0.03195 0.00000 0.00000 0.00000 0.02404 0.00000 0.00000 0.00000 0.01297 0.00000 0.00000 0.00000 Saul, F.A. Rovira, P. Boulot, G. Van Damme, E.J.M. Peumans, W.J. Truffa-Bachi, P. Bentley, G.A. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90.00 90.00 90.00 31.300 41.600 77.100 C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H8 N2 O3 132.118 y ASPARAGINE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking C3 H7 N O2 S 121.158 y CYSTEINE L-peptide linking C5 H10 N2 O3 146.144 y GLUTAMINE L-peptide linking C5 H9 N O4 147.129 y GLUTAMIC ACID L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking C6 H10 N3 O2 1 156.162 y HISTIDINE L-peptide linking H2 O 18.015 WATER non-polymer C6 H13 N O2 131.173 y ISOLEUCINE L-peptide linking C6 H13 N O2 131.173 y LEUCINE L-peptide linking C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking C5 H7 N O3 129.114 n PYROGLUTAMIC ACID L-peptide linking C5 H9 N O2 115.130 y PROLINE L-peptide linking C3 H7 N O3 105.093 y SERINE L-peptide linking C4 H9 N O3 119.119 y THREONINE L-peptide linking C11 H12 N2 O2 204.225 y TRYPTOPHAN L-peptide linking C9 H11 N O3 181.189 y TYROSINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking UK Structure Fold.Des. FODEFH 1263 0969-2126 8 593 603 10.1016/S0969-2126(00)00142-8 10873861 Crystal structure of Urtica dioica agglutinin, a superantigen presented by MHC molecules of class I and class II. 2000 NE Plant Mol.Biol. PMBIDB 2006 0167-4412 39 335 347 10.1023/A:1006134932290 Characterisation of Urtica dioica Agglutinin Isolectins and the Encoding Gene Family 1999 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 298.0 1 IMAGE PLATE 1998-09-21 MARRESEARCH SINGLE WAVELENGTH M x-ray 1 1.375 1.0 D41A LURE 1.375 SYNCHROTRON LURE BEAMLINE D41A TWO ISOFORMS ARE PRESENT IN THE CRYSTAL: ISOLECTIN VI AND ISOLECTIN V 9350.269 PROTEIN (AGGLUTININ ISOLECTIN VI/AGGLUTININ ISOLECTIN V) 1 nat polymer 18.015 water 49 nat water UDA no yes (PCA)RCGSQGGGSTCPGLRCCSIWGWCGDSEPYCGRTCENKCWSGERSDHRCGAAVGNPPCGQDRCCSVHGWCGGGNDY CSGGNCQYRCSSS QRCGSQGGGSTCPGLRCCSIWGWCGDSEPYCGRTCENKCWSGERSDHRCGAAVGNPPCGQDRCCSVHGWCGGGNDYCSGG NCQYRCSSS A polypeptide(L) n n n n n n n n n y y n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n great nettle PURIFIED FROM THE RHIZOMES Urtica sample 3501 Urtica dioica 3 2.68 54.16 VAPOR DIFFUSION, SITTING DROP 6.0 PEG 6000, sodium acetate, sodium chloride , pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 290.0K 290.0 entity_poly pdbx_struct_mod_residue pdbx_unobs_or_zero_occ_atoms struct_conn struct_ref_seq_dif repository Initial release Version format compliance Version format compliance Advisory Database references Derived calculations Polymer sequence 1 0 2000-06-21 1 1 2008-04-27 1 2 2011-07-13 2 0 2019-12-25 _entity_poly.pdbx_seq_one_letter_code_can _pdbx_struct_mod_residue.parent_comp_id _struct_conn.pdbx_leaving_atom_flag UDA TETRASACCHARIDE COMPLEX UDA TRISACCHARIDE COMPLEX RCSB Y RCSB 2000-02-28 REL REL HOH water The structure comprises two hevein-like domains, each homologous to those of Wheat Germ Agglutinin (PDB code: 9wga). Each domain contains a saccharide-binding site. The N-terminal residue is pyrrolidone carboxylic acid (PCA). A dual conformation is seen at Gly79, Gly80. No electron density is seen for the side chain of Arg33 beyond the CB atom. No interpretable density is seen for C-terminal residues Ser87, Ser88, and Ser89. WAT 1 2 HOH HOH 90 A WAT 2 2 HOH HOH 91 A WAT 3 2 HOH HOH 92 A WAT 4 2 HOH HOH 93 A WAT 5 2 HOH HOH 94 A WAT 6 2 HOH HOH 95 A WAT 7 2 HOH HOH 96 A WAT 8 2 HOH HOH 97 A WAT 9 2 HOH HOH 98 A WAT 10 2 HOH HOH 99 A WAT 11 2 HOH HOH 100 A WAT 12 2 HOH HOH 101 A WAT 13 2 HOH HOH 102 A WAT 14 2 HOH HOH 103 A WAT 15 2 HOH HOH 104 A WAT 16 2 HOH HOH 105 A WAT 17 2 HOH HOH 106 A WAT 18 2 HOH HOH 107 A WAT 19 2 HOH HOH 108 A WAT 20 2 HOH HOH 109 A WAT 21 2 HOH HOH 110 A WAT 23 2 HOH HOH 111 A WAT 24 2 HOH HOH 112 A WAT 25 2 HOH HOH 113 A WAT 26 2 HOH HOH 114 A WAT 27 2 HOH HOH 115 A WAT 28 2 HOH HOH 116 A WAT 29 2 HOH HOH 117 A WAT 30 2 HOH HOH 118 A WAT 31 2 HOH HOH 119 A WAT 32 2 HOH HOH 120 A WAT 33 2 HOH HOH 121 A WAT 34 2 HOH HOH 122 A WAT 35 2 HOH HOH 123 A WAT 36 2 HOH HOH 124 A WAT 37 2 HOH HOH 125 A WAT 38 2 HOH HOH 126 A WAT 39 2 HOH HOH 127 A WAT 40 2 HOH HOH 128 A WAT 42 2 HOH HOH 129 A WAT 43 2 HOH HOH 130 A WAT 46 2 HOH HOH 131 A WAT 47 2 HOH HOH 132 A WAT 48 2 HOH HOH 133 A WAT 49 2 HOH HOH 134 A WAT 50 2 HOH HOH 135 A WAT 51 2 HOH HOH 136 A WAT 52 2 HOH HOH 137 A WAT 53 2 HOH HOH 138 A PCA 1 n 1 PCA 1 A ARG 2 n 2 ARG 2 A CYS 3 n 3 CYS 3 A GLY 4 n 4 GLY 4 A SER 5 n 5 SER 5 A GLN 6 n 6 GLN 6 A GLY 7 n 7 GLY 7 A GLY 8 n 8 GLY 8 A GLY 9 n 9 GLY 9 A SER 10 y 10 SER 10 A GLY 10 y 10 GLY 10 A THR 11 n 11 THR 11 A CYS 12 n 12 CYS 12 A PRO 13 n 13 PRO 13 A GLY 14 n 14 GLY 14 A LEU 15 n 15 LEU 15 A ARG 16 n 16 ARG 16 A CYS 17 n 17 CYS 17 A CYS 18 n 18 CYS 18 A SER 19 n 19 SER 19 A ILE 20 n 20 ILE 20 A TRP 21 n 21 TRP 21 A GLY 22 n 22 GLY 22 A TRP 23 n 23 TRP 23 A CYS 24 n 24 CYS 24 A GLY 25 n 25 GLY 25 A ASP 26 n 26 ASP 26 A SER 27 n 27 SER 27 A GLU 28 n 28 GLU 28 A PRO 29 n 29 PRO 29 A TYR 30 n 30 TYR 30 A CYS 31 n 31 CYS 31 A GLY 32 n 32 GLY 32 A ARG 33 n 33 ARG 33 A THR 34 n 34 THR 34 A CYS 35 n 35 CYS 35 A GLN 36 n 36 GLU 36 A ASN 37 n 37 ASN 37 A LYS 38 n 38 LYS 38 A CYS 39 n 39 CYS 39 A TRP 40 n 40 TRP 40 A SER 41 n 41 SER 41 A GLY 42 n 42 GLY 42 A GLU 43 n 43 GLU 43 A ARG 44 n 44 ARG 44 A SER 45 n 45 SER 45 A ASP 46 n 46 ASP 46 A HIS 47 n 47 HIS 47 A ARG 48 n 48 ARG 48 A CYS 49 n 49 CYS 49 A GLY 50 n 50 GLY 50 A ALA 51 n 51 ALA 51 A ALA 52 n 52 ALA 52 A VAL 53 n 53 VAL 53 A GLY 54 n 54 GLY 54 A ASN 55 n 55 ASN 55 A PRO 56 n 56 PRO 56 A PRO 57 n 57 PRO 57 A CYS 58 n 58 CYS 58 A GLY 59 n 59 GLY 59 A GLN 60 n 60 GLN 60 A ASP 61 n 61 ASP 61 A ARG 62 n 62 ARG 62 A CYS 63 n 63 CYS 63 A CYS 64 n 64 CYS 64 A SER 65 n 65 SER 65 A VAL 66 n 66 VAL 66 A HIS 67 n 67 HIS 67 A GLY 68 n 68 GLY 68 A TRP 69 n 69 TRP 69 A CYS 70 n 70 CYS 70 A GLY 71 n 71 GLY 71 A GLY 72 n 72 GLY 72 A GLY 73 n 73 GLY 73 A ASN 74 n 74 ASN 74 A ASP 75 n 75 ASP 75 A TYR 76 n 76 TYR 76 A CYS 77 n 77 CYS 77 A SER 78 n 78 SER 78 A GLY 79 n 79 GLY 79 A GLY 80 n 80 GLY 80 A ASN 81 n 81 ASN 81 A CYS 82 n 82 CYS 82 A GLN 83 n 83 GLN 83 A TYR 84 n 84 TYR 84 A ARG 85 n 85 ARG 85 A CYS 86 n 86 CYS 86 A n 87 87 A n 88 88 A n 89 89 A author_defined_assembly 1 monomeric A PCA 1 PYROGLUTAMIC ACID A PCA 1 GLN 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 A N GLY 25 A N GLY 25 A O CYS 17 A O CYS 17 A O CYS 18 A O CYS 18 A N GLU 36 A N GLU 36 A O GLY 71 A O GLY 71 A N CYS 63 A N CYS 63 A O CYS 64 A O CYS 64 A N GLN 83 A N GLN 83 1 A SER 87 A SER 87 1 Y 1 A SER 88 A SER 88 1 Y 1 A SER 89 A SER 89 1 Y 1 A A OG O SER HOH 10 97 1.97 A 1 3.65 0.50 120.30 123.95 A A A NE CZ NH2 ARG ARG ARG 33 33 33 N The structure was determined to 2.45A resolution by MIR methods based on 4 Hg derivatives (rotating-anode X-ray source) with solvent flattening, and refined to 1.66A resolution with synchrotron data using a bulk solvent correction and anisotropic scale factor. 0.249 0.191 0.207 0.207 1.66 18.0 602 11689 11689 95.4 RANDOM 1 0 0 MIR Engh & Huber 1.66 18.0 49 680 0 0 631 0.017 0.02 0.016 0.02 0.0220 0.03 0.0116 0.02 0.185 0.15 0.149 0.30 0.162 0.30 0.00 15.0 4.90 7.00 13.7 15.0 27.4 20.0 1.814 2.00 2.864 3.00 3.397 3.00 4.916 4.00 30.8 1.66 18.0 1EIS 11689 11689 0.0 0.0 0.056 1 24.7 12.5 95.4 0.352 1.66 1.72 1015 8.9 84.7 data reduction DENZO data scaling SCALEPACK phasing MLPHARE model building DM refinement REFMAC phasing DM AGGLUTININ ISOLECTIN VI/AGGLUTININ ISOLECTIN V UDA UNCOMPLEXED FORM. CRYSTAL STRUCTURE OF URTICA DIOICA AGGLUTININ, A SUPERANTIGEN PRESENTED BY MHC MOLECULES OF CLASS I AND CLASS II 1 N N 2 N N A CYS 12 A CYS 12 HELX_P A ARG 16 A ARG 16 5 1 5 A SER 27 A SER 27 HELX_P A GLY 32 A GLY 32 1 2 6 A CYS 39 A CYS 39 HELX_P A GLU 43 A GLU 43 5 3 5 A GLY 50 A GLY 50 HELX_P A GLY 54 A GLY 54 5 4 5 A GLY 73 A GLY 73 HELX_P A SER 78 A SER 78 1 5 6 disulf 2.012 A CYS 3 A SG CYS 3 1_555 A CYS 18 A SG CYS 18 1_555 disulf 2.029 A CYS 12 A SG CYS 12 1_555 A CYS 24 A SG CYS 24 1_555 disulf 2.030 A CYS 17 A SG CYS 17 1_555 A CYS 31 A SG CYS 31 1_555 disulf 2.010 A CYS 35 A SG CYS 35 1_555 A CYS 39 A SG CYS 39 1_555 disulf 2.038 A CYS 49 A SG CYS 49 1_555 A CYS 64 A SG CYS 64 1_555 disulf 2.017 A CYS 58 A SG CYS 58 1_555 A CYS 70 A SG CYS 70 1_555 disulf 2.041 A CYS 63 A SG CYS 63 1_555 A CYS 77 A SG CYS 77 1_555 disulf 2.026 A CYS 82 A SG CYS 82 1_555 A CYS 86 A SG CYS 86 1_555 covale 1.360 both A PCA 1 A C PCA 1 1_555 A ARG 2 A N ARG 2 1_555 SUGAR BINDING PROTEIN LECTIN, HEVEIN DOMAIN, UDA, SUPERANTIGEN, SUGAR BINDING PROTEIN Q9SYR5_URTDI UNP 1 24 Q9SYR5 QRCGSQGGGSTCPGLRCCSIWGWCGDSEPYCGRTCENKCWSGERSDHRCGAAVGNPPCGQDRCCSVHGWCGGGNDYCSGG NCQYRCSSS 24 112 1EIS 1 89 Q9SYR5 A 1 1 89 1 SER microheterogeneity GLY 10 1EIS A Q9SYR5 UNP 33 10 3 3 anti-parallel anti-parallel anti-parallel anti-parallel A CYS 24 A CYS 24 A GLY 25 A GLY 25 A CYS 17 A CYS 17 A SER 19 A SER 19 A CYS 35 A CYS 35 A ASN 37 A ASN 37 A CYS 70 A CYS 70 A GLY 71 A GLY 71 A CYS 63 A CYS 63 A SER 65 A SER 65 A CYS 82 A CYS 82 A TYR 84 A TYR 84 19 P 21 21 21