data_5MF1 # _model_server_result.job_id etGrhto8aQu2xVGWAUqqqw _model_server_result.datetime_utc '2024-10-20 00:27:49' _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 5mf1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":1002}' # _entry.id 5MF1 # _exptl.entry_id 5MF1 _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-galactopyranose _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 5MF1 _cell.length_a 103.97 _cell.length_b 114.06 _cell.length_c 137.42 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5MF1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 E N N ? 3 G N N ? 3 I N N # 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 13 A CYS 33 1_555 A SG CYS 24 A CYS 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf2 A SG CYS 116 A CYS 136 1_555 A SG CYS 144 A CYS 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf3 A SG CYS 127 A CYS 147 1_555 A SG CYS 190 A CYS 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf4 A SG CYS 145 A CYS 165 1_555 A SG CYS 363 A CYS 383 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf5 A SG CYS 147 A CYS 167 1_555 A SG CYS 170 A CYS 190 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf6 A SG CYS 346 A CYS 366 1_555 A SG CYS 370 A CYS 390 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf7 A SG CYS 455 A CYS 475 1_555 A SG CYS 462 A CYS 482 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf8 A SG CYS 495 A CYS 515 1_555 A SG CYS 536 A CYS 556 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf9 B SG CYS 13 B CYS 33 1_555 B SG CYS 24 B CYS 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf10 B SG CYS 116 B CYS 136 1_555 B SG CYS 144 B CYS 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf11 B SG CYS 127 B CYS 147 1_555 B SG CYS 190 B CYS 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf12 B SG CYS 145 B CYS 165 1_555 B SG CYS 363 B CYS 383 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf13 B SG CYS 147 B CYS 167 1_555 B SG CYS 170 B CYS 190 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf14 B SG CYS 346 B CYS 366 1_555 B SG CYS 370 B CYS 390 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf15 B SG CYS 455 B CYS 475 1_555 B SG CYS 462 B CYS 482 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf16 B SG CYS 495 B CYS 515 1_555 B SG CYS 536 B CYS 556 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf17 C SG CYS 13 C CYS 33 1_555 C SG CYS 24 C CYS 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf18 C SG CYS 116 C CYS 136 1_555 C SG CYS 144 C CYS 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf19 C SG CYS 127 C CYS 147 1_555 C SG CYS 190 C CYS 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf20 C SG CYS 145 C CYS 165 1_555 C SG CYS 363 C CYS 383 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf21 C SG CYS 147 C CYS 167 1_555 C SG CYS 170 C CYS 190 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf22 C SG CYS 346 C CYS 366 1_555 C SG CYS 370 C CYS 390 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf23 C SG CYS 455 C CYS 475 1_555 C SG CYS 462 C CYS 482 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf24 C SG CYS 495 C CYS 515 1_555 C SG CYS 536 C CYS 556 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? covale ? covale1 A ND2 ASN 477 A ASN 497 1_555 D C1 NAG . A NAG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale2 A OG1 THR 557 A THR 577 1_555 E C1 NGA . A NGA 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale3 B ND2 ASN 477 B ASN 497 1_555 F C1 NAG . B NAG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale4 B OG1 THR 557 B THR 577 1_555 G C1 NGA . B NGA 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale5 C ND2 ASN 477 C ASN 497 1_555 H C1 NAG . C NAG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale6 C OG1 THR 557 C THR 577 1_555 I C1 NGA . C NGA 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.46 ? # _chem_comp.formula 'C8 H15 N O6' _chem_comp.formula_weight 221.208 _chem_comp.id NGA _chem_comp.mon_nstd_flag . _chem_comp.name 2-acetamido-2-deoxy-beta-D-galactopyranose _chem_comp.type 'd-saccharide, beta linking' _chem_comp.pdbx_synonyms ? # 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 NGA DGalpNAcb 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 NGA N-acetyl-b-D-galactopyranosamine 'COMMON NAME' GMML 1 NGA b-D-GalpNAc 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 NGA GalNAc 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 5MF1 _atom_sites.fract_transf_matrix[1][1] 0.009618 _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] 0.008767 _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] 0.007277 _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 2 NAG A 1 1001 1001 NAG NAG . E 3 NGA A 1 1002 1101 NGA NGA . F 2 NAG B 1 1001 1001 NAG NAG . G 3 NGA B 1 1002 1101 NGA NGA . H 2 NAG C 1 1001 1001 NAG NAG . I 3 NGA C 1 1002 1101 NGA NGA . # 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 NGA . . . I 3 -70.168 -79.119 17.277 1 99.18 ? C1 NGA 1002 C 1 HETATM 2 C C2 NGA . . . I 3 -71.642 -79.443 17.521 1 100.61 ? C2 NGA 1002 C 1 HETATM 3 C C3 NGA . . . I 3 -71.899 -79.125 18.998 1 100.37 ? C3 NGA 1002 C 1 HETATM 4 C C4 NGA . . . I 3 -71.027 -79.987 19.915 1 100.18 ? C4 NGA 1002 C 1 HETATM 5 C C5 NGA . . . I 3 -69.57 -80.069 19.442 1 100.28 ? C5 NGA 1002 C 1 HETATM 6 C C6 NGA . . . I 3 -68.768 -81.24 20.009 1 96.28 ? C6 NGA 1002 C 1 HETATM 7 C C7 NGA . . . I 3 -73.455 -79.21 15.857 1 99.84 ? C7 NGA 1002 C 1 HETATM 8 C C8 NGA . . . I 3 -74.288 -78.24 15.073 1 98.98 ? C8 NGA 1002 C 1 HETATM 9 N N2 NGA . . . I 3 -72.519 -78.665 16.658 1 101.36 ? N2 NGA 1002 C 1 HETATM 10 O O3 NGA . . . I 3 -73.272 -79.341 19.312 1 100.41 ? O3 NGA 1002 C 1 HETATM 11 O O4 NGA . . . I 3 -71.623 -81.262 20.128 1 100.72 ? O4 NGA 1002 C 1 HETATM 12 O O5 NGA . . . I 3 -69.482 -80.159 17.998 1 102.49 ? O5 NGA 1002 C 1 HETATM 13 O O6 NGA . . . I 3 -68.846 -81.376 21.424 1 92.48 ? O6 NGA 1002 C 1 HETATM 14 O O7 NGA . . . I 3 -73.621 -80.426 15.772 1 98.43 ? O7 NGA 1002 C 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 314 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 14 #