data_6C5M # _model_server_result.job_id OHFyEXr5ZVEwpMdQ-Suy2Q _model_server_result.datetime_utc '2024-11-27 04:08:11' _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 6c5m # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":301}' # _entry.id 6C5M # _exptl.entry_id 6C5M _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 106.31 _cell.angle_gamma 90 _cell.entry_id 6C5M _cell.length_a 41.576 _cell.length_b 98.348 _cell.length_c 55.399 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6C5M _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 3 oligosaccharide 4 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 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 4 3 2 BMA NAG C1 O1 . O4 HO4 . sing 4 ? 4 4 3 MAN BMA C1 O1 . O3 HO3 . sing 5 ? 4 5 3 MAN BMA C1 O1 . O6 HO6 . sing 6 ? 4 6 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 3 n C NAG 1 C 1 NAG A 301 NAG 3 n C NAG 2 C 2 NAG A 302 NAG 4 n D NAG 1 D 1 NAG A 310 NAG 4 n D NAG 2 D 2 NAG A 311 NAG 4 n D BMA 3 D 3 BMA A 312 BMA 4 n D MAN 4 D 4 MAN A 313 MAN 4 n D MAN 5 D 5 MAN A 314 MAN 4 n D FUC 6 D 6 FUC A 315 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 104 A CYS 104 1_555 A SG CYS 168 A CYS 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? disulf ? disulf2 A SG CYS 208 A CYS 208 1_555 A SG CYS 263 A CYS 263 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf3 B SG CYS 25 B CYS 25 1_555 B SG CYS 80 B CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? covale ? covale1 A ND2 ASN 20 A ASN 20 1_555 E C1 NAG . A NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale2 A ND2 ASN 42 A ASN 42 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale3 A ND2 ASN 165 A ASN 165 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale4 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale5 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale6 D O6 NAG . D NAG 1 1_555 D C1 FUC . D FUC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale7 D O4 NAG . D NAG 2 1_555 D C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale8 D O3 BMA . D BMA 3 1_555 D C1 MAN . D MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale9 D O6 BMA . D BMA 3 1_555 D C1 MAN . D MAN 5 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 411 n n C1 O1 NAG sing 412 n n C1 O5 NAG sing 413 n n C1 H1 NAG sing 414 n n C2 C3 NAG sing 415 n n C2 N2 NAG sing 416 n n C2 H2 NAG sing 417 n n C3 C4 NAG sing 418 n n C3 O3 NAG sing 419 n n C3 H3 NAG sing 420 n n C4 C5 NAG sing 421 n n C4 O4 NAG sing 422 n n C4 H4 NAG sing 423 n n C5 C6 NAG sing 424 n n C5 O5 NAG sing 425 n n C5 H5 NAG sing 426 n n C6 O6 NAG sing 427 n n C6 H61 NAG sing 428 n n C6 H62 NAG sing 429 n n C7 C8 NAG sing 430 n n C7 N2 NAG sing 431 n n C7 O7 NAG doub 432 n n C8 H81 NAG sing 433 n n C8 H82 NAG sing 434 n n C8 H83 NAG sing 435 n n N2 HN2 NAG sing 436 n n O1 HO1 NAG sing 437 n n O3 HO3 NAG sing 438 n n O4 HO4 NAG sing 439 n n O6 HO6 NAG sing 440 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 6C5M _atom_sites.fract_transf_matrix[1][1] 0.024052 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.007039 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010168 _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] 0.018808 _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 NAG A 1 301 300 NAG NAG . F 6 J81 A 1 302 501 J81 J81 . G 7 PLM A 1 303 502 PLM PLM . H 8 HOH A 1 401 66 HOH HOH . H 8 HOH A 2 402 62 HOH HOH . H 8 HOH A 3 403 64 HOH HOH . H 8 HOH A 4 404 58 HOH HOH . H 8 HOH A 5 405 50 HOH HOH . H 8 HOH A 6 406 57 HOH HOH . H 8 HOH A 7 407 41 HOH HOH . H 8 HOH A 8 408 53 HOH HOH . H 8 HOH A 9 409 68 HOH HOH . H 8 HOH A 10 410 51 HOH HOH . H 8 HOH A 11 411 39 HOH HOH . H 8 HOH A 12 412 42 HOH HOH . H 8 HOH A 13 413 63 HOH HOH . H 8 HOH A 14 414 22 HOH HOH . H 8 HOH A 15 415 5 HOH HOH . H 8 HOH A 16 416 28 HOH HOH . H 8 HOH A 17 417 35 HOH HOH . H 8 HOH A 18 418 27 HOH HOH . H 8 HOH A 19 419 34 HOH HOH . H 8 HOH A 20 420 67 HOH HOH . H 8 HOH A 21 421 1 HOH HOH . H 8 HOH A 22 422 46 HOH HOH . H 8 HOH A 23 423 56 HOH HOH . H 8 HOH A 24 424 36 HOH HOH . H 8 HOH A 25 425 30 HOH HOH . H 8 HOH A 26 426 18 HOH HOH . H 8 HOH A 27 427 24 HOH HOH . H 8 HOH A 28 428 16 HOH HOH . H 8 HOH A 29 429 40 HOH HOH . H 8 HOH A 30 430 48 HOH HOH . H 8 HOH A 31 431 38 HOH HOH . H 8 HOH A 32 432 2 HOH HOH . H 8 HOH A 33 433 52 HOH HOH . H 8 HOH A 34 434 11 HOH HOH . H 8 HOH A 35 435 47 HOH HOH . H 8 HOH A 36 436 14 HOH HOH . H 8 HOH A 37 437 23 HOH HOH . H 8 HOH A 38 438 21 HOH HOH . H 8 HOH A 39 439 19 HOH HOH . H 8 HOH A 40 440 31 HOH HOH . H 8 HOH A 41 441 4 HOH HOH . H 8 HOH A 42 442 26 HOH HOH . H 8 HOH A 43 443 12 HOH HOH . I 8 HOH B 1 101 49 HOH HOH . I 8 HOH B 2 102 43 HOH HOH . I 8 HOH B 3 103 3 HOH HOH . I 8 HOH B 4 104 61 HOH HOH . I 8 HOH B 5 105 6 HOH HOH . I 8 HOH B 6 106 37 HOH HOH . I 8 HOH B 7 107 33 HOH HOH . I 8 HOH B 8 108 45 HOH HOH . I 8 HOH B 9 109 7 HOH HOH . I 8 HOH B 10 110 65 HOH HOH . I 8 HOH B 11 111 25 HOH HOH . I 8 HOH B 12 112 13 HOH HOH . I 8 HOH B 13 113 8 HOH HOH . I 8 HOH B 14 114 20 HOH HOH . I 8 HOH B 15 115 60 HOH HOH . I 8 HOH B 16 116 59 HOH HOH . I 8 HOH B 17 117 15 HOH HOH . I 8 HOH B 18 118 32 HOH HOH . I 8 HOH B 19 119 17 HOH HOH . I 8 HOH B 20 120 44 HOH HOH . I 8 HOH B 21 121 29 HOH HOH . I 8 HOH B 22 122 10 HOH HOH . I 8 HOH B 23 123 9 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 5 11.959 9.634 23.702 1 75.89 ? C1 NAG 301 A 1 HETATM 2 C C2 NAG . . . E 5 11.723 10.901 22.859 1 79.02 ? C2 NAG 301 A 1 HETATM 3 C C3 NAG . . . E 5 10.317 10.99 22.267 1 80.08 ? C3 NAG 301 A 1 HETATM 4 C C4 NAG . . . E 5 9.863 9.651 21.688 1 78.29 ? C4 NAG 301 A 1 HETATM 5 C C5 NAG . . . E 5 9.938 8.602 22.79 1 76.26 ? C5 NAG 301 A 1 HETATM 6 C C6 NAG . . . E 5 9.419 7.227 22.375 1 74.35 ? C6 NAG 301 A 1 HETATM 7 C C7 NAG . . . E 5 13.09 12.816 23.661 1 81.39 ? C7 NAG 301 A 1 HETATM 8 C C8 NAG . . . E 5 13.097 14.01 24.578 1 80.32 ? C8 NAG 301 A 1 HETATM 9 N N2 NAG . . . E 5 11.956 12.098 23.665 1 81.66 ? N2 NAG 301 A 1 HETATM 10 O O3 NAG . . . E 5 10.319 12.01 21.261 1 83.58 ? O3 NAG 301 A 1 HETATM 11 O O4 NAG . . . E 5 8.533 9.76 21.175 1 77.81 ? O4 NAG 301 A 1 HETATM 12 O O5 NAG . . . E 5 11.309 8.471 23.164 1 76.26 ? O5 NAG 301 A 1 HETATM 13 O O6 NAG . . . E 5 10.354 6.604 21.49 1 71.18 ? O6 NAG 301 A 1 HETATM 14 O O7 NAG . . . E 5 14.063 12.543 22.975 1 77.08 ? O7 NAG 301 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 294 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #