1TYR - Header Asymmetric Unit

HEADER RETINOL-BINDING 12-MAY-95 1TYR

TITLE TRANSTHYRETIN COMPLEX WITH RETINOIC ACID

COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSTHYRETIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PREALBUMIN

SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606

KEYWDS RETINOL-BINDING PROTEIN, RETINOL-BINDING

EXPDTA X-RAY DIFFRACTION

AUTHOR G.ZANOTTI,M.R.D'ACUNTO,G.MALPELI,C.FOLLI,R.BERNI

REVDAT 3 09-NOV-16 1TYR 1 HET HETATM HETNAM VERSN REVDAT 2 24-FEB-09 1TYR 1 VERSN REVDAT 1 15-SEP-95 1TYR 0

JRNL AUTH G.ZANOTTI,M.R.D'ACUNTO,G.MALPELI,C.FOLLI,R.BERNI JRNL TITL CRYSTAL STRUCTURE OF THE TRANSTHYRETIN--RETINOIC-ACID JRNL TITL 2 COMPLEX JRNL REF EUR.J.BIOCHEM. V. 234 563 1995 JRNL REFN ISSN 0014-2956 JRNL PMID 8536704 JRNL DOI 10.1111/J.1432-1033.1995.563_B.X

REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH G.ZANOTTI,M.MARCELLO,G.MALPELI,C.FOLLI,G.SARTORI,R.BERNI REMARK 1 TITL CRYSTALLOGRAPHIC STUDIES ON COMPLEXES BETWEEN RETINOIDS AND REMARK 1 TITL 2 PLASMA RETINOL-BINDING PROTEIN REMARK 1 REF J.BIOL.CHEM. V. 269 29613 1994 REMARK 1 REFN ISSN 0021-9258 REMARK 1 REFERENCE 2 REMARK 1 AUTH E.CISZAK,V.CODY,J.R.LUFT REMARK 1 TITL CRYSTAL STRUCTURE DETERMINATION AT 2.3 ANGSTROMS OF HUMAN REMARK 1 TITL 2 TRANSTHYRETIN-3',5'-DIBROMO-2',4,4', 6-TETRA-HYDROXYAURONE REMARK 1 TITL 3 COMPLEX REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 89 6644 1992 REMARK 1 REFN ISSN 0027-8424 REMARK 1 REFERENCE 3 REMARK 1 AUTH A.WOJTCZAK,J.LUFT,V.CODY REMARK 1 TITL MECHANISM OF MOLECULAR RECOGNITION. STRUCTURAL ASPECTS OF REMARK 1 TITL 2 3,3'-DIIODO-L-THYRONINE BINDING TO HUMAN SERUM TRANSTHYRETIN REMARK 1 REF J.BIOL.CHEM. V. 267 353 1992 REMARK 1 REFN ISSN 0021-9258 REMARK 1 REFERENCE 4 REMARK 1 AUTH C.C.F.BLAKE,S.J.OATLEY REMARK 1 TITL PROTEIN-DNA AND PROTEIN-HORMONE INTERACTIONS IN PREALBUMIN: REMARK 1 TITL 2 A MODEL OF THE THYROID HORMONE NUCLEAR RECEPTOR? REMARK 1 REF NATURE V. 268 115 1977 REMARK 1 REFN ISSN 0028-0836 REMARK 1 REFERENCE 5 REMARK 1 AUTH C.C.F.BLAKE,M.J.GEISOW,I.D.A.SWAN,C.RERAT,B.RERAT REMARK 1 TITL STRUCTURE OF HUMAN PLASMA PREALBUMIN AT 2.5 ANGSTROMS REMARK 1 TITL 2 RESOLUTION, A PRELIMINARY REPORT ON THE POLYPEPTIDE CHAIN REMARK 1 TITL 3 CONFORMATION, QUATERNARY STRUCTURE AND THYROXINE BINDING REMARK 1 REF J.MOL.BIOL. V. 88 1 1974 REMARK 1 REFN ISSN 0022-2836

REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 9.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 85.0 REMARK 3 NUMBER OF REFLECTIONS : 20172 REMARK 3 REMARK 3 USING DATA ABOVE SIGMA CUTOFF. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.196 REMARK 3 R VALUE (WORKING SET) : NULL REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 USING ALL DATA, NO SIGMA CUTOFF. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1944 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 44 REMARK 3 SOLVENT ATOMS : 97 REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : 0.016 ; NULL ; NULL REMARK 3 BOND ANGLES (DEGREES) : 3.800 ; NULL ; NULL REMARK 3 TORSION ANGLES (DEGREES) : 19.600; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES (A) : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES (A) : 0.001 ; NULL ; NULL REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS (A) : NULL ; NULL ; NULL REMARK 3 REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : NULL REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE ENTRY CONTAINS RETINOIC ACID MOLECULES IN BOTH BINDING REMARK 3 SITES. THE OCCUPANCIES OF SITES WERE NOT REFINED, SINCE REMARK 3 THE ELECTRON DENSITY REFLECTS THE PRESENCE OF THE REMARK 3 CRYSTALLOGRAPHIC TWO-FOLD AXIS. IN THE FUNCTIONAL REMARK 3 TETRAMER THE RETINOIC ACID MOLECULES ARE DISORDERED DUE TO REMARK 3 THE CRYSTALLOGRAPHIC TWO-FOLD RUNNING THROUGH THE BINDING REMARK 3 SITE. REMARK 3 REMARK 3 RESIDUES 1 - 9 OF BOTH CHAINS, AS WELL AS 126 - 127 OF REMARK 3 CHAIN B, ARE ILL-DEFINED IN THE ELECTRON DENSITY. THEY REMARK 3 HAVE BEEN INCLUDED, BUT THE TEMPERATURE FACTORS ARE VERY REMARK 3 HIGH.

REMARK 4 REMARK 4 1TYR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.

REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NOV-94 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : SIEMENS-NICOLET X100 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SAINT REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL

REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL

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 21.90000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.11000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.90000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.11000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL

REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 300 REMARK: THE ENTIRE PROTEIN IS A TETRAMER, BUT THE ASYMMETRIC UNIT REMARK 300 CONTAINS A DIMER. THE TWO DIMERS ARE RELATED BY A TWO FODL REMARK 300 AXIS, WHILST THE TWO INDEPENDENT MONOMERS IN THE DIMER ARE REMARK 300 RELATED BY A PSEUDO TWO-FOLD AXIS. THE LIGAND IS BOUND IN REMARK 300 THE INTERNAL CHANNEL, MADE UP BY THE TWO INDEPENDENT REMARK 300 MONOMERS. A CRYSTALLOGRAPHIC TWO-FOLD AXIS RUNS THROUGH REMARK 300 THE CHANNEL, MAKING IT SYMMETRIC. MOREOVER, PERPENDICULAR REMARK 300 TO THE PREVIOUS ONE, THERE IS THE PSEUDO TWO-FOLD, WHICH REMARK 300 MAKES THE TWO HALFS OF THE CHANNEL NEARLY IDENTICAL. AS A REMARK 300 RESULT OF ALL THAT, TWO INDEPENDENT BINDING SITES ARE REMARK 300 PRESENT PER TERAMER, BUT, SINCE THE LIGAND IN THIS CASE REMARK 300 DOES NOT PRESENT ANY SYMMETRY, EACH LIGAND IN THE CRYSTAL REMARK 300 APPEARS TO BE SUPERIMPOSED TO ITS SYMMETRY-RELATED. IN REMARK 300 CONCLUSION, FOUR RETINOIC ACID BOUND MOLECULES ARE SEEN, REMARK 300 EACH PAIRS SUPERIMPOSED. IN ADDITION, SOLUTION DATA REMARK 300 STRONGLY SUGGEST THAT ONLY ONE LIGAND MOLECULE IS BOUND TO REMARK 300 A TTR TETRAMER. IN CONCLUSION, THE COORDINATES OF TWO 9CR REMARK 300 MOLECULES ARE GIVEN, WHICH APPLYING THE CRYSTALLOGRAPHIC REMARK 300 SYMMETRY, BECOMES FOUR, BUT ONLY ONE MUST BE CONSIDERED REMARK 300 STATISTICALLY PRESENT IN THE TETRAMER.

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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2430 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12390 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9270 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -35.0 KCAL/MOL 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 43.80000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 86.22000 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 C8 9CR A 131 LIES ON A SPECIAL POSITION.

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 C10 9CR B 130 O HOH B 274 0.32 REMARK 500 C14 9CR B 130 O HOH B 281 0.96 REMARK 500 C9 9CR B 130 O HOH B 274 1.21 REMARK 500 C15 9CR B 130 O HOH B 281 1.24 REMARK 500 O2 9CR A 131 O HOH A 220 1.26 REMARK 500 C4 9CR B 130 O HOH B 260 1.29 REMARK 500 C13 9CR B 130 O HOH B 281 1.50 REMARK 500 C5 9CR B 130 O HOH B 260 1.52 REMARK 500 C11 9CR B 130 O HOH B 274 1.59 REMARK 500 C18 9CR B 130 O HOH B 260 1.84 REMARK 500 O1 9CR B 130 O HOH B 281 1.89 REMARK 500 C12 9CR B 130 O HOH B 281 1.98 REMARK 500 OXT GLU B 127 O HOH B 281 2.01 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 C17 9CR B 130 C18 9CR B 130 2665 0.39 REMARK 500 C9 9CR A 131 C9 9CR A 131 2665 0.39 REMARK 500 C8 9CR B 130 C8 9CR B 130 2665 0.46 REMARK 500 C2 9CR B 130 O HOH B 260 2665 0.61 REMARK 500 C3 9CR B 130 C4 9CR B 130 2665 0.71 REMARK 500 C1 9CR A 131 C18 9CR A 131 2665 0.80 REMARK 500 C4 9CR A 131 C4 9CR A 131 2665 0.81 REMARK 500 C3 9CR A 131 C4 9CR A 131 2665 0.84 REMARK 500 C10 9CR A 131 C19 9CR A 131 2665 0.85 REMARK 500 C9 9CR B 130 C9 9CR B 130 2665 0.97 REMARK 500 C17 9CR A 131 C18 9CR A 131 2665 1.09 REMARK 500 C9 9CR A 131 C10 9CR A 131 2665 1.12 REMARK 500 C3 9CR B 130 O HOH B 260 2665 1.19 REMARK 500 C19 9CR B 130 O HOH B 274 2665 1.23 REMARK 500 C5 9CR A 131 C5 9CR A 131 2665 1.25 REMARK 500 C5 9CR A 131 C6 9CR A 131 2665 1.26 REMARK 500 C10 9CR B 130 C19 9CR B 130 2665 1.36 REMARK 500 C1 9CR B 130 C18 9CR B 130 2665 1.37 REMARK 500 C1 9CR B 130 O HOH B 260 2665 1.38 REMARK 500 C8 9CR A 131 C9 9CR A 131 2665 1.41 REMARK 500 C3 9CR B 130 C3 9CR B 130 2665 1.43 REMARK 500 C9 9CR B 130 C10 9CR B 130 2665 1.45 REMARK 500 C7 9CR A 131 C8 9CR A 131 2665 1.51 REMARK 500 C7 9CR B 130 C8 9CR B 130 2665 1.56 REMARK 500 C8 9CR B 130 C9 9CR B 130 2665 1.58 REMARK 500 C6 9CR B 130 C6 9CR B 130 2665 1.58 REMARK 500 C6 9CR A 131 C6 9CR A 131 2665 1.61 REMARK 500 C6 9CR A 131 C18 9CR A 131 2665 1.62 REMARK 500 O HOH B 274 O HOH B 274 2665 1.69 REMARK 500 C1 9CR B 130 C5 9CR B 130 2665 1.70 REMARK 500 C5 9CR B 130 C6 9CR B 130 2665 1.74 REMARK 500 C4 9CR B 130 C4 9CR B 130 2665 1.74 REMARK 500 C2 9CR B 130 C4 9CR B 130 2665 1.75 REMARK 500 C5 9CR B 130 C17 9CR B 130 2665 1.82 REMARK 500 C4 9CR A 131 C5 9CR A 131 2665 1.82 REMARK 500 C2 9CR A 131 C18 9CR A 131 2665 1.82 REMARK 500 C9 9CR A 131 C19 9CR A 131 2665 1.90 REMARK 500 C1 9CR A 131 C5 9CR A 131 2665 1.90 REMARK 500 C11 9CR A 131 C19 9CR A 131 2665 1.92 REMARK 500 C7 9CR A 131 C7 9CR A 131 2665 1.94 REMARK 500 C10 9CR A 131 C10 9CR A 131 2665 1.95 REMARK 500 C3 9CR A 131 C5 9CR A 131 2665 1.95 REMARK 500 C2 9CR A 131 C4 9CR A 131 2665 1.98 REMARK 500 C3 9CR B 130 C5 9CR B 130 2665 2.01 REMARK 500 C7 9CR B 130 C7 9CR B 130 2665 2.05 REMARK 500 C2 9CR B 130 C5 9CR B 130 2665 2.12 REMARK 500 C5 9CR B 130 C5 9CR B 130 2665 2.12 REMARK 500 C2 9CR B 130 C18 9CR B 130 2665 2.17 REMARK 500 C9 9CR B 130 C19 9CR B 130 2665 2.18 REMARK 500 C19 9CR A 131 C20 9CR A 131 2665 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 7 CD GLU A 7 OE2 0.073 REMARK 500 GLU A 42 CD GLU A 42 OE1 0.086 REMARK 500 GLU A 61 CD GLU A 61 OE2 0.072 REMARK 500 GLU A 62 CD GLU A 62 OE2 0.074 REMARK 500 GLU A 66 CD GLU A 66 OE2 0.073 REMARK 500 GLU A 89 CD GLU A 89 OE1 -0.073 REMARK 500 GLU A 92 CD GLU A 92 OE2 0.078 REMARK 500 GLU A 127 CD GLU A 127 OE1 0.067 REMARK 500 GLU A 127 C GLU A 127 OXT 4.278 REMARK 500 GLU B 7 CD GLU B 7 OE1 0.090 REMARK 500 GLU B 42 CD GLU B 42 OE1 0.074 REMARK 500 GLU B 51 CD GLU B 51 OE2 0.074 REMARK 500 GLU B 62 CD GLU B 62 OE2 0.072 REMARK 500 GLU B 63 CD GLU B 63 OE1 0.085 REMARK 500 GLU B 127 CD GLU B 127 OE1 0.081 REMARK 500 GLU B 127 C GLU B 127 OXT 1.509 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 PRO A 2 C - N - CA ANGL. DEV. = 10.1 DEGREES REMARK 500 CYS A 10 CA - CB - SG ANGL. DEV. = -12.4 DEGREES REMARK 500 ASP A 18 CB - CG - OD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 PHE A 33 CB - CG - CD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 ARG A 34 CG - CD - NE ANGL. DEV. = -12.7 DEGREES REMARK 500 ARG A 34 NE - CZ - NH1 ANGL. DEV. = 5.3 DEGREES REMARK 500 ARG A 34 NE - CZ - NH2 ANGL. DEV. = -6.8 DEGREES REMARK 500 ASP A 38 CB - CG - OD2 ANGL. DEV. = -5.6 DEGREES REMARK 500 ASP A 39 CB - CG - OD2 ANGL. DEV. = -8.6 DEGREES REMARK 500 SER A 46 N - CA - CB ANGL. DEV. = 9.4 DEGREES REMARK 500 THR A 60 CA - CB - CG2 ANGL. DEV. = -10.8 DEGREES REMARK 500 PRO A 86 N - CA - CB ANGL. DEV. = -7.5 DEGREES REMARK 500 ARG A 103 NE - CZ - NH1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ARG A 103 NE - CZ - NH2 ANGL. DEV. = -5.3 DEGREES REMARK 500 TYR A 116 N - CA - CB ANGL. DEV. = 12.1 DEGREES REMARK 500 TYR A 116 CB - CG - CD2 ANGL. DEV. = -7.0 DEGREES REMARK 500 SER A 117 N - CA - CB ANGL. DEV. = -10.8 DEGREES REMARK 500 THR A 119 OG1 - CB - CG2 ANGL. DEV. = -18.6 DEGREES REMARK 500 PRO B 2 C - N - CD ANGL. DEV. = -14.4 DEGREES REMARK 500 THR B 3 CA - CB - OG1 ANGL. DEV. = 13.3 DEGREES REMARK 500 CYS B 10 CA - CB - SG ANGL. DEV. = -14.2 DEGREES REMARK 500 ASP B 18 CB - CG - OD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 ARG B 21 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 PRO B 24 N - CA - CB ANGL. DEV. = 8.3 DEGREES REMARK 500 ASP B 38 CB - CG - OD1 ANGL. DEV. = 5.4 DEGREES REMARK 500 ASP B 38 CB - CG - OD2 ANGL. DEV. = -7.0 DEGREES REMARK 500 ASP B 39 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ASP B 39 CB - CG - OD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 GLU B 42 N - CA - CB ANGL. DEV. = -14.0 DEGREES REMARK 500 SER B 46 N - CA - CB ANGL. DEV. = 9.9 DEGREES REMARK 500 TYR B 78 CB - CG - CD2 ANGL. DEV. = 3.6 DEGREES REMARK 500 ASN B 98 CB - CA - C ANGL. DEV. = -12.7 DEGREES REMARK 500 ASP B 99 CB - CG - OD1 ANGL. DEV. = 6.4 DEGREES REMARK 500 ARG B 103 NE - CZ - NH1 ANGL. DEV. = 5.0 DEGREES REMARK 500 SER B 117 N - CA - CB ANGL. DEV. = -9.4 DEGREES REMARK 500 THR B 119 CA - CB - OG1 ANGL. DEV. = -13.9 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 PRO A 2 176.63 -23.70 REMARK 500 LYS A 9 29.54 -159.18 REMARK 500 CYS A 10 84.80 39.39 REMARK 500 ASP A 38 38.91 -82.56 REMARK 500 HIS A 90 -179.95 -170.50 REMARK 500 PRO A 125 -174.23 -54.32 REMARK 500 LYS A 126 147.97 130.73 REMARK 500 PRO B 2 -151.97 -114.66 REMARK 500 THR B 3 -157.67 -175.23 REMARK 500 THR B 5 53.74 -61.54 REMARK 500 SER B 8 -137.53 -130.88 REMARK 500 CYS B 10 74.02 67.77 REMARK 500 PHE B 44 -51.00 -127.27 REMARK 500 PRO B 125 -156.72 -84.70 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG B 103 0.17 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 THR A 5 21.0 L L OUTSIDE RANGE REMARK 500 CYS A 10 24.6 L L OUTSIDE RANGE REMARK 500 ASP A 39 23.2 L L OUTSIDE RANGE REMARK 500 GLU A 62 23.6 L L OUTSIDE RANGE REMARK 500 TYR A 116 24.7 L L OUTSIDE RANGE REMARK 500 GLU A 127 22.9 L L OUTSIDE RANGE REMARK 500 THR B 5 23.1 L L OUTSIDE RANGE REMARK 500 GLU B 7 21.8 L L OUTSIDE RANGE REMARK 500 ARG B 103 24.6 L L OUTSIDE RANGE REMARK 500 LYS B 126 19.7 L L OUTSIDE RANGE REMARK 500 GLU B 127 18.9 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL

REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 274 DISTANCE = 5.80 ANGSTROMS

REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: A1 REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: NULL REMARK 800 REMARK 800 SITE_IDENTIFIER: B1 REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: NULL REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 9CR B 130 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 9CR A 131

REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2PAB RELATED DB: PDB REMARK 900 NATIVE TRANSTHYRETIN

DBREF 1TYR A 1 127 UNP P02766 TTHY_HUMAN 21 147 DBREF 1TYR 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 9CR B 130 22 HET 9CR A 131 22

HETNAM 9CR (9CIS)-RETINOIC ACID

FORMUL 3 9CR 2(C20 H28 O2) FORMUL 5 HOH *97(H2 O)

HELIX 1 AA THR A 75 GLY A 83 1 9 HELIX 2 AB THR B 75 GLY B 83 1 9

SHEET 1 IA 4 GLY A 53 LEU A 55 0 SHEET 2 IA 4 PRO A 11 ALA A 19 -1 O VAL A 14 N LEU A 55 SHEET 3 IA 4 TYR A 105 SER A 112 1 N ILE A 107 O MET A 13 SHEET 4 IA 4 TYR A 114 VAL A 121 -1 N THR A 119 O ALA A 108 SHEET 1 IB 4 GLY B 53 LEU B 55 0 SHEET 2 IB 4 PRO B 11 ALA B 19 -1 O VAL B 14 N LEU B 55 SHEET 3 IB 4 TYR B 105 SER B 112 1 N ILE B 107 O MET B 13 SHEET 4 IB 4 TYR B 114 VAL B 121 -1 N THR B 119 O ALA B 108 SHEET 1 X1A 4 GLU A 42 GLU A 42 0 SHEET 2 X1A 4 VAL A 28 LYS A 35 -1 O ARG A 34 N GLU A 42 SHEET 3 X1A 4 GLY A 67 ASP A 74 -1 N GLU A 72 O HIS A 31 SHEET 4 X1A 4 ALA A 91 ALA A 97 -1 N VAL A 93 O VAL A 71 SHEET 1 X2A 4 ALA A 45 THR A 49 0 SHEET 2 X2A 4 VAL A 28 LYS A 35 -1 O VAL A 30 N GLY A 47 SHEET 3 X2A 4 GLY A 67 ASP A 74 -1 N GLU A 72 O HIS A 31 SHEET 4 X2A 4 ALA A 91 ALA A 97 -1 N VAL A 93 O VAL A 71 SHEET 1 X1B 4 GLU B 42 GLU B 42 0 SHEET 2 X1B 4 VAL B 28 LYS B 35 -1 O ARG B 34 N GLU B 42 SHEET 3 X1B 4 GLY B 67 ASP B 74 -1 N GLU B 72 O HIS B 31 SHEET 4 X1B 4 ALA B 91 ALA B 97 -1 N VAL B 93 O VAL B 71 SHEET 1 X2B 4 ALA B 45 THR B 49 0 SHEET 2 X2B 4 VAL B 28 LYS B 35 -1 O VAL B 30 N GLY B 47 SHEET 3 X2B 4 GLY B 67 ASP B 74 -1 N GLU B 72 O HIS B 31 SHEET 4 X2B 4 ALA B 91 ALA B 97 -1 N VAL B 93 O VAL B 71

LINK OXT GLU B 127 O1 9CR B 130 1555 1555 2.03

SITE 1 A1 13 LYS A 15 VAL A 16 LEU A 17 THR A 106 SITE 2 A1 13 ILE A 107 ALA A 108 ALA A 109 LEU A 110 SITE 3 A1 13 SER A 117 THR A 118 THR A 119 ALA A 120 SITE 4 A1 13 VAL A 121 SITE 1 B1 13 LYS B 15 VAL B 16 LEU B 17 THR B 106 SITE 2 B1 13 ILE B 107 ALA B 108 ALA B 109 LEU B 110 SITE 3 B1 13 SER B 117 THR B 118 THR B 119 ALA B 120 SITE 4 B1 13 VAL B 121 SITE 1 AC1 11 LYS B 15 LEU B 17 ALA B 108 LEU B 110 SITE 2 AC1 11 SER B 117 THR B 119 VAL B 121 GLU B 127 SITE 3 AC1 11 HOH B 260 HOH B 274 HOH B 281 SITE 1 AC2 10 LYS A 15 LEU A 17 THR A 106 ALA A 108 SITE 2 AC2 10 ALA A 109 LEU A 110 SER A 117 THR A 119 SITE 3 AC2 10 VAL A 121 HOH A 220

CRYST1 43.800 86.220 65.780 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 0.022831 0.000000 0.000000 0.00000

SCALE2 0.000000 0.011598 0.000000 0.00000

SCALE3 0.000000 0.000000 0.015202 0.00000