HEADER TRANSPORT PROTEIN 22-FEB-15 4YDM TITLE HIGH RESOLUTION CRYSTAL STRUCTURE OF HUMAN TRANSTHYRETIN BOUND TO TITLE 2 LIGAND AND CONJUGATES OF 3-(5-(3,5-DICHLORO-4-HYDROXYPHENYL)-1,3,4- TITLE 3 OXADIAZOL-2-YL)PHENYL FLUOROSULFATE 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 GENE: TTR, PALB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: EPICURIAN GOLD; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PMMHA KEYWDS TRANSTHYRETIN, HORMONE TRANSPORT PROTEIN, THYROXINE, RETINOL, KEYWDS 2 TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.CONNELLY,N.C.BRADBURY REVDAT 2 01-NOV-17 4YDM 1 SOURCE REMARK REVDAT 1 15-JUL-15 4YDM 0 JRNL AUTH A.BARANCZAK,Y.LIU,S.CONNELLY,W.G.DU,E.R.GREINER, JRNL AUTH 2 J.C.GENEREUX,R.L.WISEMAN,Y.S.EISELE,N.C.BRADBURY,J.DONG, JRNL AUTH 3 L.NOODLEMAN,K.B.SHARPLESS,I.A.WILSON,S.E.ENCALADA,J.W.KELLY JRNL TITL A FLUOROGENIC ARYL FLUOROSULFATE FOR INTRAORGANELLAR JRNL TITL 2 TRANSTHYRETIN IMAGING IN LIVING CELLS AND IN CAENORHABDITIS JRNL TITL 3 ELEGANS. JRNL REF J.AM.CHEM.SOC. V. 137 7404 2015 JRNL REFN ESSN 1520-5126 JRNL PMID 26051248 JRNL DOI 10.1021/JACS.5B03042 REMARK 2 REMARK 2 RESOLUTION. 1.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 63.54 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 61174 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.147 REMARK 3 R VALUE (WORKING SET) : 0.146 REMARK 3 FREE R VALUE : 0.172 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3263 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.25 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.28 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4141 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.73 REMARK 3 BIN R VALUE (WORKING SET) : 0.2300 REMARK 3 BIN FREE R VALUE SET COUNT : 219 REMARK 3 BIN FREE R VALUE : 0.2180 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1793 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 42 REMARK 3 SOLVENT ATOMS : 197 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.42 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.94000 REMARK 3 B22 (A**2) : 0.85000 REMARK 3 B33 (A**2) : 0.08000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.042 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.041 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.026 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.338 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.977 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.970 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2042 ; 0.015 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 1859 ; 0.000 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2822 ; 1.738 ; 1.985 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4332 ; 2.970 ; 3.002 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 274 ; 6.095 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 88 ;31.893 ;24.091 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 314 ;14.080 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;19.002 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 312 ; 0.101 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2344 ; 0.011 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 460 ; 0.014 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 977 ; 2.086 ; 1.627 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 976 ; 2.024 ; 1.623 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1233 ; 2.692 ; 2.444 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1234 ; 2.707 ; 2.447 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1065 ; 3.693 ; 2.121 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1066 ; 3.692 ; 2.120 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1569 ; 4.146 ; 3.017 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2344 ; 7.438 ;15.858 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2345 ; 7.437 ;15.858 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 3901 ; 6.560 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 58 ;59.370 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 3966 ;13.420 ; 5.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 4YDM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-FEB-15. REMARK 100 THE DEPOSITION ID IS D_1000207272. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JAN-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL11-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97945 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.15 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 64492 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.250 REMARK 200 RESOLUTION RANGE LOW (A) : 38.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.02900 REMARK 200 FOR THE DATA SET : 25.5000 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) : 1.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.8 REMARK 200 DATA REDUNDANCY IN SHELL : 6.20 REMARK 200 R MERGE FOR SHELL (I) : 0.49800 REMARK 200 R SYM FOR SHELL (I) : 0.49800 REMARK 200 FOR SHELL : 1.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 2QGB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: THE WT-TTR WAS CONCENTRATED TO 4 MG/ML REMARK 280 IN 10 MM NAPI, 100 MM KCL, AT PH 7.6 AND CO-CRYSTALLIZED AT ROOM REMARK 280 TEMPERATURE USING THE VAPOR-DIFFUSION SITTING DROP METHOD. REMARK 280 CRYSTALS WERE GROWN FROM 1.395 M SODIUM CITRATE, 3.5% V/V REMARK 280 GLYCEROL AT PH 5.5. THE CRYSTALS WERE FROZEN USING A CRYO- REMARK 280 PROTECTANT SOLUTION OF 1.395 M SODIUM CITRATE, PH 5.5, REMARK 280 CONTAINING 10% V/V GLYCEROL, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K 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 21.35450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.71000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.35450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.71000 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 300 REMARK: TETRAMER CONFIRMED BY BY SIZE EXCLUSION CHROMATOGRAPHY 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 TOTAL BURIED SURFACE AREA: 6330 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19210 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 15.3 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 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 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 CAU 4AJ A 201 LIES ON A SPECIAL POSITION. REMARK 375 CAR 4AJ A 201 LIES ON A SPECIAL POSITION. REMARK 375 CAS 4AJ A 201 LIES ON A SPECIAL POSITION. REMARK 375 OAB 4AJ A 201 LIES ON A SPECIAL POSITION. REMARK 375 CAE 4AJ B 201 LIES ON A SPECIAL POSITION. REMARK 375 CAS 4AJ B 201 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 305 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 OE1 GLU A 92 OE1 GLU B 92 2.00 REMARK 500 O HOH A 362 O HOH A 394 2.13 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 ASP A 99 O HOH A 394 4545 2.10 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 VAL A 14 C 4AK A 15 N 0.167 REMARK 500 VAL A 14 C 4AK A 15 N 0.173 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 B 102 CB - CA - C ANGL. DEV. = -19.3 DEGREES 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 A 397 DISTANCE = 5.87 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 4AJ A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 4AJ B 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4YDN RELATED DB: PDB DBREF 4YDM A 1 127 UNP P02766 TTHY_HUMAN 21 147 DBREF 4YDM 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 4AK 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 4AK 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 MODRES 4YDM 4AK A 15 LYS MODIFIED RESIDUE MODRES 4YDM 4AK B 15 LYS MODIFIED RESIDUE HET 4AK A 15 22 HET 4AK B 15 22 HET 4AJ A 201 21 HET 4AJ B 201 21 HETNAM 4AK N~6~-SULFO-L-LYSINE HETNAM 4AJ 2,6-DICHLORO-4-[5-(3-HYDROXYPHENYL)-1,3,4-OXADIAZOL-2- HETNAM 2 4AJ YL]PHENOL FORMUL 1 4AK 2(C6 H14 N2 O5 S) FORMUL 3 4AJ 2(C14 H8 CL2 N2 O3) FORMUL 5 HOH *197(H2 O) HELIX 1 AA1 ASP A 74 LEU A 82 1 9 HELIX 2 AA2 ASP B 74 LEU B 82 1 9 SHEET 1 AA1 8 SER A 23 PRO A 24 0 SHEET 2 AA1 8 LEU A 12 ASP A 18 -1 N ASP A 18 O SER A 23 SHEET 3 AA1 8 ARG A 104 SER A 112 1 O LEU A 111 N LEU A 17 SHEET 4 AA1 8 SER A 115 THR A 123 -1 O SER A 115 N SER A 112 SHEET 5 AA1 8 SER B 115 THR B 123 -1 O THR B 118 N TYR A 116 SHEET 6 AA1 8 ARG B 104 SER B 112 -1 N SER B 112 O SER B 115 SHEET 7 AA1 8 LEU B 12 ASP B 18 1 N MET B 13 O ILE B 107 SHEET 8 AA1 8 SER B 23 PRO B 24 -1 O SER B 23 N ASP B 18 SHEET 1 AA2 8 GLU A 54 LEU A 55 0 SHEET 2 AA2 8 LEU A 12 ASP A 18 -1 N VAL A 14 O LEU A 55 SHEET 3 AA2 8 ARG A 104 SER A 112 1 O LEU A 111 N LEU A 17 SHEET 4 AA2 8 SER A 115 THR A 123 -1 O SER A 115 N SER A 112 SHEET 5 AA2 8 SER B 115 THR B 123 -1 O THR B 118 N TYR A 116 SHEET 6 AA2 8 ARG B 104 SER B 112 -1 N SER B 112 O SER B 115 SHEET 7 AA2 8 LEU B 12 ASP B 18 1 N MET B 13 O ILE B 107 SHEET 8 AA2 8 GLU B 54 LEU B 55 -1 O LEU B 55 N VAL B 14 SHEET 1 AA3 8 TRP A 41 LYS A 48 0 SHEET 2 AA3 8 ALA A 29 LYS A 35 -1 N VAL A 32 O ALA A 45 SHEET 3 AA3 8 GLY A 67 ILE A 73 -1 O GLU A 72 N HIS A 31 SHEET 4 AA3 8 HIS A 88 ALA A 97 -1 O ALA A 91 N ILE A 73 SHEET 5 AA3 8 HIS B 88 ALA B 97 -1 O VAL B 94 N GLU A 89 SHEET 6 AA3 8 GLY B 67 ILE B 73 -1 N ILE B 73 O ALA B 91 SHEET 7 AA3 8 ALA B 29 LYS B 35 -1 N HIS B 31 O GLU B 72 SHEET 8 AA3 8 TRP B 41 LYS B 48 -1 O ALA B 45 N VAL B 32 LINK C VAL A 14 N A4AK A 15 1555 1555 1.50 LINK C VAL A 14 N B4AK A 15 1555 1555 1.51 LINK C A4AK A 15 N VAL A 16 1555 1555 1.33 LINK C B4AK A 15 N VAL A 16 1555 1555 1.33 LINK C VAL B 14 N A4AK B 15 1555 1555 1.32 LINK C VAL B 14 N B4AK B 15 1555 1555 1.33 LINK C A4AK B 15 N VAL B 16 1555 1555 1.28 LINK C B4AK B 15 N VAL B 16 1555 1555 1.25 SITE 1 AC1 7 4AK A 15 LEU A 17 THR A 106 ALA A 108 SITE 2 AC1 7 SER A 117 THR A 118 VAL A 121 SITE 1 AC2 9 4AK B 15 LEU B 17 THR B 106 ALA B 108 SITE 2 AC2 9 LEU B 110 SER B 117 THR B 118 THR B 119 SITE 3 AC2 9 HOH B 305 CRYST1 42.709 85.420 63.537 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 0.023414 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011707 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015739 0.00000 MASTER 386 0 4 2 24 0 5 6 0 0 0 20 END