data_3GHM # _model_server_result.job_id RspbgQ4x6RH7yK_hc9RiVg _model_server_result.datetime_utc '2025-02-05 10:39:50' _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 3ghm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":900}' # _entry.id 3GHM # _exptl.entry_id 3GHM _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 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 111.35 _cell.angle_gamma 90 _cell.entry_id 3GHM _cell.length_a 152.667 _cell.length_b 52.914 _cell.length_c 76.218 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3GHM _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 ? 3 2 1 BGC FUC C1 O1 . O3 HO3 . 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 B NAG 1 B 1 NAG A 901 NAG 2 n B NAG 2 B 2 NAG A 902 NAG 3 n C FUC 1 C 1 FUC A 905 FUC 3 n C BGC 2 C 2 BGC A 906 BGC # 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 27 A CYS 311 1_555 A SG CYS 53 A CYS 337 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf2 A SG CYS 38 A CYS 322 1_555 A SG CYS 63 A CYS 347 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf3 A SG CYS 48 A CYS 332 1_555 A SG CYS 82 A CYS 366 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf4 A SG CYS 76 A CYS 360 1_555 A SG CYS 87 A CYS 371 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf5 A SG CYS 112 A CYS 396 1_555 A SG CYS 149 A CYS 433 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf6 A SG CYS 116 A CYS 400 1_555 A SG CYS 154 A CYS 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf7 A SG CYS 127 A CYS 411 1_555 A SG CYS 139 A CYS 423 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf8 A SG CYS 166 A CYS 450 1_555 A SG CYS 203 A CYS 487 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf9 A SG CYS 199 A CYS 483 1_555 A SG CYS 238 A CYS 522 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf10 A SG CYS 224 A CYS 508 1_555 A SG CYS 243 A CYS 527 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf11 A SG CYS 248 A CYS 532 1_555 A SG CYS 264 A CYS 548 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? disulf ? disulf12 A SG CYS 261 A CYS 545 1_555 A SG CYS 271 A CYS 555 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? covale ? covale1 A OG SER 115 A SER 399 1_555 C C1 FUC . C FUC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.387 ? covale ? covale2 A ND2 ASN 268 A ASN 552 1_555 D C1 NAG . A NAG 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale3 A ND2 ASN 330 A ASN 614 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale4 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.386 ? covale ? covale5 C O3 FUC . C FUC 1 1_555 C C1 BGC . C BGC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.399 ? # _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 284 n n C1 O1 NAG sing 285 n n C1 O5 NAG sing 286 n n C1 H1 NAG sing 287 n n C2 C3 NAG sing 288 n n C2 N2 NAG sing 289 n n C2 H2 NAG sing 290 n n C3 C4 NAG sing 291 n n C3 O3 NAG sing 292 n n C3 H3 NAG sing 293 n n C4 C5 NAG sing 294 n n C4 O4 NAG sing 295 n n C4 H4 NAG sing 296 n n C5 C6 NAG sing 297 n n C5 O5 NAG sing 298 n n C5 H5 NAG sing 299 n n C6 O6 NAG sing 300 n n C6 H61 NAG sing 301 n n C6 H62 NAG sing 302 n n C7 C8 NAG sing 303 n n C7 N2 NAG sing 304 n n C7 O7 NAG doub 305 n n C8 H81 NAG sing 306 n n C8 H82 NAG sing 307 n n C8 H83 NAG sing 308 n n N2 HN2 NAG sing 309 n n O1 HO1 NAG sing 310 n n O3 HO3 NAG sing 311 n n O4 HO4 NAG sing 312 n n O6 HO6 NAG sing 313 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 3GHM _atom_sites.fract_transf_matrix[1][1] 0.00655 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00256 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018899 _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] 0.014087 _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 D 4 NAG A 1 900 900 NAG NAG . E 5 HOH A 1 1 1 HOH TIP . E 5 HOH A 2 2 2 HOH TIP . E 5 HOH A 3 3 3 HOH TIP . E 5 HOH A 4 4 4 HOH TIP . E 5 HOH A 5 5 5 HOH TIP . E 5 HOH A 6 6 6 HOH TIP . E 5 HOH A 7 7 7 HOH TIP . E 5 HOH A 8 8 8 HOH TIP . E 5 HOH A 9 9 9 HOH TIP . E 5 HOH A 10 10 10 HOH TIP . E 5 HOH A 11 11 11 HOH TIP . E 5 HOH A 12 12 12 HOH TIP . E 5 HOH A 13 13 13 HOH TIP . E 5 HOH A 14 14 14 HOH TIP . E 5 HOH A 15 15 15 HOH TIP . E 5 HOH A 16 16 16 HOH TIP . E 5 HOH A 17 17 17 HOH TIP . E 5 HOH A 18 18 18 HOH TIP . E 5 HOH A 19 19 19 HOH TIP . E 5 HOH A 20 20 20 HOH TIP . E 5 HOH A 21 21 21 HOH TIP . E 5 HOH A 22 22 22 HOH TIP . E 5 HOH A 23 23 23 HOH TIP . E 5 HOH A 24 24 24 HOH TIP . E 5 HOH A 25 25 25 HOH TIP . E 5 HOH A 26 26 26 HOH TIP . E 5 HOH A 27 27 27 HOH TIP . E 5 HOH A 28 28 28 HOH TIP . E 5 HOH A 29 29 29 HOH TIP . # 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 . . . D 4 -29.206 -42.297 7.59 1 81.35 ? C1 NAG 900 A 1 HETATM 2 C C2 NAG . . . D 4 -28.052 -42.854 8.42 1 88.18 ? C2 NAG 900 A 1 HETATM 3 C C3 NAG . . . D 4 -26.765 -42.78 7.596 1 88.21 ? C3 NAG 900 A 1 HETATM 4 C C4 NAG . . . D 4 -26.953 -43.512 6.263 1 89.04 ? C4 NAG 900 A 1 HETATM 5 C C5 NAG . . . D 4 -28.19 -42.974 5.532 1 87.46 ? C5 NAG 900 A 1 HETATM 6 C C6 NAG . . . D 4 -28.493 -43.756 4.267 1 88.54 ? C6 NAG 900 A 1 HETATM 7 C C7 NAG . . . D 4 -28.457 -42.545 10.773 1 105.91 ? C7 NAG 900 A 1 HETATM 8 C C8 NAG . . . D 4 -27.593 -43.418 11.67 1 101.16 ? C8 NAG 900 A 1 HETATM 9 N N2 NAG . . . D 4 -27.908 -42.097 9.648 1 100.27 ? N2 NAG 900 A 1 HETATM 10 O O3 NAG . . . D 4 -25.696 -43.369 8.321 1 89.79 ? O3 NAG 900 A 1 HETATM 11 O O4 NAG . . . D 4 -25.801 -43.336 5.449 1 84.92 ? O4 NAG 900 A 1 HETATM 12 O O5 NAG . . . D 4 -29.355 -43.062 6.386 1 88.37 ? O5 NAG 900 A 1 HETATM 13 O O6 NAG . . . D 4 -29.873 -44.079 4.174 1 90.34 ? O6 NAG 900 A 1 HETATM 14 O O7 NAG . . . D 4 -29.615 -42.284 11.101 1 95.96 ? O7 NAG 900 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 329 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #