data_6F39 # _model_server_result.job_id WfFcC1lFgUzbQMS1DUs1HQ _model_server_result.datetime_utc '2025-08-31 22:39:16' _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 6f39 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":305}' # _entry.id 6F39 # _exptl.entry_id 6F39 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 5 _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 99.9 _cell.angle_gamma 90 _cell.entry_id 6F39 _cell.length_a 140.563 _cell.length_b 54.62 _cell.length_c 138.18 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6F39 _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details 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 _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 5 _struct_asym.id I _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 2 _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 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 2 4 3 MAN BMA C1 O1 . O3 HO3 . sing 4 ? 2 5 4 GAL MAN C1 O1 . O4 HO4 . sing 5 ? 2 6 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 2 n C NAG 1 C 1 NAG A 319 NAG 2 n C NAG 2 C 2 NAG A 318 NAG 2 n C BMA 3 C 3 BMA A 317 BMA 2 n C MAN 4 C 4 MAN A 316 MAN 2 n C GAL 5 C 5 GAL A 315 GAL 2 n C MAN 6 C 6 MAN A 321 MAN 2 n D NAG 1 D 1 NAG B 319 NAG 2 n D NAG 2 D 2 NAG B 322 NAG 2 n D BMA 3 D 3 BMA B 323 BMA 2 n D MAN 4 D 4 MAN B 324 MAN 2 n D GAL 5 D 5 GAL B 325 GAL 2 n D MAN 6 D 6 MAN B 326 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 50 A CYS 54 1_555 A SG CYS 68 A CYS 72 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf2 A SG CYS 125 A CYS 129 1_555 A SG CYS 144 A CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? disulf ? disulf3 A SG CYS 140 A CYS 144 1_555 A SG CYS 153 A CYS 157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf4 A SG CYS 155 A CYS 159 1_555 A SG CYS 168 A CYS 172 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? disulf ? disulf5 A SG CYS 172 A CYS 176 1_555 A SG CYS 199 A CYS 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf6 A SG CYS 229 A CYS 233 1_555 A SG CYS 247 A CYS 251 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf7 B SG CYS 50 B CYS 54 1_555 B SG CYS 68 B CYS 72 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf8 B SG CYS 125 B CYS 129 1_555 B SG CYS 144 B CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf9 B SG CYS 140 B CYS 144 1_555 B SG CYS 153 B CYS 157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.006 ? disulf ? disulf10 B SG CYS 155 B CYS 159 1_555 B SG CYS 168 B CYS 172 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? disulf ? disulf11 B SG CYS 172 B CYS 176 1_555 B SG CYS 199 B CYS 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf12 B SG CYS 229 B CYS 233 1_555 B SG CYS 247 B CYS 251 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? covale ? covale1 A ND2 ASN 104 A ASN 108 1_555 I C1 NAG . A NAG 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.472 ? covale ? covale2 A ND2 ASN 200 A ASN 204 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale3 B ND2 ASN 200 B ASN 204 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale4 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? covale ? covale5 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale6 C O3 BMA . C BMA 3 1_555 C C1 MAN . C MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? covale ? covale7 C O6 BMA . C BMA 3 1_555 C C1 MAN . C MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale8 C O4 MAN . C MAN 4 1_555 C C1 GAL . C GAL 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale9 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.465 ? covale ? covale10 D O4 NAG . D NAG 2 1_555 D C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? covale ? covale11 D O3 BMA . D BMA 3 1_555 D C1 MAN . D MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale12 D O6 BMA . D BMA 3 1_555 D C1 MAN . D MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale13 D O4 MAN . D MAN 4 1_555 D C1 GAL . D GAL 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.46 ? metalc ? metalc1 A OD1 ASP 53 A ASP 57 1_555 E CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.652 ? metalc ? metalc2 A OD2 ASP 53 A ASP 57 1_555 E CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.812 ? metalc ? metalc3 A O SER 100 A SER 104 1_555 E CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.532 ? metalc ? metalc4 A OD1 ASP 123 A ASP 127 1_555 F CA CA . A CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.239 ? metalc ? metalc5 A OD2 ASP 123 A ASP 127 1_555 F CA CA . A CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.311 ? metalc ? metalc6 A O TYR 147 A TYR 151 1_555 F CA CA . A CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.225 ? metalc ? metalc7 A O GLY 150 A GLY 154 1_555 F CA CA . A CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.151 ? metalc ? metalc8 A OG SER 186 A SER 190 1_555 H NA NA . A NA 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.61 ? metalc ? metalc9 A OD2 ASP 222 A ASP 226 1_555 G CA CA . A CA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.43 ? metalc ? metalc10 A O ARG 275 A ARG 279 1_555 H NA NA . A NA 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.511 ? metalc ? metalc11 B OD1 ASN 19 B ASN 23 1_555 J CA CA . B CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.646 ? metalc ? metalc12 B OD2 ASP 53 B ASP 57 1_555 J CA CA . B CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.079 ? metalc ? metalc13 B O LEU 122 B LEU 126 1_555 K CA CA . B CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.537 ? metalc ? metalc14 B OD1 ASP 123 B ASP 127 1_555 K CA CA . B CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? metalc ? metalc15 B O GLY 150 B GLY 154 1_555 K CA CA . B CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? metalc ? metalc16 B OG SER 186 B SER 190 1_555 M NA NA . B NA 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.258 ? metalc ? metalc17 B OH TYR 193 B TYR 197 1_555 L CA CA . B CA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.176 ? metalc ? metalc18 B OD2 ASP 222 B ASP 226 1_555 L CA CA . B CA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.947 ? metalc ? metalc19 B OD2 ASP 232 B ASP 236 1_555 L CA CA . B CA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.163 ? metalc ? metalc20 B OD2 ASP 269 B ASP 273 1_555 L CA CA . B CA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.211 ? metalc ? metalc21 B O ARG 275 B ARG 279 1_555 M NA NA . B NA 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.418 ? # _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 307 n n C1 O1 NAG sing 308 n n C1 O5 NAG sing 309 n n C1 H1 NAG sing 310 n n C2 C3 NAG sing 311 n n C2 N2 NAG sing 312 n n C2 H2 NAG sing 313 n n C3 C4 NAG sing 314 n n C3 O3 NAG sing 315 n n C3 H3 NAG sing 316 n n C4 C5 NAG sing 317 n n C4 O4 NAG sing 318 n n C4 H4 NAG sing 319 n n C5 C6 NAG sing 320 n n C5 O5 NAG sing 321 n n C5 H5 NAG sing 322 n n C6 O6 NAG sing 323 n n C6 H61 NAG sing 324 n n C6 H62 NAG sing 325 n n C7 C8 NAG sing 326 n n C7 N2 NAG sing 327 n n C7 O7 NAG doub 328 n n C8 H81 NAG sing 329 n n C8 H82 NAG sing 330 n n C8 H83 NAG sing 331 n n N2 HN2 NAG sing 332 n n O1 HO1 NAG sing 333 n n O3 HO3 NAG sing 334 n n O4 HO4 NAG sing 335 n n O6 HO6 NAG sing 336 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 6F39 _atom_sites.fract_transf_matrix[1][1] 0.007114 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001242 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018308 _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] 0.007346 _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 E 3 CA A 1 301 301 CA CA . F 3 CA A 1 302 302 CA CA . G 3 CA A 1 303 303 CA CA . H 4 NA A 1 304 304 NA NA . I 5 NAG A 1 305 310 NAG NAG . J 3 CA B 1 301 301 CA CA . K 3 CA B 1 302 302 CA CA . L 3 CA B 1 303 303 CA CA . M 4 NA B 1 304 304 NA NA . # 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 . . . I 5 161.302 115.767 -5.062 1 320.23 ? C1 NAG 305 A 1 HETATM 2 C C2 NAG . . . I 5 160.167 116.681 -5.611 1 320.23 ? C2 NAG 305 A 1 HETATM 3 C C3 NAG . . . I 5 160.754 117.957 -6.215 1 320.23 ? C3 NAG 305 A 1 HETATM 4 C C4 NAG . . . I 5 161.799 118.541 -5.28 1 320.23 ? C4 NAG 305 A 1 HETATM 5 C C5 NAG . . . I 5 163.013 117.624 -5.276 1 320.23 ? C5 NAG 305 A 1 HETATM 6 C C6 NAG . . . I 5 163.781 117.635 -3.973 1 320.23 ? C6 NAG 305 A 1 HETATM 7 C C7 NAG . . . I 5 158.059 116.083 -6.755 1 320.23 ? C7 NAG 305 A 1 HETATM 8 C C8 NAG . . . I 5 157.369 117.017 -5.808 1 320.23 ? C8 NAG 305 A 1 HETATM 9 N N2 NAG . . . I 5 159.385 115.966 -6.61 1 320.23 ? N2 NAG 305 A 1 HETATM 10 O O3 NAG . . . I 5 159.733 118.915 -6.475 1 320.23 ? O3 NAG 305 A 1 HETATM 11 O O4 NAG . . . I 5 162.193 119.83 -5.737 1 320.23 ? O4 NAG 305 A 1 HETATM 12 O O5 NAG . . . I 5 162.633 116.26 -5.541 1 320.23 ? O5 NAG 305 A 1 HETATM 13 O O6 NAG . . . I 5 165.147 117.976 -4.179 1 320.23 ? O6 NAG 305 A 1 HETATM 14 O O7 NAG . . . I 5 157.443 115.458 -7.613 1 320.23 ? O7 NAG 305 A 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 389 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 14 #