NAG 1003 B 1 HETATM 11 O O4 NAG . . . H 4 2.287 -40.452 15.171 1 90.81 ? O4 NAG 1003 B 1 HETATM 12 O O5 NAG . . . H 4 3.072 -36.959 14.164 1 93.47 ? O5 NAG 1003 B 1 HETATM 13 O O6 NAG . . . H 4 3.641 -37.232 16.745 1 92.19 ? O6 NAG 1003 B 1 HETATM 14 O O7 NAG . . . H 4 5.631 -38.867 10.657 1 80.44 ? O7 NAG 1003 B 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 384 _model_server_stats.encode_time_ms 21 _model_server_stats.element_count 14 #