data_1YAE # _model_server_result.job_id OYtcDKaBbd1QukvFZQy2mA _model_server_result.datetime_utc '2024-11-15 14:30:35' _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 1yae # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":1303}' # _entry.id 1YAE # _exptl.entry_id 1YAE _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 311.33 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2S,3S,4S)-2-CARBOXY-4-[(1Z,3E,5R)-5-CARBOXY-1-METHYL-1,3-HEXADIENYL]-3-PYRROLIDINEACETIC ACID' _entity.pdbx_number_of_molecules 6 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 133.19 _cell.angle_gamma 90 _cell.entry_id 1YAE _cell.length_a 246.36 _cell.length_b 106.57 _cell.length_c 172.69 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1YAE _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 ? monomeric 1 author_defined_assembly 3 ? monomeric 1 author_defined_assembly 4 ? monomeric 1 author_defined_assembly 5 PISA monomeric 1 author_and_software_defined_assembly 6 PISA dimeric 2 software_defined_assembly 7 PISA dimeric 2 software_defined_assembly 8 PISA dimeric 2 software_defined_assembly 9 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,G,H,W 1 1 B,I,J,K,X 2 1 C,L,M,N,Y 3 1 D,O,P,Q,Z 4 1 E,R,S,T,AA 5 1 F,U,V,BA 6 1 B,D,I,J,K,O,P,Q,X,Z 7 1 A,G,H,W 8 1,2 C,L,M,N,Y 9 1 E,R,S,T,AA 9 3 # 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' 2_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 3 'crystal symmetry operation' 4_455 -x-1/2,y+1/2,-z -1 0 0 0 1 0 0 0 -1 -123.18 53.285 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 H N N ? 3 K N N ? 3 N N N ? 3 Q N N ? 3 T N N ? 3 V 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 FUC _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 O6 _pdbx_entity_branch_link.leaving_atom_id_2 HO6 _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 G NAG 1 G 1 NAG T 1 NAG 2 n G FUC 2 G 2 FUC T 2 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 237 A CYS 750 1_555 A SG CYS 291 A CYS 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf2 B SG CYS 237 B CYS 750 1_555 B SG CYS 291 B CYS 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? disulf ? disulf3 D SG CYS 237 D CYS 750 1_555 D SG CYS 291 D CYS 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? covale ? covale1 A ND2 ASN 5 A ASN 423 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale2 B ND2 ASN 5 B ASN 423 1_555 I C1 NAG . B NAG 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale3 B ND2 ASN 238 B ASN 751 1_555 J C1 NAG . B NAG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale4 C ND2 ASN 5 C ASN 423 1_555 L C1 NAG . C NAG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale5 C ND2 ASN 238 C ASN 751 1_555 M C1 NAG . C NAG 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale6 D ND2 ASN 5 D ASN 423 1_555 O C1 NAG . D NAG 1401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale7 D ND2 ASN 238 D ASN 751 1_555 P C1 NAG . D NAG 1402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale8 E ND2 ASN 5 E ASN 423 1_555 R C1 NAG . E NAG 1501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale9 E ND2 ASN 238 E ASN 751 1_555 S C1 NAG . E NAG 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale10 F ND2 ASN 5 F ASN 423 1_555 U C1 NAG . F NAG 1601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale11 F ND2 ASN 5 F ASN 423 1_555 U O5 NAG . F NAG 1601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.847 ? covale ? covale12 G O6 NAG . G NAG 1 1_555 G C1 FUC . G FUC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.466 ? # _chem_comp.formula 'C15 H21 N O6' _chem_comp.formula_weight 311.33 _chem_comp.id DOQ _chem_comp.mon_nstd_flag . _chem_comp.name '(2S,3S,4S)-2-CARBOXY-4-[(1Z,3E,5R)-5-CARBOXY-1-METHYL-1,3-HEXADIENYL]-3-PYRROLIDINEACETIC ACID' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '(2S,3S,4S)-3-CARBOXYMETHYL-4-[(1Z,3E,5R)-5-CARBOXY-1-METHYL-HEXA-1,3-DIENYL]-PYRROLIDINE-2-CARBOXYLIC ACID;DOMOIC ACID' # 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 OAD CAQ DOQ doub 83 n n CAQ OAG DOQ sing 84 n n CAQ CAS DOQ sing 85 n n OAG HAG DOQ sing 86 n n CAS CAB DOQ sing 87 n n CAS CAK DOQ sing 88 n n CAS HAS DOQ sing 89 n n CAB HAB1 DOQ sing 90 n n CAB HAB2 DOQ sing 91 n n CAB HAB3 DOQ sing 92 n n CAK CAI DOQ doub 93 e n CAK HAK DOQ sing 94 n n CAI CAJ DOQ sing 95 n n CAI HAI DOQ sing 96 n n CAJ CAP DOQ doub 97 z n CAJ HAJ DOQ sing 98 n n CAP CAA DOQ sing 99 n n CAP CAT DOQ sing 100 n n CAA HAA1 DOQ sing 101 n n CAA HAA2 DOQ sing 102 n n CAA HAA3 DOQ sing 103 n n CAT CAL DOQ sing 104 n n CAT CB DOQ sing 105 n n CAT HAT DOQ sing 106 n n CAL N DOQ sing 107 n n CAL HAL1 DOQ sing 108 n n CAL HAL2 DOQ sing 109 n n N CA DOQ sing 110 n n N HN DOQ sing 111 n n CA C DOQ sing 112 n n CA CB DOQ sing 113 n n CA HA DOQ sing 114 n n C OXT DOQ doub 115 n n C O DOQ sing 116 n n O HO DOQ sing 117 n n CB CG DOQ sing 118 n n CB HB DOQ sing 119 n n CG CD DOQ sing 120 n n CG HG1 DOQ sing 121 n n CG HG2 DOQ sing 122 n n CD OE2 DOQ sing 123 n n CD OE1 DOQ doub 124 n n OE2 HE2 DOQ sing 125 n n # _atom_sites.entry_id 1YAE _atom_sites.fract_transf_matrix[1][1] 0.004059 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00381 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009384 _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] 0.007942 _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 H 3 DOQ A 1 1103 1 DOQ DOM . I 4 NAG B 1 1201 1 NAG NAG . J 4 NAG B 1 1202 2 NAG NAG . K 3 DOQ B 1 1203 1 DOQ DOM . L 4 NAG C 1 1301 1 NAG NAG . M 4 NAG C 1 1302 2 NAG NAG . N 3 DOQ C 1 1303 1 DOQ DOM . O 4 NAG D 1 1401 1 NAG NAG . P 4 NAG D 1 1402 2 NAG NAG . Q 3 DOQ D 1 1403 1 DOQ DOM . R 4 NAG E 1 1501 1 NAG NAG . S 4 NAG E 1 1502 2 NAG NAG . T 3 DOQ E 1 1503 1 DOQ DOM . U 4 NAG F 1 1601 1 NAG NAG . V 3 DOQ F 1 1603 1 DOQ DOM . W 5 HOH A 1 1104 1 HOH HOH . W 5 HOH A 2 1105 17 HOH HOH . W 5 HOH A 3 1106 27 HOH HOH . W 5 HOH A 4 1107 28 HOH HOH . W 5 HOH A 5 1108 38 HOH HOH . W 5 HOH A 6 1109 39 HOH HOH . W 5 HOH A 7 1110 44 HOH HOH . W 5 HOH A 8 1111 45 HOH HOH . W 5 HOH A 9 1112 58 HOH HOH . W 5 HOH A 10 1113 61 HOH HOH . W 5 HOH A 11 1114 66 HOH HOH . W 5 HOH A 12 1115 77 HOH HOH . W 5 HOH A 13 1116 78 HOH HOH . X 5 HOH B 1 2 2 HOH HOH . X 5 HOH B 2 6 6 HOH HOH . X 5 HOH B 3 8 8 HOH HOH . X 5 HOH B 4 10 10 HOH HOH . X 5 HOH B 5 11 11 HOH HOH . X 5 HOH B 6 16 16 HOH HOH . X 5 HOH B 7 20 20 HOH HOH . X 5 HOH B 8 21 21 HOH HOH . X 5 HOH B 9 22 22 HOH HOH . X 5 HOH B 10 25 25 HOH HOH . X 5 HOH B 11 30 30 HOH HOH . X 5 HOH B 12 48 48 HOH HOH . X 5 HOH B 13 54 54 HOH HOH . X 5 HOH B 14 56 56 HOH HOH . X 5 HOH B 15 62 62 HOH HOH . X 5 HOH B 16 64 64 HOH HOH . X 5 HOH B 17 67 67 HOH HOH . X 5 HOH B 18 68 68 HOH HOH . X 5 HOH B 19 75 75 HOH HOH . Y 5 HOH C 1 12 12 HOH HOH . Y 5 HOH C 2 18 18 HOH HOH . Y 5 HOH C 3 19 19 HOH HOH . Y 5 HOH C 4 23 23 HOH HOH . Y 5 HOH C 5 29 29 HOH HOH . Y 5 HOH C 6 31 31 HOH HOH . Y 5 HOH C 7 35 35 HOH HOH . Y 5 HOH C 8 41 41 HOH HOH . Y 5 HOH C 9 43 43 HOH HOH . Y 5 HOH C 10 53 53 HOH HOH . Y 5 HOH C 11 63 63 HOH HOH . Y 5 HOH C 12 69 69 HOH HOH . Y 5 HOH C 13 70 70 HOH HOH . Y 5 HOH C 14 71 71 HOH HOH . Z 5 HOH D 1 7 7 HOH HOH . Z 5 HOH D 2 13 13 HOH HOH . Z 5 HOH D 3 14 14 HOH HOH . Z 5 HOH D 4 24 24 HOH HOH . Z 5 HOH D 5 34 34 HOH HOH . Z 5 HOH D 6 36 36 HOH HOH . Z 5 HOH D 7 37 37 HOH HOH . Z 5 HOH D 8 40 40 HOH HOH . Z 5 HOH D 9 49 49 HOH HOH . Z 5 HOH D 10 51 51 HOH HOH . Z 5 HOH D 11 52 52 HOH HOH . Z 5 HOH D 12 57 57 HOH HOH . Z 5 HOH D 13 60 60 HOH HOH . Z 5 HOH D 14 72 72 HOH HOH . Z 5 HOH D 15 73 73 HOH HOH . Z 5 HOH D 16 76 76 HOH HOH . AA 5 HOH E 1 3 3 HOH HOH . AA 5 HOH E 2 5 5 HOH HOH . AA 5 HOH E 3 26 26 HOH HOH . AA 5 HOH E 4 46 46 HOH HOH . AA 5 HOH E 5 47 47 HOH HOH . AA 5 HOH E 6 50 50 HOH HOH . AA 5 HOH E 7 59 59 HOH HOH . AA 5 HOH E 8 65 65 HOH HOH . AA 5 HOH E 9 74 74 HOH HOH . BA 5 HOH F 1 4 4 HOH HOH . BA 5 HOH F 2 9 9 HOH HOH . BA 5 HOH F 3 15 15 HOH HOH . BA 5 HOH F 4 32 32 HOH HOH . BA 5 HOH F 5 33 33 HOH HOH . BA 5 HOH F 6 42 42 HOH HOH . BA 5 HOH F 7 55 55 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 O OAD DOQ . . . N 3 -42.606 -0.877 -4.442 1 49.12 ? OAD DOQ 1303 C 1 HETATM 2 C CAQ DOQ . . . N 3 -42.313 -2.047 -4.173 1 48.13 ? CAQ DOQ 1303 C 1 HETATM 3 O OAG DOQ . . . N 3 -41.121 -2.37 -4.16 1 49.06 ? OAG DOQ 1303 C 1 HETATM 4 C CAS DOQ . . . N 3 -43.417 -3.086 -3.861 1 45.76 ? CAS DOQ 1303 C 1 HETATM 5 C CAB DOQ . . . N 3 -43.521 -3.234 -2.341 1 45.58 ? CAB DOQ 1303 C 1 HETATM 6 C CAK DOQ . . . N 3 -43.076 -4.434 -4.522 1 44.54 ? CAK DOQ 1303 C 1 HETATM 7 C CAI DOQ . . . N 3 -43.287 -4.648 -5.881 1 44.04 ? CAI DOQ 1303 C 1 HETATM 8 C CAJ DOQ . . . N 3 -42.955 -5.877 -6.462 1 44.6 ? CAJ DOQ 1303 C 1 HETATM 9 C CAP DOQ . . . N 3 -43.122 -6.196 -7.819 1 44.53 ? CAP DOQ 1303 C 1 HETATM 10 C CAA DOQ . . . N 3 -42.703 -7.594 -8.304 1 44.3 ? CAA DOQ 1303 C 1 HETATM 11 C CAT DOQ . . . N 3 -43.716 -5.135 -8.792 1 43.68 ? CAT DOQ 1303 C 1 HETATM 12 C CAL DOQ . . . N 3 -43.156 -5.184 -10.223 1 42.93 ? CAL DOQ 1303 C 1 HETATM 13 N N DOQ . . . N 3 -44.269 -4.723 -11.073 1 42.83 ? N DOQ 1303 C 1 HETATM 14 C CA DOQ . . . N 3 -45.363 -4.308 -10.175 1 42.76 ? CA DOQ 1303 C 1 HETATM 15 C C DOQ . . . N 3 -45.132 -2.871 -9.709 1 42.66 ? C DOQ 1303 C 1 HETATM 16 O OXT DOQ . . . N 3 -44.611 -2.061 -10.481 1 42.71 ? OXT DOQ 1303 C 1 HETATM 17 O O DOQ . . . N 3 -45.47 -2.528 -8.574 1 42.18 ? O DOQ 1303 C 1 HETATM 18 C CB DOQ . . . N 3 -45.238 -5.237 -9 1 42.75 ? CB DOQ 1303 C 1 HETATM 19 C CG DOQ . . . N 3 -45.753 -6.613 -9.399 1 43.13 ? CG DOQ 1303 C 1 HETATM 20 C CD DOQ . . . N 3 -47.193 -6.874 -8.949 1 44.36 ? CD DOQ 1303 C 1 HETATM 21 O OE2 DOQ . . . N 3 -47.691 -6.272 -7.987 1 43.63 ? OE2 DOQ 1303 C 1 HETATM 22 O OE1 DOQ . . . N 3 -47.859 -7.724 -9.552 1 45.83 ? OE1 DOQ 1303 C 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 36 _model_server_stats.query_time_ms 299 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 22 #