HEADER SUGAR BINDING PROTEIN 29-DEC-15 5H9P TITLE CRYSTAL STRUCTURE OF HUMAN GALECTIN-3 CRD IN COMPLEX WITH TD139 COMPND MOL_ID: 1; COMPND 2 MOLECULE: GALECTIN-3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CARBOHYDRATE-RECOGNITION DOMAIN, UNP RESIDUES 113-250; COMPND 5 SYNONYM: GAL-3,35 KDA LECTIN,CARBOHYDRATE-BINDING PROTEIN 35,CBP 35, COMPND 6 GALACTOSE-SPECIFIC LECTIN 3,GALACTOSIDE-BINDING PROTEIN,GALBP,IGE- COMPND 7 BINDING PROTEIN,L-31,LAMININ-BINDING PROTEIN,LECTIN L-29,MAC-2 COMPND 8 ANTIGEN; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: LGALS3, MAC2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 866768; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-GOLD(DE3)PLYSS AG KEYWDS GALECTIN, THIO-DIGALACTOSIDE (TDG), PI-ARGININE INTERACTION, SUGAR KEYWDS 2 BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.J.HSIEH,H.Y.LIN,C.H.LIN REVDAT 3 08-NOV-23 5H9P 1 REMARK REVDAT 2 27-JUL-16 5H9P 1 JRNL REVDAT 1 29-JUN-16 5H9P 0 JRNL AUTH T.J.HSIEH,H.Y.LIN,Z.TU,T.C.LIN,S.C.WU,Y.Y.TSENG,F.T.LIU, JRNL AUTH 2 S.T.DANNY HSU,C.H.LIN JRNL TITL DUAL THIO-DIGALACTOSIDE-BINDING MODES OF HUMAN GALECTINS AS JRNL TITL 2 THE STRUCTURAL BASIS FOR THE DESIGN OF POTENT AND SELECTIVE JRNL TITL 3 INHIBITORS JRNL REF SCI REP V. 6 29457 2016 JRNL REFN ESSN 2045-2322 JRNL PMID 27416897 JRNL DOI 10.1038/SREP29457 REMARK 2 REMARK 2 RESOLUTION. 2.04 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.04 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.07 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 8824 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.050 REMARK 3 FREE R VALUE TEST SET COUNT : 887 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 26.0688 - 3.6980 1.00 1447 162 0.1631 0.1636 REMARK 3 2 3.6980 - 2.9365 1.00 1376 153 0.1544 0.1965 REMARK 3 3 2.9365 - 2.5657 0.99 1344 148 0.1701 0.2308 REMARK 3 4 2.5657 - 2.3313 0.98 1323 146 0.1741 0.2036 REMARK 3 5 2.3313 - 2.1643 0.95 1284 144 0.1722 0.2400 REMARK 3 6 2.1643 - 2.0367 0.88 1163 134 0.1859 0.2434 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.400 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.74 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.005 1184 REMARK 3 ANGLE : 1.025 1612 REMARK 3 CHIRALITY : 0.039 171 REMARK 3 PLANARITY : 0.005 207 REMARK 3 DIHEDRAL : 28.846 493 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5H9P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-JAN-16. REMARK 100 THE DEPOSITION ID IS D_1000216701. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-NOV-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5-8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : BL13B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : PHENIX REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9047 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.040 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 10.50 REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.04 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.1 REMARK 200 DATA REDUNDANCY IN SHELL : 7.80 REMARK 200 R MERGE FOR SHELL (I) : 0.35500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 2NMN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS PH 8.0, 0.2 M LISO4, 30% REMARK 280 (W/V) PEG 4000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 18.58400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.82550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.57250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.82550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.58400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.57250 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7470 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 93 REMARK 465 SER A 94 REMARK 465 SER A 95 REMARK 465 HIS A 96 REMARK 465 HIS A 97 REMARK 465 HIS A 98 REMARK 465 HIS A 99 REMARK 465 HIS A 100 REMARK 465 HIS A 101 REMARK 465 SER A 102 REMARK 465 SER A 103 REMARK 465 GLY A 104 REMARK 465 LEU A 105 REMARK 465 VAL A 106 REMARK 465 PRO A 107 REMARK 465 ARG A 108 REMARK 465 GLY A 109 REMARK 465 SER A 110 REMARK 465 HIS A 111 REMARK 465 MET A 112 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 436 O HOH A 477 1.81 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TD2 A 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4XBN RELATED DB: PDB REMARK 900 4XBN CONTAINS THE SAME PROTEIN COMPLEX WITH TYPE I N- REMARK 900 ACETYLLACTOSAMINE REMARK 900 RELATED ID: 5H9Q RELATED DB: PDB REMARK 900 RELATED ID: 5H9R RELATED DB: PDB REMARK 900 RELATED ID: 5H9S RELATED DB: PDB DBREF 5H9P A 113 250 UNP P17931 LEG3_HUMAN 113 250 SEQADV 5H9P GLY A 93 UNP P17931 EXPRESSION TAG SEQADV 5H9P SER A 94 UNP P17931 EXPRESSION TAG SEQADV 5H9P SER A 95 UNP P17931 EXPRESSION TAG SEQADV 5H9P HIS A 96 UNP P17931 EXPRESSION TAG SEQADV 5H9P HIS A 97 UNP P17931 EXPRESSION TAG SEQADV 5H9P HIS A 98 UNP P17931 EXPRESSION TAG SEQADV 5H9P HIS A 99 UNP P17931 EXPRESSION TAG SEQADV 5H9P HIS A 100 UNP P17931 EXPRESSION TAG SEQADV 5H9P HIS A 101 UNP P17931 EXPRESSION TAG SEQADV 5H9P SER A 102 UNP P17931 EXPRESSION TAG SEQADV 5H9P SER A 103 UNP P17931 EXPRESSION TAG SEQADV 5H9P GLY A 104 UNP P17931 EXPRESSION TAG SEQADV 5H9P LEU A 105 UNP P17931 EXPRESSION TAG SEQADV 5H9P VAL A 106 UNP P17931 EXPRESSION TAG SEQADV 5H9P PRO A 107 UNP P17931 EXPRESSION TAG SEQADV 5H9P ARG A 108 UNP P17931 EXPRESSION TAG SEQADV 5H9P GLY A 109 UNP P17931 EXPRESSION TAG SEQADV 5H9P SER A 110 UNP P17931 EXPRESSION TAG SEQADV 5H9P HIS A 111 UNP P17931 EXPRESSION TAG SEQADV 5H9P MET A 112 UNP P17931 EXPRESSION TAG SEQRES 1 A 158 GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY LEU SEQRES 2 A 158 VAL PRO ARG GLY SER HIS MET PRO LEU ILE VAL PRO TYR SEQRES 3 A 158 ASN LEU PRO LEU PRO GLY GLY VAL VAL PRO ARG MET LEU SEQRES 4 A 158 ILE THR ILE LEU GLY THR VAL LYS PRO ASN ALA ASN ARG SEQRES 5 A 158 ILE ALA LEU ASP PHE GLN ARG GLY ASN ASP VAL ALA PHE SEQRES 6 A 158 HIS PHE ASN PRO ARG PHE ASN GLU ASN ASN ARG ARG VAL SEQRES 7 A 158 ILE VAL CYS ASN THR LYS LEU ASP ASN ASN TRP GLY ARG SEQRES 8 A 158 GLU GLU ARG GLN SER VAL PHE PRO PHE GLU SER GLY LYS SEQRES 9 A 158 PRO PHE LYS ILE GLN VAL LEU VAL GLU PRO ASP HIS PHE SEQRES 10 A 158 LYS VAL ALA VAL ASN ASP ALA HIS LEU LEU GLN TYR ASN SEQRES 11 A 158 HIS ARG VAL LYS LYS LEU ASN GLU ILE SER LYS LEU GLY SEQRES 12 A 158 ILE SER GLY ASP ILE ASP LEU THR SER ALA SER TYR THR SEQRES 13 A 158 MET ILE HET TD2 A 301 45 HETNAM TD2 3-DEOXY-3-[4-(3-FLUOROPHENYL)-1H-1,2,3-TRIAZOL-1-YL]- HETNAM 2 TD2 BETA-D-GALACTOPYRANOSYL 3-DEOXY-3-[4-(3-FLUOROPHENYL)- HETNAM 3 TD2 1H-1,2,3-TRIAZOL-1-YL]-1-THIO-BETA-D-GALACTOPYRANOSIDE FORMUL 2 TD2 C28 H30 F2 N6 O8 S FORMUL 3 HOH *84(H2 O) HELIX 1 AA1 LYS A 227 ILE A 231 5 5 SHEET 1 AA1 6 TYR A 118 PRO A 121 0 SHEET 2 AA1 6 LYS A 233 GLY A 238 -1 O ILE A 236 N TYR A 118 SHEET 3 AA1 6 ILE A 145 ARG A 151 -1 N ASP A 148 O GLY A 235 SHEET 4 AA1 6 ASP A 154 GLU A 165 -1 O PHE A 157 N PHE A 149 SHEET 5 AA1 6 ARG A 168 LEU A 177 -1 O VAL A 170 N ARG A 162 SHEET 6 AA1 6 ASN A 180 TRP A 181 -1 O ASN A 180 N LEU A 177 SHEET 1 AA2 6 TYR A 118 PRO A 121 0 SHEET 2 AA2 6 LYS A 233 GLY A 238 -1 O ILE A 236 N TYR A 118 SHEET 3 AA2 6 ILE A 145 ARG A 151 -1 N ASP A 148 O GLY A 235 SHEET 4 AA2 6 ASP A 154 GLU A 165 -1 O PHE A 157 N PHE A 149 SHEET 5 AA2 6 ARG A 168 LEU A 177 -1 O VAL A 170 N ARG A 162 SHEET 6 AA2 6 GLU A 185 GLN A 187 -1 O GLU A 185 N CYS A 173 SHEET 1 AA3 5 ALA A 216 ASN A 222 0 SHEET 2 AA3 5 HIS A 208 VAL A 213 -1 N VAL A 211 O LEU A 219 SHEET 3 AA3 5 PRO A 197 VAL A 204 -1 N GLN A 201 O ALA A 212 SHEET 4 AA3 5 MET A 130 VAL A 138 -1 N GLY A 136 O PHE A 198 SHEET 5 AA3 5 ILE A 240 MET A 249 -1 O THR A 248 N LEU A 131 CISPEP 1 VAL A 116 PRO A 117 0 2.48 SITE 1 AC1 12 PRO A 113 ILE A 115 ARG A 144 ILE A 145 SITE 2 AC1 12 ALA A 146 HIS A 158 ASN A 160 ARG A 162 SITE 3 AC1 12 ASN A 174 GLU A 184 ARG A 186 HOH A 466 CRYST1 37.168 57.145 63.651 90.00 90.00 90.00 P 21 21 21 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.026905 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017499 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015711 0.00000