HEADER NUCLEAR PROTEIN 23-DEC-17 5Z12 TITLE A STRUCTURE OF FXR/RXR COMPND MOL_ID: 1; COMPND 2 MOLECULE: BILE ACID RECEPTOR; COMPND 3 CHAIN: A, D; COMPND 4 FRAGMENT: UNP RESIDUES 259-486; COMPND 5 SYNONYM: FARNESOID X-ACTIVATED RECEPTOR,FARNESOL RECEPTOR HRR-1, COMPND 6 NUCLEAR RECEPTOR SUBFAMILY 1 GROUP H MEMBER 4,RETINOID X RECEPTOR- COMPND 7 INTERACTING PROTEIN 14,RXR-INTERACTING PROTEIN 14; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: RETINOIC ACID RECEPTOR RXR-ALPHA; COMPND 12 CHAIN: C, B; COMPND 13 FRAGMENT: UNP RESIDUES 228-458; COMPND 14 SYNONYM: NUCLEAR RECEPTOR SUBFAMILY 2 GROUP B MEMBER 1,RETINOID X COMPND 15 RECEPTOR ALPHA; COMPND 16 ENGINEERED: YES; COMPND 17 MOL_ID: 3; COMPND 18 MOLECULE: PEPTIDE FROM NUCLEAR RECEPTOR COACTIVATOR 2; COMPND 19 CHAIN: F, I; COMPND 20 ENGINEERED: YES; COMPND 21 MOL_ID: 4; COMPND 22 MOLECULE: PEPTIDE FROM NUCLEAR RECEPTOR COACTIVATOR 2; COMPND 23 CHAIN: J, H; COMPND 24 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: NR1H4, BAR, FXR, HRR1, RIP14; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: RXRA, NR2B1; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 18 ORGANISM_TAXID: 9606; SOURCE 19 MOL_ID: 4; SOURCE 20 SYNTHETIC: YES; SOURCE 21 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 22 ORGANISM_TAXID: 9606 KEYWDS COMPLEX, NUCLEAR PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.LU,Y.LI REVDAT 5 27-MAR-24 5Z12 1 REMARK REVDAT 4 25-DEC-19 5Z12 1 REMARK REVDAT 3 22-AUG-18 5Z12 1 JRNL REVDAT 2 25-JUL-18 5Z12 1 JRNL REVDAT 1 04-JUL-18 5Z12 0 JRNL AUTH W.ZHENG,Y.LU,S.TIAN,F.MA,Y.WEI,S.XU,Y.LI JRNL TITL STRUCTURAL INSIGHTS INTO THE HETERODIMERIC COMPLEX OF THE JRNL TITL 2 NUCLEAR RECEPTORS FXR AND RXR JRNL REF J. BIOL. CHEM. V. 293 12535 2018 JRNL REFN ESSN 1083-351X JRNL PMID 29934308 JRNL DOI 10.1074/JBC.RA118.004188 REMARK 2 REMARK 2 RESOLUTION. 2.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0189 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) : 2.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 70.9 REMARK 3 NUMBER OF REFLECTIONS : 17944 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) : 0.233 REMARK 3 R VALUE (WORKING SET) : 0.230 REMARK 3 FREE R VALUE : 0.290 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 968 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) : 2.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.82 REMARK 3 REFLECTION IN BIN (WORKING SET) : 435 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 23.75 REMARK 3 BIN R VALUE (WORKING SET) : 0.3020 REMARK 3 BIN FREE R VALUE SET COUNT : 26 REMARK 3 BIN FREE R VALUE : 0.3560 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7228 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 108 REMARK 3 SOLVENT ATOMS : 69 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.76 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.59000 REMARK 3 B22 (A**2) : -0.45000 REMARK 3 B33 (A**2) : -0.14000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.586 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.409 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 20.894 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.903 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.858 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7487 ; 0.010 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 7172 ; 0.006 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 10116 ; 1.601 ; 1.991 REMARK 3 BOND ANGLES OTHERS (DEGREES): 16633 ; 1.065 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 884 ; 6.535 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 338 ;39.905 ;24.260 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1381 ;19.401 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 43 ;21.914 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1144 ; 0.076 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 8081 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1472 ; 0.007 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 5Z12 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-DEC-17. REMARK 100 THE DEPOSITION ID IS D_1300006194. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-DEC-15 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25979 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.750 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 12.30 REMARK 200 R MERGE (I) : 0.13200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 3.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 77.7 REMARK 200 DATA REDUNDANCY IN SHELL : 9.20 REMARK 200 R MERGE FOR SHELL (I) : 0.94500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 4% V/V TACSIMATE PH 8.0, 12% W/V REMARK 280 POLYETHYLENE GLYCOL 3,350, VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 44.93650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 58.36050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 47.74200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 58.36050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 44.93650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 47.74200 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 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, J, B, I 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 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, F, D, H 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 ARG A 469 REMARK 465 VAL A 470 REMARK 465 ASN A 471 REMARK 465 ASP A 472 REMARK 465 HIS A 473 REMARK 465 GLU C 228 REMARK 465 ASP C 229 REMARK 465 MET C 230 REMARK 465 PRO C 231 REMARK 465 VAL C 232 REMARK 465 PRO C 244 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 ASN C 262 REMARK 465 ASP C 263 REMARK 465 GLU C 456 REMARK 465 ALA C 457 REMARK 465 PRO C 458 REMARK 465 ARG D 469 REMARK 465 VAL D 470 REMARK 465 ASN D 471 REMARK 465 ASP D 472 REMARK 465 HIS D 473 REMARK 465 THR B 248 REMARK 465 TYR B 249 REMARK 465 VAL B 250 REMARK 465 GLU B 251 REMARK 465 ALA B 252 REMARK 465 ASN B 253 REMARK 465 MET B 254 REMARK 465 GLY B 255 REMARK 465 LEU B 256 REMARK 465 ASN B 257 REMARK 465 PRO B 258 REMARK 465 SER B 259 REMARK 465 SER B 260 REMARK 465 PRO B 261 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 C 233 CG CD OE1 OE2 REMARK 470 ARG C 234 CG CD NE CZ NH1 NH2 REMARK 470 LYS D 289 CG CD CE NZ REMARK 470 GLU D 291 CG CD OE1 OE2 REMARK 470 GLN D 486 CG CD OE1 NE2 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 OE2 GLU D 481 N HIS H 746 2.17 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 CYS A 446 CA - CB - SG ANGL. DEV. = 6.9 DEGREES REMARK 500 CYS A 480 CA - CB - SG ANGL. DEV. = 8.8 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 GLU A 290 56.53 -141.54 REMARK 500 GLU A 291 48.14 34.27 REMARK 500 ARG C 234 13.52 -68.32 REMARK 500 HIS C 288 3.35 56.18 REMARK 500 GLN C 361 63.67 36.06 REMARK 500 ASP C 444 -5.13 61.07 REMARK 500 PRO C 446 101.09 -57.27 REMARK 500 GLU D 291 90.73 -48.10 REMARK 500 PRO D 320 108.40 -48.71 REMARK 500 PRO D 355 170.05 -57.76 REMARK 500 LYS D 390 58.89 39.85 REMARK 500 CYS D 480 -38.26 -36.46 REMARK 500 LEU H 749 -144.33 -115.71 REMARK 500 HIS H 750 -101.25 112.77 REMARK 500 ASP B 229 32.34 -73.53 REMARK 500 MET B 230 72.85 -166.23 REMARK 500 ALA B 241 21.20 -78.18 REMARK 500 VAL B 242 19.96 -142.63 REMARK 500 GLU B 243 -80.88 -115.16 REMARK 500 GLN B 361 68.80 30.19 REMARK 500 PRO B 446 103.09 -56.88 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 PRO A 320 GLY A 321 -31.29 REMARK 500 VAL C 320 LYS C 321 148.77 REMARK 500 LYS C 321 ASP C 322 -149.92 REMARK 500 HIS H 746 LYS H 747 146.89 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 33Y A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 9CR C 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 33Y D 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 9CR B 501 DBREF 5Z12 A 259 486 UNP Q96RI1 NR1H4_HUMAN 259 486 DBREF 5Z12 C 228 458 UNP P19793 RXRA_HUMAN 228 458 DBREF 5Z12 F 630 638 PDB 5Z12 5Z12 630 638 DBREF 5Z12 J 746 751 PDB 5Z12 5Z12 746 751 DBREF 5Z12 D 259 486 UNP Q96RI1 NR1H4_HUMAN 259 486 DBREF 5Z12 H 746 751 PDB 5Z12 5Z12 746 751 DBREF 5Z12 B 228 458 UNP P19793 RXRA_HUMAN 228 458 DBREF 5Z12 I 687 695 PDB 5Z12 5Z12 687 695 SEQRES 1 A 228 LEU THR PRO ASP GLN GLN THR LEU LEU HIS PHE ILE MET SEQRES 2 A 228 ASP SER TYR ASN LYS GLN ARG MET PRO GLN GLU ILE THR SEQRES 3 A 228 ASN LYS ILE LEU LYS GLU GLU PHE SER ALA GLU GLU ASN SEQRES 4 A 228 PHE LEU ILE LEU THR GLU MET ALA THR ASN HIS VAL GLN SEQRES 5 A 228 VAL LEU VAL GLU PHE THR LYS LYS LEU PRO GLY PHE GLN SEQRES 6 A 228 THR LEU ASP HIS GLU ASP GLN ILE ALA LEU LEU LYS GLY SEQRES 7 A 228 SER ALA VAL GLU ALA MET PHE LEU ARG SER ALA GLU ILE SEQRES 8 A 228 PHE ASN LYS LYS LEU PRO SER GLY HIS SER ASP LEU LEU SEQRES 9 A 228 GLU GLU ARG ILE ARG ASN SER GLY ILE SER ASP GLU TYR SEQRES 10 A 228 ILE THR PRO MET PHE SER PHE TYR LYS SER ILE GLY GLU SEQRES 11 A 228 LEU LYS MET THR GLN GLU GLU TYR ALA LEU LEU THR ALA SEQRES 12 A 228 ILE VAL ILE LEU SER PRO ASP ARG GLN TYR ILE LYS ASP SEQRES 13 A 228 ARG GLU ALA VAL GLU LYS LEU GLN GLU PRO LEU LEU ASP SEQRES 14 A 228 VAL LEU GLN LYS LEU CYS LYS ILE HIS GLN PRO GLU ASN SEQRES 15 A 228 PRO GLN HIS PHE ALA CYS LEU LEU GLY ARG LEU THR GLU SEQRES 16 A 228 LEU ARG THR PHE ASN HIS HIS HIS ALA GLU MET LEU MET SEQRES 17 A 228 SER TRP ARG VAL ASN ASP HIS LYS PHE THR PRO LEU LEU SEQRES 18 A 228 CYS GLU ILE TRP ASP VAL GLN SEQRES 1 C 231 GLU ASP MET PRO VAL GLU ARG ILE LEU GLU ALA GLU LEU SEQRES 2 C 231 ALA VAL GLU PRO LYS THR GLU THR TYR VAL GLU ALA ASN SEQRES 3 C 231 MET GLY LEU ASN PRO SER SER PRO ASN ASP PRO VAL THR SEQRES 4 C 231 ASN ILE CYS GLN ALA ALA ASP LYS GLN LEU PHE THR LEU SEQRES 5 C 231 VAL GLU TRP ALA LYS ARG ILE PRO HIS PHE SER GLU LEU SEQRES 6 C 231 PRO LEU ASP ASP GLN VAL ILE LEU LEU ARG ALA GLY TRP SEQRES 7 C 231 ASN GLU LEU LEU ILE ALA SER PHE SER HIS ARG SER ILE SEQRES 8 C 231 ALA VAL LYS ASP GLY ILE LEU LEU ALA THR GLY LEU HIS SEQRES 9 C 231 VAL HIS ARG ASN SER ALA HIS SER ALA GLY VAL GLY ALA SEQRES 10 C 231 ILE PHE ASP ARG VAL LEU THR GLU LEU VAL SER LYS MET SEQRES 11 C 231 ARG ASP MET GLN MET ASP LYS THR GLU LEU GLY CYS LEU SEQRES 12 C 231 ARG ALA ILE VAL LEU PHE ASN PRO ASP SER LYS GLY LEU SEQRES 13 C 231 SER ASN PRO ALA GLU VAL GLU ALA LEU ARG GLU LYS VAL SEQRES 14 C 231 TYR ALA SER LEU GLU ALA TYR CYS LYS HIS LYS TYR PRO SEQRES 15 C 231 GLU GLN PRO GLY ARG PHE ALA LYS LEU LEU LEU ARG LEU SEQRES 16 C 231 PRO ALA LEU ARG SER ILE GLY LEU LYS CYS LEU GLU HIS SEQRES 17 C 231 LEU PHE PHE PHE LYS LEU ILE GLY ASP THR PRO ILE ASP SEQRES 18 C 231 THR PHE LEU MET GLU MET LEU GLU ALA PRO SEQRES 1 F 9 HIS LYS ILE LEU HIS ARG LEU LEU GLN SEQRES 1 J 6 HIS LYS ILE LEU HIS ARG SEQRES 1 D 228 LEU THR PRO ASP GLN GLN THR LEU LEU HIS PHE ILE MET SEQRES 2 D 228 ASP SER TYR ASN LYS GLN ARG MET PRO GLN GLU ILE THR SEQRES 3 D 228 ASN LYS ILE LEU LYS GLU GLU PHE SER ALA GLU GLU ASN SEQRES 4 D 228 PHE LEU ILE LEU THR GLU MET ALA THR ASN HIS VAL GLN SEQRES 5 D 228 VAL LEU VAL GLU PHE THR LYS LYS LEU PRO GLY PHE GLN SEQRES 6 D 228 THR LEU ASP HIS GLU ASP GLN ILE ALA LEU LEU LYS GLY SEQRES 7 D 228 SER ALA VAL GLU ALA MET PHE LEU ARG SER ALA GLU ILE SEQRES 8 D 228 PHE ASN LYS LYS LEU PRO SER GLY HIS SER ASP LEU LEU SEQRES 9 D 228 GLU GLU ARG ILE ARG ASN SER GLY ILE SER ASP GLU TYR SEQRES 10 D 228 ILE THR PRO MET PHE SER PHE TYR LYS SER ILE GLY GLU SEQRES 11 D 228 LEU LYS MET THR GLN GLU GLU TYR ALA LEU LEU THR ALA SEQRES 12 D 228 ILE VAL ILE LEU SER PRO ASP ARG GLN TYR ILE LYS ASP SEQRES 13 D 228 ARG GLU ALA VAL GLU LYS LEU GLN GLU PRO LEU LEU ASP SEQRES 14 D 228 VAL LEU GLN LYS LEU CYS LYS ILE HIS GLN PRO GLU ASN SEQRES 15 D 228 PRO GLN HIS PHE ALA CYS LEU LEU GLY ARG LEU THR GLU SEQRES 16 D 228 LEU ARG THR PHE ASN HIS HIS HIS ALA GLU MET LEU MET SEQRES 17 D 228 SER TRP ARG VAL ASN ASP HIS LYS PHE THR PRO LEU LEU SEQRES 18 D 228 CYS GLU ILE TRP ASP VAL GLN SEQRES 1 H 6 HIS LYS ILE LEU HIS ARG SEQRES 1 B 231 GLU ASP MET PRO VAL GLU ARG ILE LEU GLU ALA GLU LEU SEQRES 2 B 231 ALA VAL GLU PRO LYS THR GLU THR TYR VAL GLU ALA ASN SEQRES 3 B 231 MET GLY LEU ASN PRO SER SER PRO ASN ASP PRO VAL THR SEQRES 4 B 231 ASN ILE CYS GLN ALA ALA ASP LYS GLN LEU PHE THR LEU SEQRES 5 B 231 VAL GLU TRP ALA LYS ARG ILE PRO HIS PHE SER GLU LEU SEQRES 6 B 231 PRO LEU ASP ASP GLN VAL ILE LEU LEU ARG ALA GLY TRP SEQRES 7 B 231 ASN GLU LEU LEU ILE ALA SER PHE SER HIS ARG SER ILE SEQRES 8 B 231 ALA VAL LYS ASP GLY ILE LEU LEU ALA THR GLY LEU HIS SEQRES 9 B 231 VAL HIS ARG ASN SER ALA HIS SER ALA GLY VAL GLY ALA SEQRES 10 B 231 ILE PHE ASP ARG VAL LEU THR GLU LEU VAL SER LYS MET SEQRES 11 B 231 ARG ASP MET GLN MET ASP LYS THR GLU LEU GLY CYS LEU SEQRES 12 B 231 ARG ALA ILE VAL LEU PHE ASN PRO ASP SER LYS GLY LEU SEQRES 13 B 231 SER ASN PRO ALA GLU VAL GLU ALA LEU ARG GLU LYS VAL SEQRES 14 B 231 TYR ALA SER LEU GLU ALA TYR CYS LYS HIS LYS TYR PRO SEQRES 15 B 231 GLU GLN PRO GLY ARG PHE ALA LYS LEU LEU LEU ARG LEU SEQRES 16 B 231 PRO ALA LEU ARG SER ILE GLY LEU LYS CYS LEU GLU HIS SEQRES 17 B 231 LEU PHE PHE PHE LYS LEU ILE GLY ASP THR PRO ILE ASP SEQRES 18 B 231 THR PHE LEU MET GLU MET LEU GLU ALA PRO SEQRES 1 I 9 HIS LYS ILE LEU HIS ARG LEU LEU GLN HET 33Y A 501 32 HET 9CR C 501 22 HET 33Y D 501 32 HET 9CR B 501 22 HETNAM 33Y 1-METHYLETHYL 3-[(3,4-DIFLUOROPHENYL)CARBONYL]-1,1- HETNAM 2 33Y DIMETHYL-1,2,3,6-TETRAHYDROAZEPINO[4,5-B]INDOLE-5- HETNAM 3 33Y CARBOXYLATE HETNAM 9CR (9CIS)-RETINOIC ACID FORMUL 9 33Y 2(C25 H24 F2 N2 O3) FORMUL 10 9CR 2(C20 H28 O2) FORMUL 13 HOH *69(H2 O) HELIX 1 AA1 THR A 260 ASN A 275 1 16 HELIX 2 AA2 MET A 279 LYS A 289 1 11 HELIX 3 AA3 GLU A 295 LYS A 318 1 24 HELIX 4 AA4 GLU A 328 ASN A 351 1 24 HELIX 5 AA5 GLY A 357 ASN A 368 1 12 HELIX 6 AA6 SER A 372 GLU A 388 1 17 HELIX 7 AA7 THR A 392 LEU A 405 1 14 HELIX 8 AA8 ASP A 414 GLN A 437 1 24 HELIX 9 AA9 GLN A 442 SER A 467 1 26 HELIX 10 AB1 THR A 476 ASP A 484 1 9 HELIX 11 AB2 ARG C 234 ALA C 241 1 8 HELIX 12 AB3 VAL C 265 ARG C 285 1 21 HELIX 13 AB4 PRO C 293 SER C 317 1 25 HELIX 14 AB5 ARG C 334 ALA C 340 1 7 HELIX 15 AB6 VAL C 342 LEU C 353 1 12 HELIX 16 AB7 LEU C 353 MET C 360 1 8 HELIX 17 AB8 ASP C 363 PHE C 376 1 14 HELIX 18 AB9 ASN C 385 TYR C 408 1 24 HELIX 19 AC1 GLY C 413 LEU C 420 1 8 HELIX 20 AC2 LEU C 420 ILE C 442 1 23 HELIX 21 AC3 ASP C 448 LEU C 455 1 8 HELIX 22 AC4 LYS F 631 GLN F 638 1 8 HELIX 23 AC5 THR D 260 ASN D 275 1 16 HELIX 24 AC6 MET D 279 LYS D 289 1 11 HELIX 25 AC7 SER D 293 LYS D 318 1 26 HELIX 26 AC8 GLU D 328 LYS D 352 1 25 HELIX 27 AC9 GLY D 357 ASN D 368 1 12 HELIX 28 AD1 SER D 372 GLU D 388 1 17 HELIX 29 AD2 THR D 392 LEU D 405 1 14 HELIX 30 AD3 ASP D 414 GLN D 437 1 24 HELIX 31 AD4 GLN D 442 SER D 467 1 26 HELIX 32 AD5 THR D 476 TRP D 483 1 8 HELIX 33 AD6 PRO B 231 ALA B 241 1 11 HELIX 34 AD7 ASP B 263 ARG B 285 1 23 HELIX 35 AD8 PRO B 293 SER B 317 1 25 HELIX 36 AD9 ARG B 334 ALA B 340 1 7 HELIX 37 AE1 VAL B 342 LEU B 353 1 12 HELIX 38 AE2 LEU B 353 MET B 360 1 8 HELIX 39 AE3 ASP B 363 PHE B 376 1 14 HELIX 40 AE4 ASN B 385 TYR B 408 1 24 HELIX 41 AE5 GLY B 413 LEU B 420 1 8 HELIX 42 AE6 LEU B 420 ILE B 442 1 23 HELIX 43 AE7 ASP B 448 GLU B 456 1 9 HELIX 44 AE8 LYS I 688 LEU I 694 1 7 SHEET 1 AA1 2 GLY C 323 LEU C 325 0 SHEET 2 AA1 2 HIS C 331 HIS C 333 -1 O VAL C 332 N ILE C 324 SHEET 1 AA2 2 GLY B 323 LEU B 325 0 SHEET 2 AA2 2 HIS B 331 HIS B 333 -1 O VAL B 332 N ILE B 324 SITE 1 AC1 12 ILE A 283 ILE A 287 LEU A 301 ALA A 305 SITE 2 AC1 12 HIS A 308 MET A 342 SER A 346 ILE A 349 SITE 3 AC1 12 LEU A 362 MET A 379 TYR A 383 TRP A 483 SITE 1 AC2 10 ILE C 268 ALA C 272 GLN C 275 PHE C 313 SITE 2 AC2 10 ARG C 316 LEU C 326 ALA C 327 VAL C 342 SITE 3 AC2 10 CYS C 432 LEU C 436 SITE 1 AC3 13 ILE D 283 ILE D 287 LEU D 301 ALA D 305 SITE 2 AC3 13 HIS D 308 MET D 342 PHE D 343 ARG D 345 SITE 3 AC3 13 SER D 346 ILE D 349 LEU D 362 TYR D 383 SITE 4 AC3 13 LEU D 465 SITE 1 AC4 10 ALA B 272 GLN B 275 TRP B 305 LEU B 309 SITE 2 AC4 10 PHE B 313 ARG B 316 LEU B 326 ALA B 327 SITE 3 AC4 10 VAL B 342 CYS B 432 CRYST1 89.873 95.484 116.721 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 0.011127 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010473 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008567 0.00000