data_6YFY # _model_server_result.job_id kymeJEDrTzoKaTfs0VR--g _model_server_result.datetime_utc '2025-03-06 09:27:22' _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 6yfy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"BA","auth_seq_id":103}' # _entry.id 6YFY # _exptl.entry_id 6YFY _exptl.method 'SOLID-STATE NMR' # _entity.details ? _entity.formula_weight 79.98 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description PHOSPHONATE _entity.pdbx_number_of_molecules 8 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details octameric _pdbx_struct_assembly.oligomeric_count 8 _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,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA _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 ? _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 ? 4 M N N ? 4 N N N ? 4 T N N ? 4 U N N ? 4 W N N ? 4 X N N ? 4 BA N N ? 4 CA N N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 3 _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 MUB _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 3 n I MUB 1 I 1 MUB C 6 NAM 3 n I NAG 2 I 2 NAG C 7 NAG 3 n J MUB 1 J 1 MUB D 6 NAM 3 n J NAG 2 J 2 NAG D 7 NAG 3 n K MUB 1 K 1 MUB G 6 NAM 3 n K NAG 2 K 2 NAG G 7 NAG 3 n L MUB 1 L 1 MUB H 6 NAM 3 n L NAG 2 L 2 NAG H 7 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 covale ? covale1 A C ZAE 1 A ZAE 1 1_555 A N ILE 2 A ILE 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale2 A C SER 3 A SER 3 1_555 A N DAR 4 A DAR 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.343 ? covale ? covale3 A C DAR 4 A DAR 4 1_555 A N 28J 5 A 28J 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.32 ? covale ? covale4 A C 28J 5 A 28J 5 1_555 A N ILE 6 A ILE 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.344 ? covale ? covale5 A C SER 7 A SER 7 1_555 A N DTH 8 A DTH 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.352 ? covale ? covale6 A C DTH 8 A DTH 8 1_555 A N ALA 9 A ALA 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale7 A OG1 DTH 8 A DTH 8 1_555 A C ILE 11 A ILE 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale8 M O3P 2PO . A 2PO 101 1_555 N P 2PO . A 2PO 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.601 ? covale ? covale9 M P 2PO . A 2PO 101 1_555 I O1 MUB . I MUB 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.636 ? covale ? covale10 N O3P 2PO . A 2PO 102 1_555 O C1 P1W . A P1W 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.425 ? covale ? covale11 O C4 P1W . A P1W 103 1_555 P C1 P1W . A P1W 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.526 ? covale ? covale12 P C4 P1W . A P1W 104 1_555 Q C1 P1W . A P1W 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.534 ? covale ? covale13 R C4 P1W . A P1W 106 1_555 S C1 P1W . A P1W 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.537 ? covale ? covale14 R C1 P1W . A P1W 106 1_555 V C4 P1W . B P1W 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.54 ? covale ? covale15 B C ZAE 1 B ZAE 1 1_555 B N ILE 2 B ILE 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.317 ? covale ? covale16 B C SER 3 B SER 3 1_555 B N DAR 4 B DAR 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale17 B C DAR 4 B DAR 4 1_555 B N 28J 5 B 28J 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale18 B C 28J 5 B 28J 5 1_555 B N ILE 6 B ILE 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.361 ? covale ? covale19 B C SER 7 B SER 7 1_555 B N DTH 8 B DTH 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.361 ? covale ? covale20 B C DTH 8 B DTH 8 1_555 B N ALA 9 B ALA 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.354 ? covale ? covale21 B OG1 DTH 8 B DTH 8 1_555 B C ILE 11 B ILE 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale22 T O3P 2PO . B 2PO 101 1_555 U P 2PO . B 2PO 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.594 ? covale ? covale23 T P 2PO . B 2PO 101 1_555 J O1 MUB . J MUB 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.63 ? covale ? covale24 U O3P 2PO . B 2PO 102 1_555 V C1 P1W . B P1W 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale25 C C ZAE 1 E ZAE 1 1_555 C N ILE 2 E ILE 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.307 ? covale ? covale26 C C SER 3 E SER 3 1_555 C N DAR 4 E DAR 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.309 ? covale ? covale27 C C DAR 4 E DAR 4 1_555 C N 28J 5 E 28J 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale28 C C 28J 5 E 28J 5 1_555 C N ILE 6 E ILE 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.34 ? covale ? covale29 C C SER 7 E SER 7 1_555 C N DTH 8 E DTH 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale30 C C DTH 8 E DTH 8 1_555 C N ALA 9 E ALA 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.344 ? covale ? covale31 C OG1 DTH 8 E DTH 8 1_555 C C ILE 11 E ILE 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.425 ? covale ? covale32 W O3P 2PO . E 2PO 101 1_555 X P 2PO . E 2PO 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.594 ? covale ? covale33 W P 2PO . E 2PO 101 1_555 K O1 MUB . K MUB 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.623 ? covale ? covale34 X O3P 2PO . E 2PO 102 1_555 Y C1 P1W . E P1W 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.42 ? covale ? covale35 Y C4 P1W . E P1W 103 1_555 Z C1 P1W . F P1W 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.542 ? covale ? covale36 D C ZAE 1 F ZAE 1 1_555 D N ILE 2 F ILE 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale37 D C SER 3 F SER 3 1_555 D N DAR 4 F DAR 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale38 D C DAR 4 F DAR 4 1_555 D N 28J 5 F 28J 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale39 D C 28J 5 F 28J 5 1_555 D N ILE 6 F ILE 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale40 D C SER 7 F SER 7 1_555 D N DTH 8 F DTH 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale41 D C DTH 8 F DTH 8 1_555 D N ALA 9 F ALA 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale42 D OG1 DTH 8 F DTH 8 1_555 D C ILE 11 F ILE 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale43 Z C4 P1W . F P1W 101 1_555 AA C1 P1W . F P1W 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.533 ? covale ? covale44 BA O3P 2PO . F 2PO 103 1_555 CA P 2PO . F 2PO 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.609 ? covale ? covale45 BA P 2PO . F 2PO 103 1_555 L O1 MUB . L MUB 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.629 ? covale ? covale46 CA O3P 2PO . F 2PO 104 1_555 DA C1 P1W . F P1W 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.428 ? covale ? covale47 DA C4 P1W . F P1W 105 1_555 EA C1 P1W . F P1W 106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.533 ? covale ? covale48 EA C4 P1W . F P1W 106 1_555 FA C1 P1W . F P1W 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.532 ? covale ? covale49 E C ALA 1 C ALA 1 1_555 E N DGL 2 C DGL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.399 ? covale ? covale50 E N ALA 1 C ALA 1 1_555 I C10 MUB . I MUB 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.371 ? covale ? covale51 E CD DGL 2 C DGL 2 1_555 E N LYS 3 C LYS 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.308 ? covale ? covale52 E C LYS 3 C LYS 3 1_555 E N DAL 4 C DAL 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.399 ? covale ? covale53 E C DAL 4 C DAL 4 1_555 E N DAL 5 C DAL 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.383 ? covale ? covale54 F C ALA 1 D ALA 1 1_555 F N DGL 2 D DGL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.36 ? covale ? covale55 F N ALA 1 D ALA 1 1_555 J C10 MUB . J MUB 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.362 ? covale ? covale56 F CD DGL 2 D DGL 2 1_555 F N LYS 3 D LYS 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.313 ? covale ? covale57 F C LYS 3 D LYS 3 1_555 F N DAL 4 D DAL 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.398 ? covale ? covale58 F C DAL 4 D DAL 4 1_555 F N DAL 5 D DAL 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.382 ? covale ? covale59 G C ALA 1 G ALA 1 1_555 G N DGL 2 G DGL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.357 ? covale ? covale60 G N ALA 1 G ALA 1 1_555 K C10 MUB . K MUB 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.364 ? covale ? covale61 G CD DGL 2 G DGL 2 1_555 G N LYS 3 G LYS 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.306 ? covale ? covale62 G C LYS 3 G LYS 3 1_555 G N DAL 4 G DAL 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.398 ? covale ? covale63 G C DAL 4 G DAL 4 1_555 G N DAL 5 G DAL 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.383 ? covale ? covale64 H C ALA 1 H ALA 1 1_555 H N DGL 2 H DGL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.355 ? covale ? covale65 H N ALA 1 H ALA 1 1_555 L C10 MUB . L MUB 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.366 ? covale ? covale66 H CD DGL 2 H DGL 2 1_555 H N LYS 3 H LYS 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.312 ? covale ? covale67 H C LYS 3 H LYS 3 1_555 H N DAL 4 H DAL 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.397 ? covale ? covale68 H C DAL 4 H DAL 4 1_555 H N DAL 5 H DAL 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.382 ? covale ? covale69 I O4 MUB . I MUB 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale70 J O4 MUB . J MUB 1 1_555 J C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale71 K O4 MUB . K MUB 1 1_555 K C1 NAG . K NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale72 L O4 MUB . L MUB 1 1_555 L C1 NAG . L NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? # _chem_comp.formula 'H O3 P -2' _chem_comp.formula_weight 79.98 _chem_comp.id 2PO _chem_comp.mon_nstd_flag . _chem_comp.name PHOSPHONATE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 P O1P 2PO sing 22 n n P O2P 2PO sing 23 n n P O3P 2PO doub 24 n n P HP 2PO sing 25 n n # _atom_sites.entry_id 6YFY _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 M 4 2PO A 1 101 8 2PO PHO . N 4 2PO A 1 102 9 2PO PHO . O 5 P1W A 1 103 10 P1W TPL . P 5 P1W A 1 104 11 P1W TPL . Q 5 P1W A 1 105 12 P1W TPL . R 5 P1W A 1 106 11 P1W TPL . S 5 P1W A 1 107 12 P1W TPL . T 4 2PO B 1 101 8 2PO PHO . U 4 2PO B 1 102 9 2PO PHO . V 5 P1W B 1 103 10 P1W TPL . W 4 2PO E 1 101 8 2PO PHO . X 4 2PO E 1 102 9 2PO PHO . Y 5 P1W E 1 103 10 P1W TPL . Z 5 P1W F 1 101 11 P1W TPL . AA 5 P1W F 1 102 12 P1W TPL . BA 4 2PO F 1 103 8 2PO PHO . CA 4 2PO F 1 104 9 2PO PHO . DA 5 P1W F 1 105 10 P1W TPL . EA 5 P1W F 1 106 11 P1W TPL . FA 5 P1W F 1 107 12 P1W TPL . # 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 P P 2PO . . . BA 4 9.31 5.868 3.819 1 0.92 ? P 2PO 103 F 1 HETATM 2 O O1P 2PO . . . BA 4 10.238 4.837 4.303 1 1.05 -1 O1P 2PO 103 F 1 HETATM 3 O O2P 2PO . . . BA 4 8.058 6.13 4.612 1 1.19 ? O2P 2PO 103 F 1 HETATM 4 O O3P 2PO . . . BA 4 8.826 5.438 2.335 1 1.06 ? O3P 2PO 103 F 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 43 _model_server_stats.query_time_ms 8995 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 4 #