HEADER TRANSPORT PROTEIN 05-MAR-15 5AKS TITLE TRANSTHYRETIN BINDING HETEROGENEITY AND ANTI-AMYLOIDOGENIC ACTIVITY OF TITLE 2 NATURAL POLYPHENOLS AND THEIR METABOLITES: RESVERATROL-3-O- TITLE 3 GLUCURONIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSTHYRETIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 21-147; COMPND 5 SYNONYM: ATTR, PREALBUMIN, TBPA; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET11B KEYWDS TRANSPORT PROTEIN, AMYLOID, FIBRILLOGENESIS, FIBRILLOGENESIS KEYWDS 2 INHIBITORS, POLYPHENOLS, POLYPHENOL METABOLITES, TRANSTHYRETIN, KEYWDS 3 NEGATIVE COOPERATIVITY EXPDTA X-RAY DIFFRACTION AUTHOR P.FLORIO,C.FOLL,M.CIANCI,D.DEL RIO,G.ZANOTTI,R.BERNI REVDAT 6 10-JAN-24 5AKS 1 REMARK REVDAT 5 15-MAY-19 5AKS 1 REMARK REVDAT 4 07-MAR-18 5AKS 1 SOURCE REMARK REVDAT 3 13-JAN-16 5AKS 1 JRNL REVDAT 2 28-OCT-15 5AKS 1 JRNL REVDAT 1 21-OCT-15 5AKS 0 JRNL AUTH P.FLORIO,C.FOLLI,M.CIANCI,D.DEL RIO,G.ZANOTTI,R.BERNI JRNL TITL TRANSTHYRETIN BINDING HETEROGENEITY AND ANTI-AMYLOIDOGENIC JRNL TITL 2 ACTIVITY OF NATURAL POLYPHENOLS AND THEIR METABOLITES JRNL REF J.BIOL.CHEM. V. 290 29769 2015 JRNL REFN ISSN 0021-9258 JRNL PMID 26468275 JRNL DOI 10.1074/JBC.M115.690172 REMARK 2 REMARK 2 RESOLUTION. 1.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 1.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 63.79 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 3 NUMBER OF REFLECTIONS : 61893 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) : 0.167 REMARK 3 FREE R VALUE : 0.188 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3120 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 63.8762 - 3.5024 0.97 2958 160 0.1494 0.1638 REMARK 3 2 3.5024 - 2.7799 0.96 2788 150 0.1566 0.1789 REMARK 3 3 2.7799 - 2.4285 0.98 2813 141 0.1537 0.1759 REMARK 3 4 2.4285 - 2.2065 0.98 2771 154 0.1507 0.1714 REMARK 3 5 2.2065 - 2.0483 0.95 2693 148 0.1492 0.1685 REMARK 3 6 2.0483 - 1.9275 0.97 2756 154 0.1532 0.1837 REMARK 3 7 1.9275 - 1.8310 0.97 2713 153 0.1648 0.1896 REMARK 3 8 1.8310 - 1.7513 0.97 2731 141 0.1809 0.1991 REMARK 3 9 1.7513 - 1.6838 0.97 2736 139 0.1805 0.2389 REMARK 3 10 1.6838 - 1.6257 0.93 2614 144 0.1884 0.2036 REMARK 3 11 1.6257 - 1.5749 0.96 2685 153 0.1813 0.1958 REMARK 3 12 1.5749 - 1.5299 0.96 2680 134 0.1928 0.1983 REMARK 3 13 1.5299 - 1.4896 0.96 2676 159 0.1906 0.2109 REMARK 3 14 1.4896 - 1.4533 0.95 2678 141 0.2027 0.2451 REMARK 3 15 1.4533 - 1.4202 0.94 2614 127 0.2131 0.2743 REMARK 3 16 1.4202 - 1.3900 0.91 2540 137 0.2203 0.2419 REMARK 3 17 1.3900 - 1.3622 0.95 2639 147 0.2148 0.2414 REMARK 3 18 1.3622 - 1.3365 0.95 2617 155 0.2239 0.2699 REMARK 3 19 1.3365 - 1.3126 0.94 2664 125 0.2447 0.2547 REMARK 3 20 1.3126 - 1.2904 0.94 2604 132 0.2549 0.2488 REMARK 3 21 1.2904 - 1.2695 0.92 2600 120 0.2589 0.2647 REMARK 3 22 1.2695 - 1.2500 0.79 2203 106 0.2542 0.2779 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.350 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.021 2308 REMARK 3 ANGLE : 2.044 3198 REMARK 3 CHIRALITY : 0.104 348 REMARK 3 PLANARITY : 0.013 415 REMARK 3 DIHEDRAL : 15.770 837 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 5AKS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-MAR-15. REMARK 100 THE DEPOSITION ID IS D_1290063203. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-AUG-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PETRA III, EMBL C/O DESY REMARK 200 BEAMLINE : P13 (MX1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.967 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : KB MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 61920 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.250 REMARK 200 RESOLUTION RANGE LOW (A) : 63.790 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.27 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.2 REMARK 200 DATA REDUNDANCY IN SHELL : 6.30 REMARK 200 R MERGE FOR SHELL (I) : 0.08000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.500 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: PDB ENTRY 1F41 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALS OF WT HUMAN TTR- LIGAND REMARK 280 COMPLEXES WERE OBTAINED AT ROOM TEMPERATURE IN ABOUT ONE WEEK BY REMARK 280 CO-CRYSTALLIZATION, USING THE HANGING-DROP VAPOR DIFFUSION REMARK 280 METHOD. THE PROTEIN (5 MG/ML), IN 20 MM SODIUM PHOSPHATE, PH 7, REMARK 280 WAS INCUBATED WITH A FOUR-FOLD MOLAR EXCESS OF LIGANDS REMARK 280 SOLUBILIZED IN DMSO. DROPS WERE FORMED BY MIXING EQUAL VOLUMES REMARK 280 OF THE SOLUTION CONTAINING LIGAND-TTR COMPLEXES AND OF THE REMARK 280 RESERVOIR/PRECIPITANT SOLUTION (2.2 M AMMONIUM SULPHATE, 0.1 M REMARK 280 KCL, 0.03 M SODIUM PHOSPHATE, PH 7.0)., VAPOR DIFFUSION, HANGING REMARK 280 DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 21.40300 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.63350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.40300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.63350 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 42.80600 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 85.26700 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 CAI R3X A1127 LIES ON A SPECIAL POSITION. 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 1 REMARK 465 PRO A 2 REMARK 465 THR A 3 REMARK 465 GLY A 4 REMARK 465 THR A 5 REMARK 465 GLY A 6 REMARK 465 GLU A 7 REMARK 465 SER A 8 REMARK 465 LYS A 9 REMARK 465 LYS A 126 REMARK 465 GLU A 127 REMARK 465 GLY B 1 REMARK 465 PRO B 2 REMARK 465 THR B 3 REMARK 465 GLY B 4 REMARK 465 THR B 5 REMARK 465 GLY B 6 REMARK 465 GLU B 7 REMARK 465 SER B 8 REMARK 465 LYS B 9 REMARK 465 PRO B 125 REMARK 465 LYS B 126 REMARK 465 GLU B 127 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 OD1 ASP B 74 O HOH B 2082 1.60 REMARK 500 OG1 THR A 60 O HOH A 2091 1.65 REMARK 500 OE2 GLU A 66 O HOH A 2108 1.66 REMARK 500 O HOH A 2029 O HOH A 2031 1.77 REMARK 500 O HOH B 2101 O HOH B 2102 1.77 REMARK 500 OH TYR A 116 O HOH A 2154 1.78 REMARK 500 O HOH A 2184 O HOH A 2185 1.82 REMARK 500 OG SER B 85 O HOH B 2104 1.85 REMARK 500 O HOH A 2188 O HOH B 2123 1.86 REMARK 500 O HOH A 2069 O HOH A 2070 1.86 REMARK 500 OD1 ASP A 99 O HOH A 2159 1.87 REMARK 500 OH TYR B 116 O HOH A 2154 1.92 REMARK 500 O HOH A 2096 O HOH A 2097 1.95 REMARK 500 N GLU A 62 O HOH A 2091 1.97 REMARK 500 ND1 HIS B 90 O HOH B 2083 1.97 REMARK 500 SG CYS A 10 O HOH A 2005 1.97 REMARK 500 OE2 GLU B 72 O HOH B 2078 1.98 REMARK 500 O6A R3X A 1127 O HOH A 2198 1.98 REMARK 500 OE2 GLU A 92 O HOH A 2157 1.98 REMARK 500 O HOH B 2074 O HOH B 2112 1.98 REMARK 500 O PRO B 102 O HOH B 2116 1.99 REMARK 500 O GLY A 83 O HOH A 2135 2.00 REMARK 500 O2 SO4 A 1125 O HOH A 2157 2.00 REMARK 500 O HOH A 2172 O HOH A 2173 2.00 REMARK 500 O HOH A 2113 O HOH A 2156 2.01 REMARK 500 O HOH B 2104 O HOH B 2106 2.01 REMARK 500 O DMS B 1128 O HOH A 2176 2.03 REMARK 500 O HOH A 2121 O HOH A 2123 2.04 REMARK 500 O3 R3X A 1127 O HOH A 2199 2.04 REMARK 500 O GLY B 83 O HOH B 2097 2.04 REMARK 500 O HOH A 2118 O HOH A 2150 2.04 REMARK 500 O HOH B 2064 O HOH B 2072 2.04 REMARK 500 OD1 ASN B 124 O HOH B 2116 2.05 REMARK 500 OD2 ASP A 99 O HOH A 2169 2.06 REMARK 500 O HOH B 2063 O HOH B 2065 2.06 REMARK 500 O HOH A 2071 O HOH A 2072 2.06 REMARK 500 O5 R3X B 1127 O HOH B 2130 2.08 REMARK 500 O HOH A 2174 O HOH A 2177 2.08 REMARK 500 O HOH A 2157 O HOH A 2196 2.09 REMARK 500 O GLY B 101 O HOH B 2114 2.09 REMARK 500 O1 SO4 B 1125 O HOH A 2062 2.10 REMARK 500 O ASP B 99 O HOH B 2114 2.10 REMARK 500 OD1 ASP A 38 O HOH A 2049 2.12 REMARK 500 NH1 ARG B 103 O HOH A 2182 2.13 REMARK 500 O HOH A 2026 O HOH A 2076 2.13 REMARK 500 N ALA A 36 O HOH A 2050 2.13 REMARK 500 O HOH A 2020 O HOH A 2044 2.14 REMARK 500 N GLU A 63 O HOH A 2091 2.14 REMARK 500 O HOH B 2097 O HOH B 2099 2.15 REMARK 500 NH1 ARG B 103 O HOH B 2114 2.15 REMARK 500 REMARK 500 THIS ENTRY HAS 66 CLOSE CONTACTS REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 2088 O HOH A 2108 4556 1.72 REMARK 500 O HOH A 2014 O HOH B 2105 2665 1.93 REMARK 500 O HOH B 2055 O HOH B 2070 4457 1.97 REMARK 500 O HOH A 2036 O HOH A 2105 4556 1.97 REMARK 500 OE2 GLU B 62 O HOH B 2083 4557 1.98 REMARK 500 O HOH A 2034 O HOH A 2065 4556 2.02 REMARK 500 O HOH A 2040 O HOH A 2095 4556 2.03 REMARK 500 O2 R3X A 1127 O HOH A 2197 2665 2.05 REMARK 500 O HOH A 2081 O HOH A 2197 2665 2.06 REMARK 500 O HOH A 2032 O HOH A 2104 4556 2.14 REMARK 500 O HOH A 2193 O HOH A 2200 2665 2.16 REMARK 500 O GLY A 83 O HOH B 2100 1655 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 GLU A 66 OE1 - CD - OE2 ANGL. DEV. = -8.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASP A 39 9.20 82.36 REMARK 500 ASP B 99 -99.94 -71.15 REMARK 500 SER B 100 77.21 52.34 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 SO4 B 1125 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1125 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS B 1128 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE R3X A 1127 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE R3X B 1127 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5AKT RELATED DB: PDB REMARK 900 TRANSTHYRETIN BINDING HETEROGENEITY AND ANTI-AMYLOIDOGENIC ACTIVITY REMARK 900 OF NATURAL POLYPHENOLS AND THEIR METABOLITES: RESVERATROL-4'-O- REMARK 900 GLUCURONIDE REMARK 900 RELATED ID: 5AKV RELATED DB: PDB REMARK 900 TRANSTHYRETIN BINDING HETEROGENEITY AND ANTI-AMYLOIDOGENIC ACTIVITY REMARK 900 OF NATURAL POLYPHENOLS AND THEIR METABOLITES: GENISTEIN-7-O- REMARK 900 GLUCURONIDE REMARK 900 RELATED ID: 5AL0 RELATED DB: PDB REMARK 900 TRANSTHYRETIN BINDING HETEROGENEITY AND ANTI-AMYLOIDOGENIC ACTIVITY REMARK 900 OF NATURAL POLYPHENOLS AND THEIR METABOLITES: RESVERATROL-3-O- REMARK 900 SULFATE REMARK 900 RELATED ID: 5AL8 RELATED DB: PDB REMARK 900 TRANSTHYRETIN BINDING HETEROGENEITY AND ANTI-AMYLOIDOGENIC ACTIVITY REMARK 900 OF NATURAL POLYPHENOLS AND THEIR METABOLITES: DAIDZEIN-7-O- REMARK 900 GLUCURONIDE DBREF 5AKS A 1 127 UNP P02766 TTHY_HUMAN 21 147 DBREF 5AKS B 1 127 UNP P02766 TTHY_HUMAN 21 147 SEQRES 1 A 127 GLY PRO THR GLY THR GLY GLU SER LYS CYS PRO LEU MET SEQRES 2 A 127 VAL LYS VAL LEU ASP ALA VAL ARG GLY SER PRO ALA ILE SEQRES 3 A 127 ASN VAL ALA VAL HIS VAL PHE ARG LYS ALA ALA ASP ASP SEQRES 4 A 127 THR TRP GLU PRO PHE ALA SER GLY LYS THR SER GLU SER SEQRES 5 A 127 GLY GLU LEU HIS GLY LEU THR THR GLU GLU GLU PHE VAL SEQRES 6 A 127 GLU GLY ILE TYR LYS VAL GLU ILE ASP THR LYS SER TYR SEQRES 7 A 127 TRP LYS ALA LEU GLY ILE SER PRO PHE HIS GLU HIS ALA SEQRES 8 A 127 GLU VAL VAL PHE THR ALA ASN ASP SER GLY PRO ARG ARG SEQRES 9 A 127 TYR THR ILE ALA ALA LEU LEU SER PRO TYR SER TYR SER SEQRES 10 A 127 THR THR ALA VAL VAL THR ASN PRO LYS GLU SEQRES 1 B 127 GLY PRO THR GLY THR GLY GLU SER LYS CYS PRO LEU MET SEQRES 2 B 127 VAL LYS VAL LEU ASP ALA VAL ARG GLY SER PRO ALA ILE SEQRES 3 B 127 ASN VAL ALA VAL HIS VAL PHE ARG LYS ALA ALA ASP ASP SEQRES 4 B 127 THR TRP GLU PRO PHE ALA SER GLY LYS THR SER GLU SER SEQRES 5 B 127 GLY GLU LEU HIS GLY LEU THR THR GLU GLU GLU PHE VAL SEQRES 6 B 127 GLU GLY ILE TYR LYS VAL GLU ILE ASP THR LYS SER TYR SEQRES 7 B 127 TRP LYS ALA LEU GLY ILE SER PRO PHE HIS GLU HIS ALA SEQRES 8 B 127 GLU VAL VAL PHE THR ALA ASN ASP SER GLY PRO ARG ARG SEQRES 9 B 127 TYR THR ILE ALA ALA LEU LEU SER PRO TYR SER TYR SER SEQRES 10 B 127 THR THR ALA VAL VAL THR ASN PRO LYS GLU HET SO4 A1125 5 HET R3X A1127 29 HET SO4 B1125 5 HET R3X B1127 29 HET DMS B1128 4 HETNAM SO4 SULFATE ION HETNAM R3X RESVERATROL-3-O-GLUCURONIDE HETNAM DMS DIMETHYL SULFOXIDE FORMUL 3 SO4 2(O4 S 2-) FORMUL 4 R3X 2(C20 H20 O9) FORMUL 7 DMS C2 H6 O S FORMUL 8 HOH *330(H2 O) HELIX 1 1 ASP A 74 LEU A 82 1 9 HELIX 2 2 ASP B 74 LEU B 82 1 9 SHEET 1 AA 2 SER A 23 PRO A 24 0 SHEET 2 AA 2 LEU A 12 ASP A 18 -1 N ASP A 18 O SER A 23 SHEET 1 AB 2 GLU A 54 LEU A 55 0 SHEET 2 AB 2 LEU A 12 ASP A 18 -1 O VAL A 14 N LEU A 55 SHEET 1 BA 2 SER B 23 PRO B 24 0 SHEET 2 BA 2 LEU B 12 ASP B 18 -1 N ASP B 18 O SER B 23 SHEET 1 BB 2 GLU B 54 LEU B 55 0 SHEET 2 BB 2 LEU B 12 ASP B 18 -1 O VAL B 14 N LEU B 55 SHEET 1 AC 8 TRP A 41 LYS A 48 0 SHEET 2 AC 8 ALA A 29 LYS A 35 -1 O VAL A 30 N GLY A 47 SHEET 3 AC 8 GLY A 67 ILE A 73 -1 O ILE A 68 N LYS A 35 SHEET 4 AC 8 HIS A 88 ALA A 97 -1 O ALA A 91 N ILE A 73 SHEET 5 AC 8 HIS B 88 ALA B 97 -1 N GLU B 89 O VAL A 94 SHEET 6 AC 8 GLY B 67 ILE B 73 -1 O GLY B 67 N ALA B 97 SHEET 7 AC 8 ALA B 29 LYS B 35 -1 O HIS B 31 N GLU B 72 SHEET 8 AC 8 TRP B 41 LYS B 48 -1 O GLU B 42 N ARG B 34 SITE 1 AC1 9 LYS A 35 TRP A 41 HOH A2062 HOH A2156 SITE 2 AC1 9 GLU B 72 HIS B 90 HOH B2078 HOH B2080 SITE 3 AC1 9 HOH B2129 SITE 1 AC2 8 LYS A 70 GLU A 72 HIS A 90 GLU A 92 SITE 2 AC2 8 HOH A2112 HOH A2153 HOH A2157 TRP B 41 SITE 1 AC3 7 ARG A 103 HOH A2015 HOH A2058 HOH A2175 SITE 2 AC3 7 HOH A2176 HOH A2177 TYR B 114 SITE 1 AC4 16 LYS A 15 THR A 106 SER A 117 THR A 119 SITE 2 AC4 16 VAL A 121 HOH A2011 HOH A2081 HOH A2082 SITE 3 AC4 16 HOH A2083 HOH A2178 HOH A2186 HOH A2187 SITE 4 AC4 16 HOH A2197 HOH A2198 HOH A2199 HOH A2200 SITE 1 AC5 11 MET B 13 LYS B 15 LEU B 17 GLU B 54 SITE 2 AC5 11 THR B 106 LEU B 110 SER B 117 THR B 119 SITE 3 AC5 11 HOH B2005 HOH B2120 HOH B2130 CRYST1 42.806 85.267 63.793 90.00 90.00 90.00 P 21 21 2 8 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 0.023361 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011728 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015676 0.00000