data_7PBD # _model_server_result.job_id 3YVfQnob_fHO_dQf68RGsg _model_server_result.datetime_utc '2024-12-26 17:41:38' _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 7pbd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Q","auth_seq_id":502}' # _entry.id 7PBD # _exptl.entry_id 7PBD _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 221.208 _entity.id 8 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 3 _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 7PBD _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7PBD _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 _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 ? _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 ? 8 M N N ? 8 O N N ? 8 Q N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 5 oligosaccharide 6 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 ? 5 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 6 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 6 3 2 BMA NAG C1 O1 . O4 HO4 . sing 4 ? 6 4 3 MAN BMA C1 O1 . O3 HO3 . sing 5 ? 6 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 5 n G NAG 1 G 1 NAG B 507 NAG 5 n G NAG 2 G 2 NAG B 508 NAG 6 n H NAG 1 H 1 NAG B 509 NAG 6 n H NAG 2 H 2 NAG B 510 NAG 6 n H BMA 3 H 3 BMA B 511 BMA 6 n H MAN 4 H 4 MAN B 512 MAN 6 n H MAN 5 H 5 MAN B 513 MAN 6 n I NAG 1 I 1 NAG C 602 NAG 6 n I NAG 2 I 2 NAG C 603 NAG 6 n I BMA 3 I 3 BMA C 604 BMA 6 n I MAN 4 I 4 MAN C 605 MAN 6 n I MAN 5 I 5 MAN C 606 MAN 5 n J NAG 1 J 1 NAG C 607 NAG 5 n J NAG 2 J 2 NAG C 608 NAG 6 n K NAG 1 K 1 NAG E 503 NAG 6 n K NAG 2 K 2 NAG E 504 NAG 6 n K BMA 3 K 3 BMA E 505 BMA 6 n K MAN 4 K 4 MAN E 506 MAN 6 n K MAN 5 K 5 MAN E 507 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 138 A CYS 139 1_555 A SG CYS 152 A CYS 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf2 B SG CYS 136 B CYS 136 1_555 B SG CYS 150 B CYS 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf3 C SG CYS 136 C CYS 136 1_555 C SG CYS 150 C CYS 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf4 D SG CYS 136 E CYS 136 1_555 D SG CYS 150 E CYS 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf5 E SG CYS 192 D CYS 139 1_555 E SG CYS 206 D CYS 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf6 F SG CYS 409 F CYS 409 1_555 F SG CYS 483 F CYS 483 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? covale ? covale1 A ND2 ASN 110 A ASN 111 1_555 M C1 NAG . A NAG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale2 B ND2 ASN 80 B ASN 80 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.54 ? covale ? covale3 B ND2 ASN 149 B ASN 149 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.475 ? covale ? covale4 C ND2 ASN 80 C ASN 80 1_555 J C1 NAG . J NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? covale ? covale5 C ND2 ASN 149 C ASN 149 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.466 ? covale ? covale6 D ND2 ASN 80 E ASN 80 1_555 O C1 NAG . E NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.521 ? covale ? covale7 D ND2 ASN 149 E ASN 149 1_555 K C1 NAG . K NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.503 ? covale ? covale8 E ND2 ASN 164 D ASN 111 1_555 Q C1 NAG . D NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.463 ? covale ? covale9 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale10 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.414 ? covale ? covale11 H O4 NAG . H NAG 2 1_555 H C1 BMA . H BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.425 ? covale ? covale12 H O3 BMA . H BMA 3 1_555 H C1 MAN . H MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale13 H O6 BMA . H BMA 3 1_555 H C1 MAN . H MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale14 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale15 I O4 NAG . I NAG 2 1_555 I C1 BMA . I BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale16 I O3 BMA . I BMA 3 1_555 I C1 MAN . I MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale17 I O6 BMA . I BMA 3 1_555 I C1 MAN . I MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale18 J O4 NAG . J NAG 1 1_555 J C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale19 K O4 NAG . K NAG 1 1_555 K C1 NAG . K NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale20 K O4 NAG . K NAG 2 1_555 K C1 BMA . K BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale21 K O3 BMA . K BMA 3 1_555 K C1 MAN . K MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale22 K O6 BMA . K BMA 3 1_555 K C1 MAN . K MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? # _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 315 n n C1 O1 NAG sing 316 n n C1 O5 NAG sing 317 n n C1 H1 NAG sing 318 n n C2 C3 NAG sing 319 n n C2 N2 NAG sing 320 n n C2 H2 NAG sing 321 n n C3 C4 NAG sing 322 n n C3 O3 NAG sing 323 n n C3 H3 NAG sing 324 n n C4 C5 NAG sing 325 n n C4 O4 NAG sing 326 n n C4 H4 NAG sing 327 n n C5 C6 NAG sing 328 n n C5 O5 NAG sing 329 n n C5 H5 NAG sing 330 n n C6 O6 NAG sing 331 n n C6 H61 NAG sing 332 n n C6 H62 NAG sing 333 n n C7 C8 NAG sing 334 n n C7 N2 NAG sing 335 n n C7 O7 NAG doub 336 n n C8 H81 NAG sing 337 n n C8 H82 NAG sing 338 n n C8 H83 NAG sing 339 n n N2 HN2 NAG sing 340 n n O1 HO1 NAG sing 341 n n O3 HO3 NAG sing 342 n n O4 HO4 NAG sing 343 n n O6 HO6 NAG sing 344 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 7PBD _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 L 7 ABU A 1 801 507 ABU ABU . M 8 NAG A 1 802 973 NAG NAG . N 9 HSM B 1 601 601 HSM HSM . O 8 NAG E 1 501 508 NAG NAG . P 7 ABU D 1 501 507 ABU ABU . Q 8 NAG D 1 502 508 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 . . . Q 8 169.041 152.218 133.501 1 118.65 ? C1 NAG 502 D 1 HETATM 2 C C2 NAG . . . Q 8 169.078 151.482 132.163 1 118.65 ? C2 NAG 502 D 1 HETATM 3 C C3 NAG . . . Q 8 169.151 152.48 131.011 1 118.65 ? C3 NAG 502 D 1 HETATM 4 C C4 NAG . . . Q 8 168.025 153.499 131.12 1 118.65 ? C4 NAG 502 D 1 HETATM 5 C C5 NAG . . . Q 8 168.039 154.149 132.5 1 118.65 ? C5 NAG 502 D 1 HETATM 6 C C6 NAG . . . Q 8 166.881 155.092 132.722 1 118.65 ? C6 NAG 502 D 1 HETATM 7 C C7 NAG . . . Q 8 171.474 150.933 132.189 1 118.65 ? C7 NAG 502 D 1 HETATM 8 C C8 NAG . . . Q 8 172.491 149.836 132.108 1 118.65 ? C8 NAG 502 D 1 HETATM 9 N N2 NAG . . . Q 8 170.194 150.552 132.104 1 118.65 ? N2 NAG 502 D 1 HETATM 10 O O3 NAG . . . Q 8 169.061 151.785 129.773 1 118.65 ? O3 NAG 502 D 1 HETATM 11 O O4 NAG . . . Q 8 168.183 154.505 130.127 1 118.65 ? O4 NAG 502 D 1 HETATM 12 O O5 NAG . . . Q 8 167.95 153.138 133.514 1 118.65 ? O5 NAG 502 D 1 HETATM 13 O O6 NAG . . . Q 8 167.293 156.262 133.415 1 118.65 ? O6 NAG 502 D 1 HETATM 14 O O7 NAG . . . Q 8 171.795 152.109 132.326 1 118.65 ? O7 NAG 502 D 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 42 _model_server_stats.query_time_ms 324 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 14 #