data_5VGJ # _model_server_result.job_id wVsOF_Yf8g_HsQFzeo96rQ _model_server_result.datetime_utc '2024-11-30 17:19:21' _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 5vgj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":1330}' # _entry.id 5VGJ # _exptl.entry_id 5VGJ _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 1 _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 120 _cell.entry_id 5VGJ _cell.length_a 106.572 _cell.length_b 106.572 _cell.length_c 129.857 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VGJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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' 6_876 -x+3,-x+y+2,-z+5/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 213.144 184.588119 216.428333 # _struct_asym.details ? _struct_asym.entity_id 6 _struct_asym.id G _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 4 oligosaccharide 5 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 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 4 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 4 4 3 MAN BMA C1 O1 . O6 HO6 . sing 4 ? 4 5 4 MAN MAN C1 O1 . O3 HO3 . sing 5 ? 4 6 4 MAN MAN C1 O1 . O6 HO6 . sing 6 ? 4 7 3 MAN BMA C1 O1 . O3 HO3 . sing 7 ? 5 2 1 NAG NAG C1 O1 . O4 HO4 . sing 8 ? 5 3 2 BMA NAG C1 O1 . O4 HO4 . sing 9 ? 5 4 3 MAN BMA C1 O1 . O3 HO3 . sing 10 ? 5 5 3 MAN BMA C1 O1 . O6 HO6 . 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 4 n D NAG 1 A 1 NAG G 1560 NAG 4 n D NAG 2 A 2 NAG G 1561 NAG 4 n D BMA 3 A 3 BMA G 1562 BMA 4 n D MAN 4 A 4 MAN G 1564 MAN 4 n D MAN 5 A 5 MAN G 1565 MAN 4 n D MAN 6 A 6 MAN G 1566 MAN 4 n D MAN 7 A 7 MAN G 1563 MAN 4 n E NAG 1 B 1 NAG G 1600 NAG 4 n E NAG 2 B 2 NAG G 1601 NAG 4 n E BMA 3 B 3 BMA G 1602 BMA 4 n E MAN 4 B 4 MAN G 1604 MAN 4 n E MAN 5 B 5 MAN G 1606 MAN 4 n E MAN 6 B 6 MAN G 1605 MAN 4 n E MAN 7 B 7 MAN G 1603 MAN 5 n F NAG 1 C 1 NAG G 1650 NAG 5 n F NAG 2 C 2 NAG G 1651 NAG 5 n F BMA 3 C 3 BMA G 1652 BMA 5 n F MAN 4 C 4 MAN G 1653 MAN 5 n F MAN 5 C 5 MAN G 1654 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 9 G CYS 126 1_555 A SG CYS 84 G CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 A SG CYS 14 G CYS 131 1_555 A SG CYS 38 G CYS 157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf3 B SG CYS 22 H CYS 22 1_555 B SG CYS 95 H CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf4 B SG CYS 151 H CYS 140 1_555 B SG CYS 207 H CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf5 C SG CYS 23 L CYS 23 1_555 C SG CYS 93 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf6 C SG CYS 140 L CYS 134 1_555 C SG CYS 200 L CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? covale ? covale1 A ND2 ASN 16 G ASN 133 1_555 G C1 NAG . G NAG 1330 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale2 A ND2 ASN 37 G ASN 156 1_555 D C1 NAG . A NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.403 ? covale ? covale3 A ND2 ASN 41 G ASN 160 1_555 E C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale4 A ND2 ASN 48 G ASN 165 1_555 F C1 NAG . C NAG 1 1_555 B ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale5 D O4 NAG . A NAG 1 1_555 D C1 NAG . A NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale6 D O4 NAG . A NAG 2 1_555 D C1 BMA . A BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale7 D O6 BMA . A BMA 3 1_555 D C1 MAN . A MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale8 D O3 BMA . A BMA 3 1_555 D C1 MAN . A MAN 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale9 D O3 MAN . A MAN 4 1_555 D C1 MAN . A MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale10 D O6 MAN . A MAN 4 1_555 D C1 MAN . A MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale11 E O4 NAG . B NAG 1 1_555 E C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale12 E O4 NAG . B NAG 2 1_555 E C1 BMA . B BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale13 E O6 BMA . B BMA 3 1_555 E C1 MAN . B MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale14 E O3 BMA . B BMA 3 1_555 E C1 MAN . B MAN 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale15 E O3 MAN . B MAN 4 1_555 E C1 MAN . B MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale16 E O6 MAN . B MAN 4 1_555 E C1 MAN . B MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale17 F O4 NAG . C NAG 1 1_555 F C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale18 F O4 NAG . C NAG 2 1_555 F C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale19 F O3 BMA . C BMA 3 1_555 F C1 MAN . C MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale20 F O6 BMA . C BMA 3 1_555 F C1 MAN . C MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? # _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 283 n n C1 O1 NAG sing 284 n n C1 O5 NAG sing 285 n n C1 H1 NAG sing 286 n n C2 C3 NAG sing 287 n n C2 N2 NAG sing 288 n n C2 H2 NAG sing 289 n n C3 C4 NAG sing 290 n n C3 O3 NAG sing 291 n n C3 H3 NAG sing 292 n n C4 C5 NAG sing 293 n n C4 O4 NAG sing 294 n n C4 H4 NAG sing 295 n n C5 C6 NAG sing 296 n n C5 O5 NAG sing 297 n n C5 H5 NAG sing 298 n n C6 O6 NAG sing 299 n n C6 H61 NAG sing 300 n n C6 H62 NAG sing 301 n n C7 C8 NAG sing 302 n n C7 N2 NAG sing 303 n n C7 O7 NAG doub 304 n n C8 H81 NAG sing 305 n n C8 H82 NAG sing 306 n n C8 H83 NAG sing 307 n n N2 HN2 NAG sing 308 n n O1 HO1 NAG sing 309 n n O3 HO3 NAG sing 310 n n O4 HO4 NAG sing 311 n n O6 HO6 NAG sing 312 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 5VGJ _atom_sites.fract_transf_matrix[1][1] 0.009383 _atom_sites.fract_transf_matrix[1][2] 0.005417 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010835 _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] 0.007701 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # _pdbx_nonpoly_scheme.asym_id G _pdbx_nonpoly_scheme.entity_id 6 _pdbx_nonpoly_scheme.mon_id NAG _pdbx_nonpoly_scheme.pdb_strand_id G _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 1330 _pdbx_nonpoly_scheme.auth_seq_num 1330 _pdbx_nonpoly_scheme.pdb_mon_id NAG _pdbx_nonpoly_scheme.auth_mon_id NAG _pdbx_nonpoly_scheme.pdb_ins_code . # 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 . . . G 6 24.561 195.237 106.047 1 162.07 ? C1 NAG 1330 G 1 HETATM 2 C C2 NAG . . . G 6 25.857 194.447 106.094 1 166.19 ? C2 NAG 1330 G 1 HETATM 3 C C3 NAG . . . G 6 26.311 194.118 104.676 1 168.15 ? C3 NAG 1330 G 1 HETATM 4 C C4 NAG . . . G 6 25.187 193.45 103.894 1 175.01 ? C4 NAG 1330 G 1 HETATM 5 C C5 NAG . . . G 6 23.88 194.236 104.022 1 168.44 ? C5 NAG 1330 G 1 HETATM 6 C C6 NAG . . . G 6 22.693 193.514 103.43 1 163.3 ? C6 NAG 1330 G 1 HETATM 7 C C7 NAG . . . G 6 27.437 194.758 107.942 1 165.89 ? C7 NAG 1330 G 1 HETATM 8 C C8 NAG . . . G 6 28.493 195.639 108.529 1 157.85 ? C8 NAG 1330 G 1 HETATM 9 N N2 NAG . . . G 6 26.89 195.184 106.801 1 166.47 ? N2 NAG 1330 G 1 HETATM 10 O O3 NAG . . . G 6 27.447 193.262 104.719 1 173.65 ? O3 NAG 1330 G 1 HETATM 11 O O4 NAG . . . G 6 25.55 193.377 102.52 1 160.67 ? O4 NAG 1330 G 1 HETATM 12 O O5 NAG . . . G 6 23.568 194.473 105.403 1 160.37 ? O5 NAG 1330 G 1 HETATM 13 O O6 NAG . . . G 6 21.47 194.079 103.882 1 163.99 ? O6 NAG 1330 G 1 HETATM 14 O O7 NAG . . . G 6 27.097 193.708 108.475 1 169.29 ? O7 NAG 1330 G 1 HETATM 15 H H2 NAG . . . G 6 25.691 193.608 106.564 1 200.05 ? H2 NAG 1330 G 1 HETATM 16 H H3 NAG . . . G 6 26.559 194.947 104.225 1 202.41 ? H3 NAG 1330 G 1 HETATM 17 H H4 NAG . . . G 6 25.051 192.546 104.237 1 210.65 ? H4 NAG 1330 G 1 HETATM 18 H H5 NAG . . . G 6 23.984 195.095 103.57 1 202.76 ? H5 NAG 1330 G 1 HETATM 19 H H61 NAG . . . G 6 22.728 192.574 103.693 1 196.59 ? H61 NAG 1330 G 1 HETATM 20 H H62 NAG . . . G 6 22.734 193.576 102.457 1 196.59 ? H62 NAG 1330 G 1 HETATM 21 H H81 NAG . . . G 6 28.113 196.518 108.72 1 190.05 ? H81 NAG 1330 G 1 HETATM 22 H H82 NAG . . . G 6 29.228 195.733 107.893 1 190.05 ? H82 NAG 1330 G 1 HETATM 23 H H83 NAG . . . G 6 28.826 195.241 109.355 1 190.05 ? H83 NAG 1330 G 1 HETATM 24 H HN2 NAG . . . G 6 27.183 195.971 106.446 1 200.4 ? HN2 NAG 1330 G 1 HETATM 25 H HO3 NAG . . . G 6 28.002 193.473 104.059 1 209.02 ? HO3 NAG 1330 G 1 HETATM 26 H HO4 NAG . . . G 6 25.172 192.663 102.151 1 193.43 ? HO4 NAG 1330 G 1 HETATM 27 H HO6 NAG . . . G 6 20.8 193.53 103.685 1 197.42 ? HO6 NAG 1330 G 1 # _model_server_stats.io_time_ms 61 _model_server_stats.parse_time_ms 26 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 225 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 27 #