HEADER GENE REGULATION 17-FEB-21 7NKE TITLE CRYSTAL STRUCTURE OF HUMAN RXRALPHA LIGAND BINDING DOMAIN IN COMPLEX TITLE 2 WITH 2,4-DI-TERT-BUTYLPHENOL AND A COACTIVATOR FRAGMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: RETINOIC ACID RECEPTOR RXR-ALPHA; COMPND 3 CHAIN: A, C; 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: NUCLEAR RECEPTOR COACTIVATOR 2; COMPND 9 CHAIN: B, D; COMPND 10 SYNONYM: NCOA-2,CLASS E BASIC HELIX-LOOP-HELIX PROTEIN 75,BHLHE75, COMPND 11 TRANSCRIPTIONAL INTERMEDIARY FACTOR 2,HTIF2; COMPND 12 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 BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; 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 NUCLEAR RECEPTOR, COMPLEX, LIGAND, COACTIVATOR, GENE REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR C.CARIVENC,W.BOURGUET REVDAT 3 07-FEB-24 7NKE 1 REMARK REVDAT 2 15-MAR-23 7NKE 1 JRNL REVDAT 1 02-MAR-22 7NKE 0 JRNL AUTH X.M.REN,R.C.CHANG,Y.HUANG,A.AMORIM AMATO,C.CARIVENC, JRNL AUTH 2 M.GRIMALDI,Y.KUO,P.BALAGUER,W.BOURGUET,B.BLUMBERG JRNL TITL 2,4-DI-TERT-BUTYLPHENOL INDUCES ADIPOGENESIS IN HUMAN JRNL TITL 2 MESENCHYMAL STEM CELLS BY ACTIVATING RETINOID X RECEPTORS. JRNL REF ENDOCRINOLOGY V. 164 2023 JRNL REFN ISSN 0013-7227 JRNL PMID 36750942 JRNL DOI 10.1210/ENDOCR/BQAD021 REMARK 2 REMARK 2 RESOLUTION. 2.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 57.24 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 18581 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) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1141 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) : 2.35 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.41 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1388 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.66 REMARK 3 BIN R VALUE (WORKING SET) : 0.2060 REMARK 3 BIN FREE R VALUE SET COUNT : 76 REMARK 3 BIN FREE R VALUE : 0.2490 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3491 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 33 REMARK 3 SOLVENT ATOMS : 120 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.43 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.18000 REMARK 3 B22 (A**2) : 1.16000 REMARK 3 B33 (A**2) : 0.03000 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): 0.412 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.263 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.175 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.344 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.911 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3633 ; 0.014 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3609 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4930 ; 1.642 ; 2.001 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8264 ; 1.028 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 444 ; 5.551 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 153 ;33.037 ;23.725 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 636 ;15.174 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;22.010 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 561 ; 0.097 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3983 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 797 ; 0.002 ; 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): 1782 ; 2.963 ; 3.606 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1783 ; 2.963 ; 3.606 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2218 ; 4.502 ; 5.380 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2219 ; 4.501 ; 5.383 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1851 ; 3.529 ; 3.927 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1850 ; 3.527 ; 3.926 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2711 ; 5.363 ; 5.770 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4158 ; 6.949 ;28.482 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4125 ; 6.955 ;28.434 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL 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 7NKE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-FEB-21. REMARK 100 THE DEPOSITION ID IS D_1292114150. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-JAN-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID30B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.96546 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19758 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.350 REMARK 200 RESOLUTION RANGE LOW (A) : 57.250 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.48 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.45800 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: REFMAC REMARK 200 STARTING MODEL: 3E94 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350 0.2 M SODIUM FORMATE, REMARK 280 VAPOR DIFFUSION, TEMPERATURE 293K 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 31.35300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.41600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.65150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.41600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.35300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.65150 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 TOTAL BURIED SURFACE AREA: 4500 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18540 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 219 REMARK 465 SER A 220 REMARK 465 HIS A 221 REMARK 465 MET A 222 REMARK 465 THR A 223 REMARK 465 SER A 224 REMARK 465 SER A 225 REMARK 465 ALA A 226 REMARK 465 ASN A 227 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 PRO A 458 REMARK 465 HIS A 459 REMARK 465 GLN A 460 REMARK 465 MET A 461 REMARK 465 THR A 462 REMARK 465 LYS B 686 REMARK 465 SER B 697 REMARK 465 SER B 698 REMARK 465 GLY C 219 REMARK 465 SER C 220 REMARK 465 HIS C 221 REMARK 465 MET C 222 REMARK 465 THR C 223 REMARK 465 SER C 224 REMARK 465 SER C 225 REMARK 465 ALA C 226 REMARK 465 ASN C 227 REMARK 465 LYS C 245 REMARK 465 THR C 246 REMARK 465 GLU C 247 REMARK 465 THR C 248 REMARK 465 TYR C 249 REMARK 465 VAL C 250 REMARK 465 GLU C 251 REMARK 465 ALA C 252 REMARK 465 ASN C 253 REMARK 465 MET C 254 REMARK 465 GLY C 255 REMARK 465 LEU C 256 REMARK 465 ASN C 257 REMARK 465 PRO C 258 REMARK 465 SER C 259 REMARK 465 SER C 260 REMARK 465 PRO C 261 REMARK 465 PRO C 458 REMARK 465 HIS C 459 REMARK 465 GLN C 460 REMARK 465 MET C 461 REMARK 465 THR C 462 REMARK 465 LYS D 686 REMARK 465 SER D 697 REMARK 465 SER D 698 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 228 CG CD OE1 OE2 REMARK 470 ASP A 229 CG OD1 OD2 REMARK 470 ARG A 234 NE CZ NH1 NH2 REMARK 470 LYS A 321 CE NZ REMARK 470 LEU A 330 CD1 CD2 REMARK 470 LYS A 407 CE NZ REMARK 470 ILE A 442 CD1 REMARK 470 ASP A 444 CG OD1 OD2 REMARK 470 GLU A 456 CG CD OE1 OE2 REMARK 470 GLU C 228 CG CD OE1 OE2 REMARK 470 ARG C 234 NE CZ NH1 NH2 REMARK 470 ILE C 318 CD1 REMARK 470 LYS C 321 CG CD CE NZ REMARK 470 ILE C 324 CD1 REMARK 470 LEU C 325 CD1 CD2 REMARK 470 THR C 328 OG1 CG2 REMARK 470 GLN C 361 CD OE1 NE2 REMARK 470 LYS C 381 CG CD CE NZ REMARK 470 ILE C 442 CD1 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLU A 243 OE1 OE2 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 625 O HOH D 702 3645 2.19 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 243 CD GLU A 243 OE1 -0.086 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 ASP A 263 CB - CG - OD1 ANGL. DEV. = 6.5 DEGREES REMARK 500 ARG A 371 NE - CZ - NH1 ANGL. DEV. = 3.0 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 HIS A 288 -7.70 73.60 REMARK 500 HIS C 288 -7.54 73.77 REMARK 500 ASP C 322 58.79 -142.33 REMARK 500 LEU C 353 -73.11 -117.98 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 GLU A 243 0.11 SIDE CHAIN 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 UGW A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue UGW C 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMT C 502 DBREF 7NKE A 223 462 UNP P19793 RXRA_HUMAN 223 462 DBREF 7NKE B 686 698 UNP Q15596 NCOA2_HUMAN 686 698 DBREF 7NKE C 223 462 UNP P19793 RXRA_HUMAN 223 462 DBREF 7NKE D 686 698 UNP Q15596 NCOA2_HUMAN 686 698 SEQADV 7NKE GLY A 219 UNP P19793 EXPRESSION TAG SEQADV 7NKE SER A 220 UNP P19793 EXPRESSION TAG SEQADV 7NKE HIS A 221 UNP P19793 EXPRESSION TAG SEQADV 7NKE MET A 222 UNP P19793 EXPRESSION TAG SEQADV 7NKE GLY C 219 UNP P19793 EXPRESSION TAG SEQADV 7NKE SER C 220 UNP P19793 EXPRESSION TAG SEQADV 7NKE HIS C 221 UNP P19793 EXPRESSION TAG SEQADV 7NKE MET C 222 UNP P19793 EXPRESSION TAG SEQRES 1 A 244 GLY SER HIS MET THR SER SER ALA ASN GLU ASP MET PRO SEQRES 2 A 244 VAL GLU ARG ILE LEU GLU ALA GLU LEU ALA VAL GLU PRO SEQRES 3 A 244 LYS THR GLU THR TYR VAL GLU ALA ASN MET GLY LEU ASN SEQRES 4 A 244 PRO SER SER PRO ASN ASP PRO VAL THR ASN ILE CYS GLN SEQRES 5 A 244 ALA ALA ASP LYS GLN LEU PHE THR LEU VAL GLU TRP ALA SEQRES 6 A 244 LYS ARG ILE PRO HIS PHE SER GLU LEU PRO LEU ASP ASP SEQRES 7 A 244 GLN VAL ILE LEU LEU ARG ALA GLY TRP ASN GLU LEU LEU SEQRES 8 A 244 ILE ALA SER PHE SER HIS ARG SER ILE ALA VAL LYS ASP SEQRES 9 A 244 GLY ILE LEU LEU ALA THR GLY LEU HIS VAL HIS ARG ASN SEQRES 10 A 244 SER ALA HIS SER ALA GLY VAL GLY ALA ILE PHE ASP ARG SEQRES 11 A 244 VAL LEU THR GLU LEU VAL SER LYS MET ARG ASP MET GLN SEQRES 12 A 244 MET ASP LYS THR GLU LEU GLY CYS LEU ARG ALA ILE VAL SEQRES 13 A 244 LEU PHE ASN PRO ASP SER LYS GLY LEU SER ASN PRO ALA SEQRES 14 A 244 GLU VAL GLU ALA LEU ARG GLU LYS VAL TYR ALA SER LEU SEQRES 15 A 244 GLU ALA TYR CYS LYS HIS LYS TYR PRO GLU GLN PRO GLY SEQRES 16 A 244 ARG PHE ALA LYS LEU LEU LEU ARG LEU PRO ALA LEU ARG SEQRES 17 A 244 SER ILE GLY LEU LYS CYS LEU GLU HIS LEU PHE PHE PHE SEQRES 18 A 244 LYS LEU ILE GLY ASP THR PRO ILE ASP THR PHE LEU MET SEQRES 19 A 244 GLU MET LEU GLU ALA PRO HIS GLN MET THR SEQRES 1 B 13 LYS HIS LYS ILE LEU HIS ARG LEU LEU GLN ASP SER SER SEQRES 1 C 244 GLY SER HIS MET THR SER SER ALA ASN GLU ASP MET PRO SEQRES 2 C 244 VAL GLU ARG ILE LEU GLU ALA GLU LEU ALA VAL GLU PRO SEQRES 3 C 244 LYS THR GLU THR TYR VAL GLU ALA ASN MET GLY LEU ASN SEQRES 4 C 244 PRO SER SER PRO ASN ASP PRO VAL THR ASN ILE CYS GLN SEQRES 5 C 244 ALA ALA ASP LYS GLN LEU PHE THR LEU VAL GLU TRP ALA SEQRES 6 C 244 LYS ARG ILE PRO HIS PHE SER GLU LEU PRO LEU ASP ASP SEQRES 7 C 244 GLN VAL ILE LEU LEU ARG ALA GLY TRP ASN GLU LEU LEU SEQRES 8 C 244 ILE ALA SER PHE SER HIS ARG SER ILE ALA VAL LYS ASP SEQRES 9 C 244 GLY ILE LEU LEU ALA THR GLY LEU HIS VAL HIS ARG ASN SEQRES 10 C 244 SER ALA HIS SER ALA GLY VAL GLY ALA ILE PHE ASP ARG SEQRES 11 C 244 VAL LEU THR GLU LEU VAL SER LYS MET ARG ASP MET GLN SEQRES 12 C 244 MET ASP LYS THR GLU LEU GLY CYS LEU ARG ALA ILE VAL SEQRES 13 C 244 LEU PHE ASN PRO ASP SER LYS GLY LEU SER ASN PRO ALA SEQRES 14 C 244 GLU VAL GLU ALA LEU ARG GLU LYS VAL TYR ALA SER LEU SEQRES 15 C 244 GLU ALA TYR CYS LYS HIS LYS TYR PRO GLU GLN PRO GLY SEQRES 16 C 244 ARG PHE ALA LYS LEU LEU LEU ARG LEU PRO ALA LEU ARG SEQRES 17 C 244 SER ILE GLY LEU LYS CYS LEU GLU HIS LEU PHE PHE PHE SEQRES 18 C 244 LYS LEU ILE GLY ASP THR PRO ILE ASP THR PHE LEU MET SEQRES 19 C 244 GLU MET LEU GLU ALA PRO HIS GLN MET THR SEQRES 1 D 13 LYS HIS LYS ILE LEU HIS ARG LEU LEU GLN ASP SER SER HET UGW A 501 30 HET UGW C 501 30 HET FMT C 502 3 HETNAM UGW 2,4-DI~{TERT}-BUTYLPHENOL HETNAM FMT FORMIC ACID FORMUL 5 UGW 2(C14 H22 O) FORMUL 7 FMT C H2 O2 FORMUL 8 HOH *120(H2 O) HELIX 1 AA1 PRO A 231 VAL A 242 1 12 HELIX 2 AA2 ASP A 263 ILE A 286 1 24 HELIX 3 AA3 PRO A 293 ARG A 316 1 24 HELIX 4 AA4 ARG A 334 ALA A 340 1 7 HELIX 5 AA5 VAL A 342 LEU A 353 1 12 HELIX 6 AA6 LEU A 353 MET A 360 1 8 HELIX 7 AA7 ASP A 363 PHE A 376 1 14 HELIX 8 AA8 ASN A 385 TYR A 408 1 24 HELIX 9 AA9 GLY A 413 LEU A 420 1 8 HELIX 10 AB1 ARG A 421 GLY A 443 1 23 HELIX 11 AB2 ASP A 448 GLU A 456 1 9 HELIX 12 AB3 LYS B 688 ASP B 696 1 9 HELIX 13 AB4 PRO C 231 VAL C 242 1 12 HELIX 14 AB5 ASP C 263 ARG C 285 1 23 HELIX 15 AB6 PRO C 293 SER C 317 1 25 HELIX 16 AB7 ARG C 334 ALA C 340 1 7 HELIX 17 AB8 VAL C 342 LEU C 353 1 12 HELIX 18 AB9 LEU C 353 MET C 360 1 8 HELIX 19 AC1 ASP C 363 PHE C 376 1 14 HELIX 20 AC2 ASN C 385 TYR C 408 1 24 HELIX 21 AC3 GLY C 413 LEU C 420 1 8 HELIX 22 AC4 ARG C 421 GLY C 443 1 23 HELIX 23 AC5 ASP C 448 LEU C 455 1 8 HELIX 24 AC6 LYS D 688 ASP D 696 1 9 SHEET 1 AA1 2 GLY A 323 LEU A 325 0 SHEET 2 AA1 2 HIS A 331 HIS A 333 -1 O VAL A 332 N ILE A 324 SHEET 1 AA2 2 GLY C 323 LEU C 326 0 SHEET 2 AA2 2 LEU C 330 HIS C 333 -1 O LEU C 330 N LEU C 326 SITE 1 AC1 7 ILE A 310 PHE A 313 VAL A 349 CYS A 432 SITE 2 AC1 7 HIS A 435 LEU A 436 PHE A 439 SITE 1 AC2 8 ALA C 272 ILE C 310 PHE C 313 ILE C 345 SITE 2 AC2 8 VAL C 349 CYS C 432 LEU C 436 PHE C 439 SITE 1 AC3 6 VAL C 242 GLN C 275 LEU C 279 TRP C 282 SITE 2 AC3 6 SER C 312 ARG C 371 CRYST1 62.706 67.303 108.832 90.00 90.00 90.00 P 21 21 21 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 0.015947 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014858 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009188 0.00000