data_5LF5 # _model_server_result.job_id N57DmLZVfk2zDyznPEQuOw _model_server_result.datetime_utc '2025-07-03 19:02:02' _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 5lf5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":601}' # _entry.id 5LF5 # _exptl.entry_id 5LF5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 180.156 _entity.id 4 _entity.src_method man _entity.type non-polymer _entity.pdbx_description alpha-D-mannopyranose _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 120 _cell.entry_id 5LF5 _cell.length_a 278.868 _cell.length_b 278.868 _cell.length_c 62.52 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5LF5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 32 2 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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 5_676 x-y+1,-y+2,-z+4/3 1 0 0 0 -1 0 0 0 -1 0 483.013545 83.36 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 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 ? 2 2 1 FUC NAG C1 O1 . O6 HO6 . sing 2 ? 3 2 1 GAL NGA C1 O1 . O3 HO3 . sing 3 ? 3 3 2 SIA GAL C2 O2 . O3 HO3 . 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 B NAG 1 B 1 NAG A 1332 NAG 2 n B FUC 2 B 2 FUC A 2332 FUC 3 n C NGA 1 C 1 NGA B 2 NGA 3 n C GAL 2 C 2 GAL B 3 GAL 3 n C SIA 3 C 3 SIA B 4 SIA # 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 20 A CYS 37 1_555 A SG CYS 148 A CYS 165 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf2 A SG CYS 25 A CYS 42 1_555 A SG CYS 83 A CYS 100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf3 A SG CYS 142 A CYS 159 1_555 A SG CYS 200 A CYS 217 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf4 A SG CYS 244 A CYS 261 1_555 A SG CYS 288 A CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf5 A SG CYS 330 A CYS 347 1_555 A SG CYS 375 A CYS 392 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf6 A SG CYS 404 A CYS 421 1_555 A SG CYS 413 A CYS 430 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf7 A SG CYS 415 A CYS 432 1_555 A SG CYS 471 A CYS 488 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? covale ? covale1 A CD1 TRP 5 A TRP 22 1_555 D C1 MAN . A MAN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.478 ? covale ? covale2 A ND2 ASN 82 A ASN 99 1_555 E C1 NAG . A NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale3 A ND2 ASN 229 A ASN 246 1_555 F C1 NAG . A NAG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale4 A ND2 ASN 298 A ASN 315 1_555 G C1 NAG . A NAG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? covale ? covale5 A ND2 ASN 315 A ASN 332 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.554 ? covale ? covale6 A ND2 ASN 389 A ASN 406 1_555 H C1 NAG . A NAG 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale7 B O6 NAG . B NAG 1 1_555 B C1 FUC . B FUC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? covale ? covale8 C O3 NGA . C NGA 1 1_555 C C1 GAL . C GAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale9 C O3 GAL . C GAL 2 1_555 C C2 SIA . C SIA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.466 ? # _chem_comp.formula 'C6 H12 O6' _chem_comp.formula_weight 180.156 _chem_comp.id MAN _chem_comp.mon_nstd_flag . _chem_comp.name alpha-D-mannopyranose _chem_comp.type 'd-saccharide, alpha linking' _chem_comp.pdbx_synonyms alpha-D-mannose;D-mannose;mannose # 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 MAN sing 263 n n C1 O1 MAN sing 264 n n C1 O5 MAN sing 265 n n C1 H1 MAN sing 266 n n C2 C3 MAN sing 267 n n C2 O2 MAN sing 268 n n C2 H2 MAN sing 269 n n C3 C4 MAN sing 270 n n C3 O3 MAN sing 271 n n C3 H3 MAN sing 272 n n C4 C5 MAN sing 273 n n C4 O4 MAN sing 274 n n C4 H4 MAN sing 275 n n C5 C6 MAN sing 276 n n C5 O5 MAN sing 277 n n C5 H5 MAN sing 278 n n C6 O6 MAN sing 279 n n C6 H61 MAN sing 280 n n C6 H62 MAN sing 281 n n O1 HO1 MAN sing 282 n n O2 HO2 MAN sing 283 n n O3 HO3 MAN sing 284 n n O4 HO4 MAN sing 285 n n O6 HO6 MAN sing 286 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 MAN DManpa 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 MAN a-D-mannopyranose 'COMMON NAME' GMML 1 MAN a-D-Manp 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 MAN Man 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 5LF5 _atom_sites.fract_transf_matrix[1][1] 0.003586 _atom_sites.fract_transf_matrix[1][2] 0.00207 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.004141 _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] 0.015995 _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 4 MAN A 1 601 1022 MAN MAN . E 5 NAG A 1 602 1099 NAG NAG . F 5 NAG A 1 603 1246 NAG NAG . G 5 NAG A 1 604 1315 NAG NAG . H 5 NAG A 1 607 1406 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 MAN . . . D 4 86.844 133.64 6.441 1 121.08 ? C1 MAN 601 A 1 HETATM 2 C C2 MAN . . . D 4 87.373 133.411 5.023 1 149.38 ? C2 MAN 601 A 1 HETATM 3 C C3 MAN . . . D 4 87.969 134.709 4.463 1 157.82 ? C3 MAN 601 A 1 HETATM 4 C C4 MAN . . . D 4 88.89 135.433 5.481 1 212.31 ? C4 MAN 601 A 1 HETATM 5 C C5 MAN . . . D 4 88.271 135.487 6.905 1 109.18 ? C5 MAN 601 A 1 HETATM 6 C C6 MAN . . . D 4 87.098 136.462 7.046 1 147.19 ? C6 MAN 601 A 1 HETATM 7 O O2 MAN . . . D 4 86.324 133.042 4.128 1 189.43 ? O2 MAN 601 A 1 HETATM 8 O O3 MAN . . . D 4 86.968 135.599 3.984 1 167.96 ? O3 MAN 601 A 1 HETATM 9 O O4 MAN . . . D 4 90.152 134.783 5.532 1 205.8 ? O4 MAN 601 A 1 HETATM 10 O O5 MAN . . . D 4 87.808 134.18 7.292 1 81.91 ? O5 MAN 601 A 1 HETATM 11 O O6 MAN . . . D 4 87.318 137.575 6.183 1 170.83 ? O6 MAN 601 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 399 _model_server_stats.encode_time_ms 21 _model_server_stats.element_count 11 #