data_5VOB # _model_server_result.job_id 1YuW8ijlCNSzdueR2njWbA _model_server_result.datetime_utc '2025-03-26 14:51:08' _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 5vob # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":301}' # _entry.id 5VOB # _exptl.entry_id 5VOB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 9 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 10 _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 5VOB _cell.length_a 124.163 _cell.length_b 145.422 _cell.length_c 173.658 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VOB _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 heptameric _pdbx_struct_assembly.oligomeric_count 7 _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 _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 ? 9 I N N ? 9 J N N ? 9 K N N ? 9 L N N ? 9 M N N ? 9 N N N ? 9 O N N ? 9 P N N ? 9 Q N N ? 9 R N N # _pdbx_entity_branch.entity_id 8 _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 ? 8 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 8 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 8 n H NAG 1 F 1 NAG E 130 NAG 8 n H NAG 2 F 2 NAG E 131 NAG 8 n H BMA 3 F 3 BMA E 132 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 59 A CYS 59 1_555 B SG CYS 54 B CYS 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf2 A SG CYS 95 A CYS 95 1_555 B SG CYS 47 B CYS 47 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf3 A SG CYS 195 A CYS 195 1_555 A SG CYS 211 A CYS 211 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? disulf ? disulf4 A SG CYS 330 A CYS 330 1_555 A SG CYS 383 A CYS 383 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf5 A SG CYS 495 A CYS 495 1_555 A SG CYS 522 A CYS 522 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? disulf ? disulf6 A SG CYS 571 A CYS 571 1_555 A SG CYS 624 A CYS 624 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? disulf ? disulf7 A SG CYS 647 A CYS 647 1_555 A SG CYS 650 A CYS 650 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf8 B SG CYS 144 B CYS 144 1_555 C SG CYS 162 C CYS 162 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf9 B SG CYS 154 B CYS 154 1_555 B SG CYS 159 B CYS 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? disulf ? disulf10 C SG CYS 30 C CYS 30 1_555 C SG CYS 49 C CYS 49 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? disulf ? disulf11 C SG CYS 31 C CYS 31 1_555 C SG CYS 64 C CYS 64 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf12 C SG CYS 43 C CYS 43 1_555 C SG CYS 58 C CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? disulf ? disulf13 C SG CYS 96 C CYS 96 1_555 C SG CYS 111 C CYS 111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf14 D SG CYS 57 D CYS 57 1_555 D SG CYS 83 D CYS 83 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf15 D SG CYS 172 D CYS 172 1_555 D SG CYS 207 D CYS 207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.985 ? disulf ? disulf16 E SG CYS 20 E CYS 20 1_555 E SG CYS 40 E CYS 40 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf17 F SG CYS 41 H CYS 22 1_555 F SG CYS 115 H CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf18 F SG CYS 168 H CYS 149 1_555 F SG CYS 224 H CYS 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf19 G SG CYS 43 L CYS 23 1_555 G SG CYS 108 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? disulf ? disulf20 G SG CYS 155 L CYS 135 1_555 G SG CYS 215 L CYS 195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? covale ? covale1 A ND2 ASN 55 A ASN 55 1_555 M C1 NAG . A NAG 805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale2 A ND2 ASN 62 A ASN 62 1_555 N C1 NAG . A NAG 806 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale3 A ND2 ASN 67 A ASN 67 1_555 J C1 NAG . A NAG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale4 A ND2 ASN 192 A ASN 192 1_555 K C1 NAG . A NAG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale5 A ND2 ASN 641 A ASN 641 1_555 I C1 NAG . A NAG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale6 A ND2 ASN 700 A ASN 700 1_555 L C1 NAG . A NAG 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale7 B ND2 ASN 74 B ASN 74 1_555 O C1 NAG . B NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale8 D ND2 ASN 85 D ASN 85 1_555 R C1 NAG . D NAG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? covale ? covale9 D ND2 ASN 118 D ASN 118 1_555 P C1 NAG . D NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.401 ? covale ? covale10 D ND2 ASN 201 D ASN 201 1_555 Q C1 NAG . D NAG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale11 E ND2 ASN 81 E ASN 81 1_555 H C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale12 H O4 NAG . F NAG 1 1_555 H C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale13 H O4 NAG . F NAG 2 1_555 H C1 BMA . F BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.466 ? # _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 259 n n C1 O1 NAG sing 260 n n C1 O5 NAG sing 261 n n C1 H1 NAG sing 262 n n C2 C3 NAG sing 263 n n C2 N2 NAG sing 264 n n C2 H2 NAG sing 265 n n C3 C4 NAG sing 266 n n C3 O3 NAG sing 267 n n C3 H3 NAG sing 268 n n C4 C5 NAG sing 269 n n C4 O4 NAG sing 270 n n C4 H4 NAG sing 271 n n C5 C6 NAG sing 272 n n C5 O5 NAG sing 273 n n C5 H5 NAG sing 274 n n C6 O6 NAG sing 275 n n C6 H61 NAG sing 276 n n C6 H62 NAG sing 277 n n C7 C8 NAG sing 278 n n C7 N2 NAG sing 279 n n C7 O7 NAG doub 280 n n C8 H81 NAG sing 281 n n C8 H82 NAG sing 282 n n C8 H83 NAG sing 283 n n N2 HN2 NAG sing 284 n n O1 HO1 NAG sing 285 n n O3 HO3 NAG sing 286 n n O4 HO4 NAG sing 287 n n O6 HO6 NAG sing 288 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 5VOB _atom_sites.fract_transf_matrix[1][1] 0.008054 _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] 0.006877 _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] 0.005758 _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 I 9 NAG A 1 801 714 NAG NAG . J 9 NAG A 1 802 715 NAG NAG . K 9 NAG A 1 803 716 NAG NAG . L 9 NAG A 1 804 717 NAG NAG . M 9 NAG A 1 805 718 NAG NAG . N 9 NAG A 1 806 719 NAG NAG . O 9 NAG B 1 301 274 NAG NAG . P 9 NAG D 1 301 215 NAG NAG . Q 9 NAG D 1 302 216 NAG NAG . R 9 NAG D 1 303 217 NAG NAG . # 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 . . . O 9 -13.947 -24.994 -6.014 1 183.45 ? C1 NAG 301 B 1 HETATM 2 C C2 NAG . . . O 9 -14.554 -24.577 -4.671 1 184.92 ? C2 NAG 301 B 1 HETATM 3 C C3 NAG . . . O 9 -15.196 -25.767 -3.955 1 186.26 ? C3 NAG 301 B 1 HETATM 4 C C4 NAG . . . O 9 -15.971 -26.634 -4.94 1 186.8 ? C4 NAG 301 B 1 HETATM 5 C C5 NAG . . . O 9 -15.02 -27.269 -5.955 1 186.54 ? C5 NAG 301 B 1 HETATM 6 C C6 NAG . . . O 9 -15.686 -27.694 -7.251 1 186.83 ? C6 NAG 301 B 1 HETATM 7 C C7 NAG . . . O 9 -13.423 -22.72 -3.486 1 183.45 ? C7 NAG 301 B 1 HETATM 8 C C8 NAG . . . O 9 -12.275 -22.356 -2.592 1 182.75 ? C8 NAG 301 B 1 HETATM 9 N N2 NAG . . . O 9 -13.492 -24.011 -3.852 1 184.27 ? N2 NAG 301 B 1 HETATM 10 O O3 NAG . . . O 9 -16.058 -25.301 -2.922 1 186.37 ? O3 NAG 301 B 1 HETATM 11 O O4 NAG . . . O 9 -16.659 -27.667 -4.239 1 186.72 ? O4 NAG 301 B 1 HETATM 12 O O5 NAG . . . O 9 -13.899 -26.413 -6.288 1 185.23 ? O5 NAG 301 B 1 HETATM 13 O O6 NAG . . . O 9 -16.141 -26.591 -8.029 1 186.76 ? O6 NAG 301 B 1 HETATM 14 O O7 NAG . . . O 9 -14.247 -21.888 -3.857 1 183.53 ? O7 NAG 301 B 1 # _model_server_stats.io_time_ms 62 _model_server_stats.parse_time_ms 173 _model_server_stats.create_model_time_ms 90 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 14 #