0.017564 0.000000 0.000000 0.000000 0.010757 0.000000 0.000000 0.000000 0.019794 0.000000 0.000000 0.000000 Su, J. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.000 90.000 90.000 56.934 92.964 50.521 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 C6 H12 O6 180.156 beta-D-glucopyranose D-saccharide, beta linking C3 H7 N O2 S 121.158 y CYSTEINE L-peptide linking C6 H12 O6 180.156 beta-D-galactopyranose D-saccharide, beta 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 H11 N O2 S 149.211 y METHIONINE L-peptide linking C9 H11 N O2 165.189 y PHENYLALANINE 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 US Biosci. Rep. 1573-4935 38 10.1042/BSR20181787 30413611 Resetting the ligand binding site of placental protein 13/galectin-13 recovers its ability to bind lactose 2018 0000-0001-8406-1676 100 1 PIXEL 2017-12-23 DECTRIS PILATUS 6M SINGLE WAVELENGTH M x-ray 1 0.977 1.0 BL18U1 SSRF 0.977 SYNCHROTRON SSRF BEAMLINE BL18U1 16004.324 Galactoside-binding soluble lectin 13 UNP residues 2-139 R53H, H57R 1 man polymer 342.297 beta-D-galactopyranose-(1-4)-beta-D-glucopyranose 1 man branched 18.015 water 98 nat water Galectin-13,Gal-13,Placental tissue protein 13,Placental protein 13 beta-lactose no no SSLPVPYKLPVSLSVGSCVIIKGTPIHSFINDPQLQVDFYTDMDEDSDIAFHFRVRFGNHVVMNRREFGIWMLEETTDYV PFEDGKQFELCIYVHYNEYEIKVNGIRIYGFVHRIPPSFVKMVQVSRDISLTSVCVCN SSLPVPYKLPVSLSVGSCVIIKGTPIHSFINDPQLQVDFYTDMDEDSDIAFHFRVRFGNHVVMNRREFGIWMLEETTDYV PFEDGKQFELCIYVHYNEYEIKVNGIRIYGFVHRIPPSFVKMVQVSRDISLTSVCVCN A polypeptide(L) 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 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 Human sample 1 138 LGALS13, PLAC8 9606 Homo sapiens 562 Escherichia coli Biological sequence 1 2.09 41.11 VAPOR DIFFUSION, HANGING DROP PEG 298 atom_site chem_comp entity entity_name_com pdbx_branch_scheme pdbx_chem_comp_identifier pdbx_entity_branch pdbx_entity_branch_descriptor pdbx_entity_branch_link pdbx_entity_branch_list pdbx_entity_nonpoly pdbx_molecule_features pdbx_nonpoly_scheme struct_conn struct_conn_type struct_site struct_site_gen repository Initial release Carbohydrate remediation repository Remediation Atomic model Data collection Derived calculations Non-polymer description Structure summary 1 0 2018-12-26 2 0 2020-07-29 _atom_site.B_iso_or_equiv _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.auth_asym_id _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.label_atom_id _atom_site.label_comp_id _chem_comp.formula _chem_comp.formula_weight _chem_comp.id _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.type _entity.formula_weight _entity.pdbx_description _entity.type China National Natural Science Foundation of China 31500637 A B4H 201 n B BGC 1 A B4H 201 n B GAL 2 DGlcpb b-D-glucopyranose b-D-Glcp Glc DGalpb b-D-galactopyranose b-D-Galp Gal N PDBJ Y PDBJ 2018-06-26 REL REL oligosaccharide DGalpb1-4DGlcpb1-ROH 2 GMML 1.0 Glycam Condensed Sequence WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2112h-1b_1-5]/1-2/a4-b1 2 PDB2Glycan 1.1.0 WURCS [][b-D-Glcp]{[(4+1)][b-D-Galp]{}} 2 PDB-CARE LINUCS C1 O4 GAL BGC 2 1 2 O1 HO4 sing n n HOH water Nutrient oligosaccharide beta-lactose Oligosaccharide HOH 48 3 HOH HOH 301 A HOH 61 3 HOH HOH 302 A HOH 86 3 HOH HOH 303 A HOH 62 3 HOH HOH 304 A HOH 87 3 HOH HOH 305 A HOH 64 3 HOH HOH 306 A HOH 33 3 HOH HOH 307 A HOH 79 3 HOH HOH 308 A HOH 72 3 HOH HOH 309 A HOH 22 3 HOH HOH 310 A HOH 19 3 HOH HOH 311 A HOH 89 3 HOH HOH 312 A HOH 31 3 HOH HOH 313 A HOH 24 3 HOH HOH 314 A HOH 96 3 HOH HOH 315 A HOH 63 3 HOH HOH 316 A HOH 3 3 HOH HOH 317 A HOH 84 3 HOH HOH 318 A HOH 75 3 HOH HOH 319 A HOH 2 3 HOH HOH 320 A HOH 8 3 HOH HOH 321 A HOH 38 3 HOH HOH 322 A HOH 83 3 HOH HOH 323 A HOH 35 3 HOH HOH 324 A HOH 44 3 HOH HOH 325 A HOH 41 3 HOH HOH 326 A HOH 73 3 HOH HOH 327 A HOH 13 3 HOH HOH 328 A HOH 54 3 HOH HOH 329 A HOH 7 3 HOH HOH 330 A HOH 15 3 HOH HOH 331 A HOH 58 3 HOH HOH 332 A HOH 60 3 HOH HOH 333 A HOH 1 3 HOH HOH 334 A HOH 34 3 HOH HOH 335 A HOH 21 3 HOH HOH 336 A HOH 91 3 HOH HOH 337 A HOH 46 3 HOH HOH 338 A HOH 23 3 HOH HOH 339 A HOH 68 3 HOH HOH 340 A HOH 45 3 HOH HOH 341 A HOH 11 3 HOH HOH 342 A HOH 80 3 HOH HOH 343 A HOH 4 3 HOH HOH 344 A HOH 53 3 HOH HOH 345 A HOH 90 3 HOH HOH 346 A HOH 28 3 HOH HOH 347 A HOH 20 3 HOH HOH 348 A HOH 78 3 HOH HOH 349 A HOH 65 3 HOH HOH 350 A HOH 50 3 HOH HOH 351 A HOH 36 3 HOH HOH 352 A HOH 5 3 HOH HOH 353 A HOH 74 3 HOH HOH 354 A HOH 70 3 HOH HOH 355 A HOH 40 3 HOH HOH 356 A HOH 39 3 HOH HOH 357 A HOH 17 3 HOH HOH 358 A HOH 32 3 HOH HOH 359 A HOH 26 3 HOH HOH 360 A HOH 69 3 HOH HOH 361 A HOH 42 3 HOH HOH 362 A HOH 37 3 HOH HOH 363 A HOH 9 3 HOH HOH 364 A HOH 43 3 HOH HOH 365 A HOH 18 3 HOH HOH 366 A HOH 97 3 HOH HOH 367 A HOH 57 3 HOH HOH 368 A HOH 16 3 HOH HOH 369 A HOH 77 3 HOH HOH 370 A HOH 51 3 HOH HOH 371 A HOH 6 3 HOH HOH 372 A HOH 12 3 HOH HOH 373 A HOH 55 3 HOH HOH 374 A HOH 30 3 HOH HOH 375 A HOH 10 3 HOH HOH 376 A HOH 93 3 HOH HOH 377 A HOH 25 3 HOH HOH 378 A HOH 56 3 HOH HOH 379 A HOH 29 3 HOH HOH 380 A HOH 81 3 HOH HOH 381 A HOH 14 3 HOH HOH 382 A HOH 82 3 HOH HOH 383 A HOH 27 3 HOH HOH 384 A HOH 67 3 HOH HOH 385 A HOH 94 3 HOH HOH 386 A HOH 88 3 HOH HOH 387 A HOH 76 3 HOH HOH 388 A HOH 49 3 HOH HOH 389 A HOH 66 3 HOH HOH 390 A HOH 95 3 HOH HOH 391 A HOH 47 3 HOH HOH 392 A HOH 71 3 HOH HOH 393 A HOH 85 3 HOH HOH 394 A HOH 59 3 HOH HOH 395 A HOH 52 3 HOH HOH 396 A HOH 98 3 HOH HOH 397 A HOH 92 3 HOH HOH 398 A SER 2 n 1 SER 2 A SER 3 n 2 SER 3 A LEU 4 n 3 LEU 4 A PRO 5 n 4 PRO 5 A VAL 6 n 5 VAL 6 A PRO 7 n 6 PRO 7 A TYR 8 n 7 TYR 8 A LYS 9 n 8 LYS 9 A LEU 10 n 9 LEU 10 A PRO 11 n 10 PRO 11 A VAL 12 n 11 VAL 12 A SER 13 n 12 SER 13 A LEU 14 n 13 LEU 14 A SER 15 n 14 SER 15 A VAL 16 n 15 VAL 16 A GLY 17 n 16 GLY 17 A SER 18 n 17 SER 18 A CYS 19 n 18 CYS 19 A VAL 20 n 19 VAL 20 A ILE 21 n 20 ILE 21 A ILE 22 n 21 ILE 22 A LYS 23 n 22 LYS 23 A GLY 24 n 23 GLY 24 A THR 25 n 24 THR 25 A PRO 26 n 25 PRO 26 A ILE 27 n 26 ILE 27 A HIS 28 n 27 HIS 28 A SER 29 n 28 SER 29 A PHE 30 n 29 PHE 30 A ILE 31 n 30 ILE 31 A ASN 32 n 31 ASN 32 A ASP 33 n 32 ASP 33 A PRO 34 n 33 PRO 34 A GLN 35 n 34 GLN 35 A LEU 36 n 35 LEU 36 A GLN 37 n 36 GLN 37 A VAL 38 n 37 VAL 38 A ASP 39 n 38 ASP 39 A PHE 40 n 39 PHE 40 A TYR 41 n 40 TYR 41 A THR 42 n 41 THR 42 A ASP 43 n 42 ASP 43 A MET 44 n 43 MET 44 A ASP 45 n 44 ASP 45 A GLU 46 n 45 GLU 46 A ASP 47 n 46 ASP 47 A SER 48 n 47 SER 48 A ASP 49 n 48 ASP 49 A ILE 50 n 49 ILE 50 A ALA 51 n 50 ALA 51 A PHE 52 n 51 PHE 52 A HIS 53 n 52 HIS 53 A PHE 54 n 53 PHE 54 A ARG 55 n 54 ARG 55 A VAL 56 n 55 VAL 56 A ARG 57 n 56 ARG 57 A PHE 58 n 57 PHE 58 A GLY 59 n 58 GLY 59 A ASN 60 n 59 ASN 60 A HIS 61 n 60 HIS 61 A VAL 62 n 61 VAL 62 A VAL 63 n 62 VAL 63 A MET 64 n 63 MET 64 A ASN 65 n 64 ASN 65 A ARG 66 n 65 ARG 66 A ARG 67 n 66 ARG 67 A GLU 68 n 67 GLU 68 A PHE 69 n 68 PHE 69 A GLY 70 n 69 GLY 70 A ILE 71 n 70 ILE 71 A TRP 72 n 71 TRP 72 A MET 73 n 72 MET 73 A LEU 74 n 73 LEU 74 A GLU 75 n 74 GLU 75 A GLU 76 n 75 GLU 76 A THR 77 n 76 THR 77 A THR 78 n 77 THR 78 A ASP 79 n 78 ASP 79 A TYR 80 n 79 TYR 80 A VAL 81 n 80 VAL 81 A PRO 82 n 81 PRO 82 A PHE 83 n 82 PHE 83 A GLU 84 n 83 GLU 84 A ASP 85 n 84 ASP 85 A GLY 86 n 85 GLY 86 A LYS 87 n 86 LYS 87 A GLN 88 n 87 GLN 88 A PHE 89 n 88 PHE 89 A GLU 90 n 89 GLU 90 A LEU 91 n 90 LEU 91 A CYS 92 n 91 CYS 92 A ILE 93 n 92 ILE 93 A TYR 94 n 93 TYR 94 A VAL 95 n 94 VAL 95 A HIS 96 n 95 HIS 96 A TYR 97 n 96 TYR 97 A ASN 98 n 97 ASN 98 A GLU 99 n 98 GLU 99 A TYR 100 n 99 TYR 100 A GLU 101 n 100 GLU 101 A ILE 102 n 101 ILE 102 A LYS 103 n 102 LYS 103 A VAL 104 n 103 VAL 104 A ASN 105 n 104 ASN 105 A GLY 106 n 105 GLY 106 A ILE 107 n 106 ILE 107 A ARG 108 n 107 ARG 108 A ILE 109 n 108 ILE 109 A TYR 110 n 109 TYR 110 A GLY 111 n 110 GLY 111 A PHE 112 n 111 PHE 112 A VAL 113 n 112 VAL 113 A HIS 114 n 113 HIS 114 A ARG 115 n 114 ARG 115 A ILE 116 n 115 ILE 116 A PRO 117 n 116 PRO 117 A PRO 118 n 117 PRO 118 A SER 119 n 118 SER 119 A PHE 120 n 119 PHE 120 A VAL 121 n 120 VAL 121 A LYS 122 n 121 LYS 122 A MET 123 n 122 MET 123 A VAL 124 n 123 VAL 124 A GLN 125 n 124 GLN 125 A VAL 126 n 125 VAL 126 A SER 127 n 126 SER 127 A ARG 128 n 127 ARG 128 A ASP 129 n 128 ASP 129 A ILE 130 n 129 ILE 130 A SER 131 n 130 SER 131 A LEU 132 n 131 LEU 132 A THR 133 n 132 THR 133 A SER 134 n 133 SER 134 A VAL 135 n 134 VAL 135 A CYS 136 n 135 CYS 136 A VAL 137 n 136 VAL 137 A CYS 138 n 137 CYS 138 A ASN 139 n 138 ASN 139 A author_and_software_defined_assembly PISA 2 dimeric gel filtration 1560 -3 12730 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 1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 4_575 x,-y+2,-z crystal symmetry operation 0.0000000000 185.9280000000 0.0000000000 A N LEU 10 A N LEU 9 A O VAL 124 A O VAL 123 A O SER 127 A O SER 126 A N GLN 37 A N GLN 36 A N LEU 36 A N LEU 35 A O VAL 56 A O VAL 55 A N ARG 57 A N ARG 56 A O HIS 61 A O HIS 60 A N GLU 68 A N GLU 67 A O ILE 71 A O ILE 70 A N LEU 10 A N LEU 9 A O VAL 124 A O VAL 123 A O SER 127 A O SER 126 A N GLN 37 A N GLN 36 A N LEU 36 A N LEU 35 A O VAL 56 A O VAL 55 A N ARG 57 A N ARG 56 A O HIS 61 A O HIS 60 A N MET 64 A N MET 63 A O GLU 76 A O GLU 75 A O ILE 109 A O ILE 108 A N ILE 102 A N ILE 101 A O LYS 103 A O LYS 102 A N CYS 92 A N CYS 91 A O PHE 89 A O PHE 88 A N GLY 24 A N GLY 23 A N THR 25 A N THR 24 A O SER 131 A O SER 130 1 A HOH 314 C HOH 1 A HOH 374 C HOH 1 A CG2 VAL 62 A CG2 VAL 61 1 Y 1 A ASN 60 -134.57 -83.43 1 A MET 73 -93.17 -156.20 1 A ARG 128 86.93 -139.29 1 A ASP 129 -96.63 58.00 73.250 26.8939 15.480 0.2089 0.1797 0.1826 1.6300 18.8940 1707 17077 10.0000 99.7600 0.1700 1 THROUGHOUT 1.360 MOLECULAR REPLACEMENT 24.0800 0.9000 1.1100 1.6300 18.8940 98 1245 45.40 34.86 23 0 1124 138 1.63 18.8940 6A63 17086 1 14.2 6.2 99.8 1.63 1.66 1 refinement PHENIX (1.10.1_2155: ???) N Galactoside-binding soluble lectin 13 Placental protein 13/galectin-13 variant R53HH57R with Lactose 1 N N 2 N N 3 N N A SER 29 A SER 28 HELX_P A ASP 33 A ASP 32 5 AA1 5 A PRO 117 A PRO 116 HELX_P A VAL 121 A VAL 120 5 AA2 5 disulf 2.052 A CYS 136 A SG CYS 135 1_555 A CYS 138 A SG CYS 137 4_575 covale 1.370 both sing B BGC 1 B O4 BGC 1_555 B GAL 2 B C1 GAL 1_555 SUGAR BINDING PROTEIN Sugar binding protein A VAL 6 A VAL 5 1 A PRO 7 A PRO 6 3.40 PP13_HUMAN UNP 1 2 Q9UHV8 SSLPVPYKLPVSLSVGSCVIIKGTPIHSFINDPQLQVDFYTDMDEDSDIAFRFRVHFGNHVVMNRREFGIWMLEETTDYV PFEDGKQFELCIYVHYNEYEIKVNGIRIYGFVHRIPPSFVKMVQVSRDISLTSVCVCN 2 139 6A63 2 139 Q9UHV8 A 1 1 138 1 ARG engineered mutation HIS 53 6A63 A Q9UHV8 UNP 53 52 1 HIS engineered mutation ARG 57 6A63 A Q9UHV8 UNP 57 56 6 6 5 anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel A TYR 8 A TYR 7 A PRO 11 A PRO 10 A MET 123 A MET 122 A ARG 128 A ARG 127 A GLN 35 A GLN 34 A TYR 41 A TYR 40 A ILE 50 A ILE 49 A ARG 57 A ARG 56 A HIS 61 A HIS 60 A GLU 68 A GLU 67 A ILE 71 A ILE 70 A TRP 72 A TRP 71 A TYR 8 A TYR 7 A PRO 11 A PRO 10 A MET 123 A MET 122 A ARG 128 A ARG 127 A GLN 35 A GLN 34 A TYR 41 A TYR 40 A ILE 50 A ILE 49 A ARG 57 A ARG 56 A HIS 61 A HIS 60 A GLU 68 A GLU 67 A GLU 76 A GLU 75 A THR 78 A THR 77 A ILE 107 A ILE 106 A VAL 113 A VAL 112 A GLU 99 A GLU 98 A VAL 104 A VAL 103 A PHE 89 A PHE 88 A VAL 95 A VAL 94 A CYS 19 A CYS 18 A PRO 26 A PRO 25 A ILE 130 A ILE 129 A CYS 138 A CYS 137 21 C 2 2 2