HEADER TRANSCRIPTION 05-DEC-16 5MKU TITLE CRYSTAL STRUCTURE OF THE RETINOID X RECEPTOR ALPHA IN COMPLEX WITH TITLE 2 SYNTHETIC HONOKIOL DERIVATIVE 4 AND A FRAGMENT OF THE TIF2 CO- TITLE 3 ACTIVATOR. COMPND MOL_ID: 1; COMPND 2 MOLECULE: RETINOIC ACID RECEPTOR RXR-ALPHA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NUCLEAR RECEPTOR SUBFAMILY 2 GROUP B MEMBER 1,RETINOID X COMPND 5 RECEPTOR ALPHA; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: HIS-LYS-ILE-LEU-HIS-ARG-LEU-LEU-GLN-ASP-SER; COMPND 9 CHAIN: B; COMPND 10 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: RXRA, NR2B1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606 KEYWDS RXR TIF2 HONOKIOL, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR S.A.ANDREI,L.BRUNSVELD,M.SCHEEPSTRA,C.OTTMANN REVDAT 3 17-JAN-24 5MKU 1 REMARK REVDAT 2 10-AUG-22 5MKU 1 REMARK ATOM REVDAT 1 08-NOV-17 5MKU 0 JRNL AUTH M.SCHEEPSTRA,S.A.ANDREI,R.M.J.M.DE VRIES,F.A.MEIJER,J.N.MA, JRNL AUTH 2 E.S.BURSTEIN,R.OLSSON,C.OTTMANN,L.G.MILROY,L.BRUNSVELD JRNL TITL LIGAND DEPENDENT SWITCH FROM RXR HOMO- TO RXR-NURR1 JRNL TITL 2 HETERODIMERIZATION. JRNL REF ACS CHEM NEUROSCI V. 8 2065 2017 JRNL REFN ESSN 1948-7193 JRNL PMID 28691794 JRNL DOI 10.1021/ACSCHEMNEURO.7B00216 REMARK 2 REMARK 2 RESOLUTION. 1.78 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.78 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.42 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 27456 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.149 REMARK 3 R VALUE (WORKING SET) : 0.148 REMARK 3 FREE R VALUE : 0.177 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1319 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 25.4194 - 3.6993 1.00 3060 152 0.1439 0.1668 REMARK 3 2 3.6993 - 2.9376 1.00 2940 149 0.1385 0.1628 REMARK 3 3 2.9376 - 2.5667 1.00 2937 124 0.1514 0.1729 REMARK 3 4 2.5667 - 2.3322 1.00 2918 142 0.1502 0.1827 REMARK 3 5 2.3322 - 2.1651 1.00 2881 149 0.1327 0.1689 REMARK 3 6 2.1651 - 2.0375 1.00 2865 168 0.1374 0.1802 REMARK 3 7 2.0375 - 1.9355 1.00 2875 141 0.1572 0.2207 REMARK 3 8 1.9355 - 1.8513 1.00 2883 140 0.1764 0.1814 REMARK 3 9 1.8513 - 1.7800 0.96 2778 154 0.1936 0.2269 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.760 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.62 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.67 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 : 0.018 1933 REMARK 3 ANGLE : 1.358 2633 REMARK 3 CHIRALITY : 0.230 297 REMARK 3 PLANARITY : 0.009 359 REMARK 3 DIHEDRAL : 16.644 1194 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 229 THROUGH 263 ) REMARK 3 ORIGIN FOR THE GROUP (A): 21.2620 0.1544 -5.7793 REMARK 3 T TENSOR REMARK 3 T11: 0.1572 T22: 0.1340 REMARK 3 T33: 0.1412 T12: -0.0522 REMARK 3 T13: -0.0285 T23: -0.0212 REMARK 3 L TENSOR REMARK 3 L11: 3.6071 L22: 4.8865 REMARK 3 L33: 1.7304 L12: -2.7909 REMARK 3 L13: -1.1814 L23: 1.2079 REMARK 3 S TENSOR REMARK 3 S11: -0.0650 S12: -0.1679 S13: 0.3882 REMARK 3 S21: 0.0900 S22: 0.1753 S23: -0.3741 REMARK 3 S31: -0.2931 S32: 0.3317 S33: -0.2233 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 264 THROUGH 293 ) REMARK 3 ORIGIN FOR THE GROUP (A): 27.6887 -10.6656 -3.4613 REMARK 3 T TENSOR REMARK 3 T11: 0.0884 T22: 0.1694 REMARK 3 T33: 0.1279 T12: -0.0274 REMARK 3 T13: -0.0206 T23: -0.0077 REMARK 3 L TENSOR REMARK 3 L11: 2.1267 L22: 1.6180 REMARK 3 L33: 1.1860 L12: -0.8994 REMARK 3 L13: -0.4705 L23: 0.2817 REMARK 3 S TENSOR REMARK 3 S11: 0.0283 S12: -0.1317 S13: 0.2984 REMARK 3 S21: 0.0672 S22: 0.0644 S23: -0.2941 REMARK 3 S31: -0.1334 S32: 0.2912 S33: -0.0896 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 294 THROUGH 342 ) REMARK 3 ORIGIN FOR THE GROUP (A): 27.1410 -15.1456 -15.0050 REMARK 3 T TENSOR REMARK 3 T11: 0.0651 T22: 0.1336 REMARK 3 T33: 0.1076 T12: 0.0033 REMARK 3 T13: 0.0059 T23: -0.0099 REMARK 3 L TENSOR REMARK 3 L11: 1.4081 L22: 1.3864 REMARK 3 L33: 0.6362 L12: -0.3253 REMARK 3 L13: -0.1039 L23: 0.1979 REMARK 3 S TENSOR REMARK 3 S11: 0.0331 S12: 0.0966 S13: -0.0205 REMARK 3 S21: -0.1831 S22: -0.0158 S23: -0.1817 REMARK 3 S31: 0.0045 S32: 0.2500 S33: 0.0026 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 343 THROUGH 375 ) REMARK 3 ORIGIN FOR THE GROUP (A): 18.9006 -9.4121 -19.3796 REMARK 3 T TENSOR REMARK 3 T11: 0.0747 T22: 0.0839 REMARK 3 T33: 0.0526 T12: -0.0040 REMARK 3 T13: 0.0018 T23: 0.0148 REMARK 3 L TENSOR REMARK 3 L11: 1.1847 L22: 1.3299 REMARK 3 L33: 1.2476 L12: -0.2362 REMARK 3 L13: -0.4231 L23: 0.1774 REMARK 3 S TENSOR REMARK 3 S11: 0.0204 S12: 0.0770 S13: 0.0619 REMARK 3 S21: -0.1945 S22: -0.0065 S23: -0.0363 REMARK 3 S31: -0.1266 S32: 0.1553 S33: -0.0035 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 376 THROUGH 442 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.6280 -12.0925 -10.0804 REMARK 3 T TENSOR REMARK 3 T11: 0.0454 T22: 0.0520 REMARK 3 T33: 0.0622 T12: -0.0112 REMARK 3 T13: 0.0031 T23: -0.0039 REMARK 3 L TENSOR REMARK 3 L11: 1.0047 L22: 0.5242 REMARK 3 L33: 0.9829 L12: -0.3589 REMARK 3 L13: -0.0324 L23: 0.0949 REMARK 3 S TENSOR REMARK 3 S11: -0.0164 S12: -0.0260 S13: -0.0137 REMARK 3 S21: 0.0021 S22: 0.0114 S23: 0.0074 REMARK 3 S31: -0.0075 S32: 0.0306 S33: 0.0085 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 443 THROUGH 458 ) REMARK 3 ORIGIN FOR THE GROUP (A): 33.3407 -23.9505 -3.7922 REMARK 3 T TENSOR REMARK 3 T11: 0.1850 T22: 0.2177 REMARK 3 T33: 0.1708 T12: 0.0512 REMARK 3 T13: -0.0312 T23: -0.0293 REMARK 3 L TENSOR REMARK 3 L11: 4.3507 L22: 4.8926 REMARK 3 L33: 2.3221 L12: -2.6290 REMARK 3 L13: -1.3332 L23: 2.4875 REMARK 3 S TENSOR REMARK 3 S11: -0.0454 S12: -0.0461 S13: -0.3769 REMARK 3 S21: 0.3392 S22: 0.1593 S23: -0.2036 REMARK 3 S31: 0.5051 S32: 0.3744 S33: -0.0822 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 473 THROUGH 481 ) REMARK 3 ORIGIN FOR THE GROUP (A): 29.6639 -14.2745 7.6523 REMARK 3 T TENSOR REMARK 3 T11: 0.1275 T22: 0.2975 REMARK 3 T33: 0.1411 T12: 0.0025 REMARK 3 T13: -0.0531 T23: -0.0190 REMARK 3 L TENSOR REMARK 3 L11: 6.9794 L22: 4.1887 REMARK 3 L33: 5.0754 L12: -2.5426 REMARK 3 L13: 0.4865 L23: -0.1254 REMARK 3 S TENSOR REMARK 3 S11: -0.0485 S12: -0.3741 S13: 0.2232 REMARK 3 S21: 0.4614 S22: 0.1508 S23: -0.4936 REMARK 3 S31: -0.0155 S32: 0.3135 S33: -0.0422 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 5MKU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-DEC-16. REMARK 100 THE DEPOSITION ID IS D_1200002623. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JAN-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-003 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.541870 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 200K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM 7.2.0 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.29 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27516 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.780 REMARK 200 RESOLUTION RANGE LOW (A) : 25.420 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 8.600 REMARK 200 R MERGE (I) : 0.12200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.78 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.82 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.1 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : 0.68500 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: PHASER 2.6.0 REMARK 200 STARTING MODEL: 5EC9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M PIPES, PH 7.0, 0.1M NACL, 22% PEG REMARK 280 2K MME, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.16067 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 27.08033 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 27.08033 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 54.16067 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 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 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -27.08033 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 HOH A 645 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 738 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 900 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 906 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 GLU A 243 REMARK 465 PRO A 244 REMARK 465 LYS A 245 REMARK 465 THR A 246 REMARK 465 GLU A 247 REMARK 465 THR A 248 REMARK 465 TYR A 249 REMARK 465 VAL A 250 REMARK 465 GLU A 251 REMARK 465 ALA A 252 REMARK 465 ASN A 253 REMARK 465 MET A 254 REMARK 465 GLY A 255 REMARK 465 LEU A 256 REMARK 465 ASN A 257 REMARK 465 PRO A 258 REMARK 465 SER A 259 REMARK 465 SER A 260 REMARK 465 PRO A 261 REMARK 465 ASN A 262 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 767 O HOH A 772 1.82 REMARK 500 O HOH A 605 O HOH A 746 1.90 REMARK 500 O HOH A 751 O HOH A 775 1.98 REMARK 500 O HOH A 835 O HOH A 879 2.01 REMARK 500 O HOH A 794 O HOH A 876 2.04 REMARK 500 O HOH A 848 O HOH A 879 2.05 REMARK 500 O HOH A 813 O HOH A 825 2.10 REMARK 500 O HOH A 846 O HOH A 875 2.10 REMARK 500 NH2 ARG A 234 OE1 GLU A 237 2.12 REMARK 500 O HOH A 835 O HOH A 848 2.16 REMARK 500 O HOH A 664 O HOH A 870 2.17 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 605 O HOH A 782 5554 1.96 REMARK 500 O HOH A 817 O HOH B 504 2544 2.04 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 ARG A 371 NE - CZ - NH1 ANGL. DEV. = 4.9 DEGREES REMARK 500 ARG A 371 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 VAL A 374 CG1 - CB - CG2 ANGL. DEV. = 11.7 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 HIS A 288 -9.84 81.97 REMARK 500 LEU A 353 -65.60 -122.13 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 902 DISTANCE = 6.09 ANGSTROMS REMARK 525 HOH A 903 DISTANCE = 6.59 ANGSTROMS REMARK 525 HOH A 904 DISTANCE = 6.68 ANGSTROMS REMARK 525 HOH A 905 DISTANCE = 6.99 ANGSTROMS REMARK 525 HOH A 906 DISTANCE = 7.17 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue J57 A 501 DBREF 5MKU A 229 456 UNP P19793 RXRA_HUMAN 229 456 DBREF 5MKU B 472 482 PDB 5MKU 5MKU 472 482 SEQRES 1 A 228 ASP MET PRO VAL GLU ARG ILE LEU GLU ALA GLU LEU ALA SEQRES 2 A 228 VAL GLU PRO LYS THR GLU THR TYR VAL GLU ALA ASN MET SEQRES 3 A 228 GLY LEU ASN PRO SER SER PRO ASN ASP PRO VAL THR ASN SEQRES 4 A 228 ILE CYS GLN ALA ALA ASP LYS GLN LEU PHE THR LEU VAL SEQRES 5 A 228 GLU TRP ALA LYS ARG ILE PRO HIS PHE SER GLU LEU PRO SEQRES 6 A 228 LEU ASP ASP GLN VAL ILE LEU LEU ARG ALA GLY TRP ASN SEQRES 7 A 228 GLU LEU LEU ILE ALA SER PHE SER HIS ARG SER ILE ALA SEQRES 8 A 228 VAL LYS ASP GLY ILE LEU LEU ALA THR GLY LEU HIS VAL SEQRES 9 A 228 HIS ARG ASN SER ALA HIS SER ALA GLY VAL GLY ALA ILE SEQRES 10 A 228 PHE ASP ARG VAL LEU THR GLU LEU VAL SER LYS MET ARG SEQRES 11 A 228 ASP MET GLN MET ASP LYS THR GLU LEU GLY CYS LEU ARG SEQRES 12 A 228 ALA ILE VAL LEU PHE ASN PRO ASP SER LYS GLY LEU SER SEQRES 13 A 228 ASN PRO ALA GLU VAL GLU ALA LEU ARG GLU LYS VAL TYR SEQRES 14 A 228 ALA SER LEU GLU ALA TYR CYS LYS HIS LYS TYR PRO GLU SEQRES 15 A 228 GLN PRO GLY ARG PHE ALA LYS LEU LEU LEU ARG LEU PRO SEQRES 16 A 228 ALA LEU ARG SER ILE GLY LEU LYS CYS LEU GLU HIS LEU SEQRES 17 A 228 PHE PHE PHE LYS LEU ILE GLY ASP THR PRO ILE ASP THR SEQRES 18 A 228 PHE LEU MET GLU MET LEU GLU SEQRES 1 B 11 HIS LYS ILE LEU HIS ARG LEU LEU GLN ASP SER HET J57 A 501 39 HETNAM J57 (~{E})-3-[4-OXIDANYL-3-(3-PROPAN-2-YLPHENYL) HETNAM 2 J57 PHENYL]PROP-2-ENOIC ACID FORMUL 3 J57 C18 H18 O3 FORMUL 4 HOH *321(H2 O) HELIX 1 AA1 PRO A 231 VAL A 242 1 12 HELIX 2 AA2 PRO A 264 ARG A 285 1 22 HELIX 3 AA3 HIS A 288 LEU A 292 5 5 HELIX 4 AA4 PRO A 293 SER A 317 1 25 HELIX 5 AA5 ILE A 318 VAL A 320 5 3 HELIX 6 AA6 HIS A 333 ALA A 340 1 8 HELIX 7 AA7 VAL A 342 LEU A 353 1 12 HELIX 8 AA8 LEU A 353 GLN A 361 1 9 HELIX 9 AA9 ASP A 363 PHE A 376 1 14 HELIX 10 AB1 ASN A 385 TYR A 408 1 24 HELIX 11 AB2 GLY A 413 LEU A 420 1 8 HELIX 12 AB3 ARG A 421 ILE A 442 1 22 HELIX 13 AB4 THR A 449 LEU A 455 1 7 HELIX 14 AB5 LYS B 473 LEU B 479 1 7 SHEET 1 AA1 2 ILE A 324 LEU A 325 0 SHEET 2 AA1 2 HIS A 331 VAL A 332 -1 O VAL A 332 N ILE A 324 SITE 1 AC1 12 ILE A 268 ALA A 271 ALA A 272 GLN A 275 SITE 2 AC1 12 ASN A 306 PHE A 313 ARG A 316 LEU A 326 SITE 3 AC1 12 ALA A 327 CYS A 432 LEU A 436 HOH A 635 CRYST1 77.650 77.650 81.241 90.00 90.00 120.00 P 32 2 1 6 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 0.012878 0.007435 0.000000 0.00000 SCALE2 0.000000 0.014871 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012309 0.00000