data_3PMH # _model_server_result.job_id N6arf_NRDRKeM4J7slB3eQ _model_server_result.datetime_utc '2024-12-03 06:48:20' _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 3pmh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":601}' # _entry.id 3PMH # _exptl.entry_id 3PMH _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 6 _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 90 _cell.angle_gamma 90 _cell.entry_id 3PMH _cell.length_a 67.657 _cell.length_b 67.657 _cell.length_c 329.73 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3PMH _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F _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 6 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 4 _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 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 4 3 2 MAN NAG C1 O1 . O4 HO4 . sing 3 ? 4 4 3 MAN MAN C1 O1 . O3 HO3 . sing 4 ? 4 5 3 MAN MAN 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 4 n D NAG 1 C 1 NAG B 501 NAG 4 n D NAG 2 C 2 NAG B 502 NAG 4 n D MAN 3 C 3 MAN B 503 MAN 4 n D MAN 4 C 4 MAN B 508 MAN 4 n D MAN 5 C 5 MAN B 504 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 9 A CYS 1 1_555 B SG CYS 119 B CYS 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf2 B SG CYS 28 B CYS 42 1_555 B SG CYS 44 B CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf3 B SG CYS 173 B CYS 168 1_555 B SG CYS 187 B CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 B SG CYS 201 B CYS 191 1_555 B SG CYS 231 B CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf5 C SG CYS 4 G CYS 4 1_555 C SG CYS 17 G CYS 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf6 C SG CYS 209 G CYS 209 1_555 C SG CYS 248 G CYS 248 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf7 C SG CYS 211 G CYS 211 1_555 C SG CYS 264 G CYS 264 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? covale ? covale1 B ND2 ASN 53 B ASN 60 1_555 D C1 NAG . C NAG 1 1_555 G ? ? ? ? ? ? ? ? ? ? ? 1.459 ? covale ? covale2 C ND2 ASN 159 G ASN 159 1_555 F C1 NAG . G NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale3 C C TYS 276 G TYS 276 1_555 C N ASP 277 G ASP 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale4 C C TYS 279 G TYS 279 1_555 C N PRO 280 G PRO 280 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.345 ? covale ? covale5 D O4 NAG . C NAG 1 1_555 D C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.391 ? covale ? covale6 D O4 NAG . C NAG 2 1_555 D C1 MAN . C MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.407 ? covale ? covale7 D O3 MAN . C MAN 3 1_555 D C1 MAN . C MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.405 ? covale ? covale8 D O6 MAN . C MAN 3 1_555 D C1 MAN . C MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.409 ? # _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 322 n n C1 O1 NAG sing 323 n n C1 O5 NAG sing 324 n n C1 H1 NAG sing 325 n n C2 C3 NAG sing 326 n n C2 N2 NAG sing 327 n n C2 H2 NAG sing 328 n n C3 C4 NAG sing 329 n n C3 O3 NAG sing 330 n n C3 H3 NAG sing 331 n n C4 C5 NAG sing 332 n n C4 O4 NAG sing 333 n n C4 H4 NAG sing 334 n n C5 C6 NAG sing 335 n n C5 O5 NAG sing 336 n n C5 H5 NAG sing 337 n n C6 O6 NAG sing 338 n n C6 H61 NAG sing 339 n n C6 H62 NAG sing 340 n n C7 C8 NAG sing 341 n n C7 N2 NAG sing 342 n n C7 O7 NAG doub 343 n n C8 H81 NAG sing 344 n n C8 H82 NAG sing 345 n n C8 H83 NAG sing 346 n n N2 HN2 NAG sing 347 n n O1 HO1 NAG sing 348 n n O3 HO3 NAG sing 349 n n O4 HO4 NAG sing 350 n n O6 HO6 NAG sing 351 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 3PMH _atom_sites.fract_transf_matrix[1][1] 0.01478 _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] 0.01478 _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] 0.003033 _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 5 0G7 B 1 301 700 0G7 0G7 . F 6 NAG G 1 601 601 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 . . . F 6 -25.613 -11.511 91.557 1 102.34 ? C1 NAG 601 G 1 HETATM 2 C C2 NAG . . . F 6 -27.124 -11.782 91.249 1 99.7 ? C2 NAG 601 G 1 HETATM 3 C C3 NAG . . . F 6 -27.502 -11.056 89.91 1 102.85 ? C3 NAG 601 G 1 HETATM 4 C C4 NAG . . . F 6 -27.065 -9.545 89.884 1 105.67 ? C4 NAG 601 G 1 HETATM 5 C C5 NAG . . . F 6 -25.603 -9.497 90.316 1 105.56 ? C5 NAG 601 G 1 HETATM 6 C C6 NAG . . . F 6 -25.015 -8.146 90.39 1 107.3 ? C6 NAG 601 G 1 HETATM 7 C C7 NAG . . . F 6 -28.154 -13.838 91.963 1 90.18 ? C7 NAG 601 G 1 HETATM 8 C C8 NAG . . . F 6 -28.302 -15.308 91.647 1 86.68 ? C8 NAG 601 G 1 HETATM 9 N N2 NAG . . . F 6 -27.355 -13.202 91.115 1 92.52 ? N2 NAG 601 G 1 HETATM 10 O O3 NAG . . . F 6 -28.898 -11.168 89.685 1 104.37 ? O3 NAG 601 G 1 HETATM 11 O O4 NAG . . . F 6 -27.211 -9.045 88.572 1 106.16 ? O4 NAG 601 G 1 HETATM 12 O O5 NAG . . . F 6 -25.422 -10.106 91.621 1 103.18 ? O5 NAG 601 G 1 HETATM 13 O O6 NAG . . . F 6 -25.892 -7.204 91.003 1 112.68 ? O6 NAG 601 G 1 HETATM 14 O O7 NAG . . . F 6 -28.725 -13.318 92.95 1 89.35 ? O7 NAG 601 G 1 # _model_server_stats.io_time_ms 43 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 14 #