data_5CM4 # _model_server_result.job_id NmnOA1-mhWuv4hI1sA914A _model_server_result.datetime_utc '2025-06-22 20:28:17' _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 5cm4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":301}' # _entry.id 5CM4 # _exptl.entry_id 5CM4 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 3 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 3 _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 5CM4 _cell.length_a 105.583 _cell.length_b 111.738 _cell.length_c 75.37 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5CM4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,G 1 1 B,E,F,H 2 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 ? 3 D N N ? 3 E N N ? 3 F N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order 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 302 NAG 2 n C NAG 2 C 2 NAG A 303 NAG # 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 6 A CYS 45 1_555 A SG CYS 67 A CYS 106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? disulf ? disulf2 A SG CYS 14 A CYS 53 1_555 A SG CYS 60 A CYS 99 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? disulf ? disulf3 A SG CYS 51 A CYS 90 1_555 A SG CYS 89 A CYS 128 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.146 ? disulf ? disulf4 A SG CYS 78 A CYS 117 1_555 A SG CYS 119 A CYS 158 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? disulf ? disulf5 A SG CYS 82 A CYS 121 1_555 A SG CYS 106 A CYS 145 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? disulf ? disulf6 B SG CYS 6 B CYS 45 1_555 B SG CYS 67 B CYS 106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? disulf ? disulf7 B SG CYS 14 B CYS 53 1_555 B SG CYS 60 B CYS 99 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? disulf ? disulf8 B SG CYS 51 B CYS 90 1_555 B SG CYS 89 B CYS 128 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? disulf ? disulf9 B SG CYS 78 B CYS 117 1_555 B SG CYS 119 B CYS 158 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? disulf ? disulf10 B SG CYS 82 B CYS 121 1_555 B SG CYS 106 B CYS 145 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? covale ? covale1 A ND2 ASN 20 A ASN 59 1_555 D C1 NAG . A NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale2 A ND2 ASN 105 A ASN 144 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.427 ? covale ? covale3 B ND2 ASN 20 B ASN 59 1_555 E C1 NAG . B NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale4 B ND2 ASN 105 B ASN 144 1_555 F C1 NAG . B NAG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale5 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? # _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 237 n n C1 O1 NAG sing 238 n n C1 O5 NAG sing 239 n n C1 H1 NAG sing 240 n n C2 C3 NAG sing 241 n n C2 N2 NAG sing 242 n n C2 H2 NAG sing 243 n n C3 C4 NAG sing 244 n n C3 O3 NAG sing 245 n n C3 H3 NAG sing 246 n n C4 C5 NAG sing 247 n n C4 O4 NAG sing 248 n n C4 H4 NAG sing 249 n n C5 C6 NAG sing 250 n n C5 O5 NAG sing 251 n n C5 H5 NAG sing 252 n n C6 O6 NAG sing 253 n n C6 H61 NAG sing 254 n n C6 H62 NAG sing 255 n n C7 C8 NAG sing 256 n n C7 N2 NAG sing 257 n n C7 O7 NAG doub 258 n n C8 H81 NAG sing 259 n n C8 H82 NAG sing 260 n n C8 H83 NAG sing 261 n n N2 HN2 NAG sing 262 n n O1 HO1 NAG sing 263 n n O3 HO3 NAG sing 264 n n O4 HO4 NAG sing 265 n n O6 HO6 NAG sing 266 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 5CM4 _atom_sites.fract_transf_matrix[1][1] 0.009471 _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] 0.00895 _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] 0.013268 _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 3 NAG A 1 301 301 NAG NAG . E 3 NAG B 1 301 301 NAG NAG . F 3 NAG B 1 302 302 NAG NAG . G 4 HOH A 1 401 38 HOH HOH . G 4 HOH A 2 402 19 HOH HOH . G 4 HOH A 3 403 5 HOH HOH . G 4 HOH A 4 404 35 HOH HOH . G 4 HOH A 5 405 36 HOH HOH . G 4 HOH A 6 406 50 HOH HOH . G 4 HOH A 7 407 44 HOH HOH . G 4 HOH A 8 408 11 HOH HOH . G 4 HOH A 9 409 2 HOH HOH . G 4 HOH A 10 410 10 HOH HOH . G 4 HOH A 11 411 1 HOH HOH . G 4 HOH A 12 412 8 HOH HOH . G 4 HOH A 13 413 7 HOH HOH . G 4 HOH A 14 414 34 HOH HOH . G 4 HOH A 15 415 14 HOH HOH . G 4 HOH A 16 416 12 HOH HOH . G 4 HOH A 17 417 31 HOH HOH . G 4 HOH A 18 418 15 HOH HOH . G 4 HOH A 19 419 4 HOH HOH . G 4 HOH A 20 420 17 HOH HOH . G 4 HOH A 21 421 45 HOH HOH . G 4 HOH A 22 422 39 HOH HOH . G 4 HOH A 23 423 18 HOH HOH . G 4 HOH A 24 424 6 HOH HOH . G 4 HOH A 25 425 9 HOH HOH . G 4 HOH A 26 426 47 HOH HOH . G 4 HOH A 27 427 13 HOH HOH . G 4 HOH A 28 428 43 HOH HOH . G 4 HOH A 29 429 51 HOH HOH . G 4 HOH A 30 430 42 HOH HOH . G 4 HOH A 31 431 16 HOH HOH . G 4 HOH A 32 432 46 HOH HOH . G 4 HOH A 33 433 3 HOH HOH . H 4 HOH B 1 401 26 HOH HOH . H 4 HOH B 2 402 48 HOH HOH . H 4 HOH B 3 403 24 HOH HOH . H 4 HOH B 4 404 33 HOH HOH . H 4 HOH B 5 405 21 HOH HOH . H 4 HOH B 6 406 23 HOH HOH . H 4 HOH B 7 407 37 HOH HOH . H 4 HOH B 8 408 40 HOH HOH . H 4 HOH B 9 409 41 HOH HOH . H 4 HOH B 10 410 32 HOH HOH . H 4 HOH B 11 411 22 HOH HOH . H 4 HOH B 12 412 25 HOH HOH . H 4 HOH B 13 413 30 HOH HOH . H 4 HOH B 14 414 20 HOH HOH . H 4 HOH B 15 415 29 HOH HOH . H 4 HOH B 16 416 27 HOH HOH . H 4 HOH B 17 417 49 HOH HOH . H 4 HOH B 18 418 28 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 . . . E 3 -8.768 -33.974 10.502 1 136.43 ? C1 NAG 301 B 1 HETATM 2 C C2 NAG . . . E 3 -9.84 -34.799 11.297 1 143.46 ? C2 NAG 301 B 1 HETATM 3 C C3 NAG . . . E 3 -9.592 -36.334 11.22 1 141.52 ? C3 NAG 301 B 1 HETATM 4 C C4 NAG . . . E 3 -9.372 -36.707 9.745 1 140.46 ? C4 NAG 301 B 1 HETATM 5 C C5 NAG . . . E 3 -8.324 -35.792 9.076 1 138.87 ? C5 NAG 301 B 1 HETATM 6 C C6 NAG . . . E 3 -8.086 -36.135 7.599 1 137.35 ? C6 NAG 301 B 1 HETATM 7 C C7 NAG . . . E 3 -11.191 -34.232 13.306 1 135.2 ? C7 NAG 301 B 1 HETATM 8 C C8 NAG . . . E 3 -11.003 -33.634 14.647 1 125.32 ? C8 NAG 301 B 1 HETATM 9 N N2 NAG . . . E 3 -10.037 -34.293 12.652 1 141.77 ? N2 NAG 301 B 1 HETATM 10 O O3 NAG . . . E 3 -10.703 -37.036 11.752 1 145.2 ? O3 NAG 301 B 1 HETATM 11 O O4 NAG . . . E 3 -8.986 -38.061 9.643 1 140.99 ? O4 NAG 301 B 1 HETATM 12 O O5 NAG . . . E 3 -8.701 -34.438 9.178 1 139.4 ? O5 NAG 301 B 1 HETATM 13 O O6 NAG . . . E 3 -7.251 -37.272 7.509 1 135.68 ? O6 NAG 301 B 1 HETATM 14 O O7 NAG . . . E 3 -12.296 -34.674 12.95 1 130.02 ? O7 NAG 301 B 1 # _model_server_stats.io_time_ms 48 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 321 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #