data_3HMG # _model_server_result.job_id mCY5o1VOMi747ipBwskXUg _model_server_result.datetime_utc '2024-11-07 07:37:06' _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 3hmg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"R","auth_seq_id":329}' # _entry.id 3HMG # _exptl.entry_id 3HMG _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 12 _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 3HMG _cell.length_a 162.8 _cell.length_b 162.8 _cell.length_c 177.3 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3HMG _symmetry.cell_setting ? _symmetry.Int_Tables_number 76 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 41' # _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,R,S,T,U,V,W,X,Y,Z,AA _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 J N N ? 4 K N N ? 4 L N N ? 4 M N N ? 4 N N N ? 4 O N N ? 4 P N N ? 4 Q N N ? 4 R N N ? 4 S N N ? 4 T N N ? 4 U N N # _pdbx_entity_branch.entity_id 3 _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 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 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 3 n G NAG 1 G 1 NAG A 339 NAG 3 n G NAG 2 G 2 NAG A 340 NAG 3 n G BMA 3 G 3 BMA A 341 MAN 3 n H NAG 1 H 1 NAG C 339 NAG 3 n H NAG 2 H 2 NAG C 340 NAG 3 n H BMA 3 H 3 BMA C 341 MAN 3 n I NAG 1 I 1 NAG E 339 NAG 3 n I NAG 2 I 2 NAG E 340 NAG 3 n I BMA 3 I 3 BMA E 341 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 14 A CYS 14 1_555 B SG CYS 137 B CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.988 ? disulf ? disulf2 A SG CYS 52 A CYS 52 1_555 A SG CYS 277 A CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? disulf ? disulf3 A SG CYS 64 A CYS 64 1_555 A SG CYS 76 A CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf4 A SG CYS 97 A CYS 97 1_555 A SG CYS 139 A CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.99 ? disulf ? disulf5 A SG CYS 281 A CYS 281 1_555 A SG CYS 305 A CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? disulf ? disulf6 B SG CYS 144 B CYS 144 1_555 B SG CYS 148 B CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? disulf ? disulf7 C SG CYS 14 C CYS 14 1_555 D SG CYS 137 D CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? disulf ? disulf8 C SG CYS 52 C CYS 52 1_555 C SG CYS 277 C CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf9 C SG CYS 64 C CYS 64 1_555 C SG CYS 76 C CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf10 C SG CYS 97 C CYS 97 1_555 C SG CYS 139 C CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.994 ? disulf ? disulf11 C SG CYS 281 C CYS 281 1_555 C SG CYS 305 C CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.993 ? disulf ? disulf12 D SG CYS 144 D CYS 144 1_555 D SG CYS 148 D CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? disulf ? disulf13 E SG CYS 14 E CYS 14 1_555 F SG CYS 137 F CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.998 ? disulf ? disulf14 E SG CYS 52 E CYS 52 1_555 E SG CYS 277 E CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? disulf ? disulf15 E SG CYS 64 E CYS 64 1_555 E SG CYS 76 E CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.99 ? disulf ? disulf16 E SG CYS 97 E CYS 97 1_555 E SG CYS 139 E CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.998 ? disulf ? disulf17 E SG CYS 281 E CYS 281 1_555 E SG CYS 305 E CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2 ? disulf ? disulf18 F SG CYS 144 F CYS 144 1_555 F SG CYS 148 F CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? covale ? covale1 A ND2 ASN 38 A ASN 38 1_555 J C1 NAG . A NAG 329 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale2 A ND2 ASN 81 A ASN 81 1_555 K C1 NAG . A NAG 334 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale3 A ND2 ASN 165 A ASN 165 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.465 ? covale ? covale4 A ND2 ASN 285 A ASN 285 1_555 L C1 NAG . A NAG 348 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale5 B ND2 ASN 154 B ASN 154 1_555 M C1 NAG . B NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale6 C ND2 ASN 38 C ASN 38 1_555 N C1 NAG . C NAG 329 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale7 C ND2 ASN 81 C ASN 81 1_555 O C1 NAG . C NAG 334 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale8 C ND2 ASN 165 C ASN 165 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? covale ? covale9 C ND2 ASN 285 C ASN 285 1_555 P C1 NAG . C NAG 348 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale10 D ND2 ASN 154 D ASN 154 1_555 Q C1 NAG . D NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 ? covale ? covale11 E ND2 ASN 38 E ASN 38 1_555 R C1 NAG . E NAG 329 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale12 E ND2 ASN 81 E ASN 81 1_555 S C1 NAG . E NAG 334 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale13 E ND2 ASN 165 E ASN 165 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 ? covale ? covale14 E ND2 ASN 285 E ASN 285 1_555 T C1 NAG . E NAG 348 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.423 ? covale ? covale15 F ND2 ASN 154 F ASN 154 1_555 U C1 NAG . F NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? covale ? covale16 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale17 G O4 NAG . G NAG 2 1_555 G C1 BMA . G BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.424 ? covale ? covale18 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale19 H O4 NAG . H NAG 2 1_555 H C1 BMA . H BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale20 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale21 I O4 NAG . I NAG 2 1_555 I C1 BMA . I BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? # _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 261 n n C1 O1 NAG sing 262 n n C1 O5 NAG sing 263 n n C1 H1 NAG sing 264 n n C2 C3 NAG sing 265 n n C2 N2 NAG sing 266 n n C2 H2 NAG sing 267 n n C3 C4 NAG sing 268 n n C3 O3 NAG sing 269 n n C3 H3 NAG sing 270 n n C4 C5 NAG sing 271 n n C4 O4 NAG sing 272 n n C4 H4 NAG sing 273 n n C5 C6 NAG sing 274 n n C5 O5 NAG sing 275 n n C5 H5 NAG sing 276 n n C6 O6 NAG sing 277 n n C6 H61 NAG sing 278 n n C6 H62 NAG sing 279 n n C7 C8 NAG sing 280 n n C7 N2 NAG sing 281 n n C7 O7 NAG doub 282 n n C8 H81 NAG sing 283 n n C8 H82 NAG sing 284 n n C8 H83 NAG sing 285 n n N2 HN2 NAG sing 286 n n O1 HO1 NAG sing 287 n n O3 HO3 NAG sing 288 n n O4 HO4 NAG sing 289 n n O6 HO6 NAG sing 290 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 3HMG _atom_sites.fract_transf_matrix[1][1] 0.006143 _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] 0.006143 _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] 0.00564 _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 J 4 NAG A 1 329 329 NAG NAG . K 4 NAG A 1 334 334 NAG NAG . L 4 NAG A 1 348 348 NAG NAG . M 4 NAG B 1 401 401 NAG NAG . N 4 NAG C 1 329 329 NAG NAG . O 4 NAG C 1 334 334 NAG NAG . P 4 NAG C 1 348 348 NAG NAG . Q 4 NAG D 1 401 401 NAG NAG . R 4 NAG E 1 329 329 NAG NAG . S 4 NAG E 1 334 334 NAG NAG . T 4 NAG E 1 348 348 NAG NAG . U 4 NAG F 1 401 401 NAG NAG . V 5 HOH A 1 349 2 HOH HOH . V 5 HOH A 2 350 3 HOH HOH . V 5 HOH A 3 351 4 HOH HOH . V 5 HOH A 4 352 5 HOH HOH . V 5 HOH A 5 353 11 HOH HOH . V 5 HOH A 6 354 12 HOH HOH . W 5 HOH B 1 402 22 HOH HOH . W 5 HOH B 2 403 23 HOH HOH . W 5 HOH B 3 404 24 HOH HOH . W 5 HOH B 4 405 27 HOH HOH . W 5 HOH B 5 406 29 HOH HOH . X 5 HOH C 1 349 2 HOH HOH . X 5 HOH C 2 350 3 HOH HOH . X 5 HOH C 3 351 4 HOH HOH . X 5 HOH C 4 352 5 HOH HOH . X 5 HOH C 5 353 11 HOH HOH . X 5 HOH C 6 354 12 HOH HOH . Y 5 HOH D 1 402 22 HOH HOH . Y 5 HOH D 2 403 23 HOH HOH . Y 5 HOH D 3 404 24 HOH HOH . Y 5 HOH D 4 405 27 HOH HOH . Y 5 HOH D 5 406 29 HOH HOH . Z 5 HOH E 1 349 2 HOH HOH . Z 5 HOH E 2 350 3 HOH HOH . Z 5 HOH E 3 351 4 HOH HOH . Z 5 HOH E 4 352 5 HOH HOH . Z 5 HOH E 5 353 11 HOH HOH . Z 5 HOH E 6 354 12 HOH HOH . AA 5 HOH F 1 402 22 HOH HOH . AA 5 HOH F 2 403 23 HOH HOH . AA 5 HOH F 3 404 24 HOH HOH . AA 5 HOH F 4 405 27 HOH HOH . AA 5 HOH F 5 406 29 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 . . . R 4 62.959 34.091 13.63 1 38.18 ? C1 NAG 329 E 1 HETATM 2 C C2 NAG . . . R 4 64.256 33.953 12.893 1 40.82 ? C2 NAG 329 E 1 HETATM 3 C C3 NAG . . . R 4 64.307 34.977 11.8 1 42.47 ? C3 NAG 329 E 1 HETATM 4 C C4 NAG . . . R 4 63.122 34.777 10.828 1 42.82 ? C4 NAG 329 E 1 HETATM 5 C C5 NAG . . . R 4 61.767 34.73 11.606 1 41.69 ? C5 NAG 329 E 1 HETATM 6 C C6 NAG . . . R 4 60.673 34.135 10.708 1 41.55 ? C6 NAG 329 E 1 HETATM 7 C C7 NAG . . . R 4 66.47 33.372 13.775 1 43.05 ? C7 NAG 329 E 1 HETATM 8 C C8 NAG . . . R 4 67.57 33.701 14.769 1 43.23 ? C8 NAG 329 E 1 HETATM 9 N N2 NAG . . . R 4 65.375 34.151 13.801 1 42.24 ? N2 NAG 329 E 1 HETATM 10 O O3 NAG . . . R 4 65.54 34.84 11.109 1 43.71 ? O3 NAG 329 E 1 HETATM 11 O O4 NAG . . . R 4 63.121 35.86 9.903 1 45.22 ? O4 NAG 329 E 1 HETATM 12 O O5 NAG . . . R 4 61.861 33.861 12.742 1 40.61 ? O5 NAG 329 E 1 HETATM 13 O O6 NAG . . . R 4 60.908 32.741 10.541 1 41.83 ? O6 NAG 329 E 1 HETATM 14 O O7 NAG . . . R 4 66.559 32.406 13.008 1 43.06 ? O7 NAG 329 E 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 346 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #