data_4D6W # _model_server_result.job_id 51p17PSt5lfCodxKRwpQiA _model_server_result.datetime_utc '2024-12-26 11:22:23' _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 4d6w # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1001}' # _entry.id 4D6W # _exptl.entry_id 4D6W _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 96.95 _cell.angle_gamma 90 _cell.entry_id 4D6W _cell.length_a 365.59 _cell.length_b 83.5 _cell.length_c 60.82 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4D6W _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 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,H,I,J _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 # 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 FUC NAG 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 2 n D NAG 1 D 1 NAG A 2001 NAG 2 n D NAG 2 D 2 NAG A 2002 NAG 3 n E NAG 1 E 1 NAG B 1002 NAG 3 n E FUC 2 E 2 FUC B 1003 FUC # 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 24 A CYS 24 1_555 A SG CYS 287 A CYS 287 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? disulf ? disulf2 A SG CYS 59 A CYS 59 1_555 A SG CYS 92 A CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf3 A SG CYS 68 A CYS 68 1_555 A SG CYS 114 A CYS 114 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf4 A SG CYS 153 A CYS 153 1_555 A SG CYS 158 A CYS 158 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? disulf ? disulf5 A SG CYS 178 A CYS 178 1_555 A SG CYS 223 A CYS 223 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf6 A SG CYS 218 A CYS 218 1_555 A SG CYS 256 A CYS 256 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? disulf ? disulf7 B SG CYS 24 B CYS 24 1_555 B SG CYS 287 B CYS 287 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf8 B SG CYS 59 B CYS 59 1_555 B SG CYS 92 B CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf9 B SG CYS 68 B CYS 68 1_555 B SG CYS 114 B CYS 114 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf10 B SG CYS 153 B CYS 153 1_555 B SG CYS 158 B CYS 158 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf11 B SG CYS 178 B CYS 178 1_555 B SG CYS 223 B CYS 223 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf12 B SG CYS 218 B CYS 218 1_555 B SG CYS 256 B CYS 256 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf13 C SG CYS 24 C CYS 24 1_555 C SG CYS 287 C CYS 287 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? disulf ? disulf14 C SG CYS 59 C CYS 59 1_555 C SG CYS 92 C CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf15 C SG CYS 68 C CYS 68 1_555 C SG CYS 114 C CYS 114 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf16 C SG CYS 153 C CYS 153 1_555 C SG CYS 158 C CYS 158 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf17 C SG CYS 178 C CYS 178 1_555 C SG CYS 223 C CYS 223 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf18 C SG CYS 218 C CYS 218 1_555 C SG CYS 256 C CYS 256 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? covale ? covale1 A ND2 ASN 323 A ASN 323 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? covale ? covale2 B ND2 ASN 163 B ASN 163 1_555 F C1 NAG . B NAG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale3 B ND2 ASN 323 B ASN 323 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.426 ? covale ? covale4 C ND2 ASN 163 C ASN 163 1_555 G C1 NAG . C NAG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale5 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? covale ? covale6 E O6 NAG . E NAG 1 1_555 E C1 FUC . E FUC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? # _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 260 n n C1 O1 NAG sing 261 n n C1 O5 NAG sing 262 n n C1 H1 NAG sing 263 n n C2 C3 NAG sing 264 n n C2 N2 NAG sing 265 n n C2 H2 NAG sing 266 n n C3 C4 NAG sing 267 n n C3 O3 NAG sing 268 n n C3 H3 NAG sing 269 n n C4 C5 NAG sing 270 n n C4 O4 NAG sing 271 n n C4 H4 NAG sing 272 n n C5 C6 NAG sing 273 n n C5 O5 NAG sing 274 n n C5 H5 NAG sing 275 n n C6 O6 NAG sing 276 n n C6 H61 NAG sing 277 n n C6 H62 NAG sing 278 n n C7 C8 NAG sing 279 n n C7 N2 NAG sing 280 n n C7 O7 NAG doub 281 n n C8 H81 NAG sing 282 n n C8 H82 NAG sing 283 n n C8 H83 NAG sing 284 n n N2 HN2 NAG sing 285 n n O1 HO1 NAG sing 286 n n O3 HO3 NAG sing 287 n n O4 HO4 NAG sing 288 n n O6 HO6 NAG sing 289 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 4D6W _atom_sites.fract_transf_matrix[1][1] 0.002735 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000333 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011976 _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] 0.016564 _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 1001 NAG NAG . G 4 NAG C 1 1004 1004 NAG NAG . H 5 HOH A 1 3001 3001 HOH HOH . H 5 HOH A 2 3002 3002 HOH HOH . I 5 HOH B 1 3001 3001 HOH HOH . J 5 HOH C 1 3001 3001 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 . . . F 4 -37.658 -22.218 -34.645 1 180.22 ? C1 NAG 1001 B 1 HETATM 2 C C2 NAG . . . F 4 -36.897 -22.854 -35.828 1 181.75 ? C2 NAG 1001 B 1 HETATM 3 C C3 NAG . . . F 4 -36.172 -24.137 -35.391 1 183.89 ? C3 NAG 1001 B 1 HETATM 4 C C4 NAG . . . F 4 -36.975 -24.911 -34.35 1 182.96 ? C4 NAG 1001 B 1 HETATM 5 C C5 NAG . . . F 4 -38.455 -24.563 -34.451 1 183.38 ? C5 NAG 1001 B 1 HETATM 6 C C6 NAG . . . F 4 -39.327 -25.382 -33.529 1 181.79 ? C6 NAG 1001 B 1 HETATM 7 C C7 NAG . . . F 4 -37.327 -23.398 -38.192 1 172.19 ? C7 NAG 1001 B 1 HETATM 8 C C8 NAG . . . F 4 -38.38 -23.615 -39.236 1 170.22 ? C8 NAG 1001 B 1 HETATM 9 N N2 NAG . . . F 4 -37.772 -23.101 -36.967 1 177.14 ? N2 NAG 1001 B 1 HETATM 10 O O3 NAG . . . F 4 -34.898 -23.793 -34.857 1 184.28 ? O3 NAG 1001 B 1 HETATM 11 O O4 NAG . . . F 4 -36.818 -26.311 -34.548 1 182.17 ? O4 NAG 1001 B 1 HETATM 12 O O5 NAG . . . F 4 -38.654 -23.184 -34.102 1 182.72 ? O5 NAG 1001 B 1 HETATM 13 O O6 NAG . . . F 4 -40.695 -25.286 -33.902 1 179.59 ? O6 NAG 1001 B 1 HETATM 14 O O7 NAG . . . F 4 -36.131 -23.486 -38.446 1 170.73 ? O7 NAG 1001 B 1 # _model_server_stats.io_time_ms 93 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 316 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 14 #