HEADER GENE REGULATION 07-FEB-18 6FOD TITLE VITAMIN D NUCLEAR RECEPTOR COMPLEX 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: VITAMIN D3 RECEPTOR A; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: VDR-A,1,25-DIHYDROXYVITAMIN D3 RECEPTOR A,NUCLEAR RECEPTOR COMPND 5 SUBFAMILY 1 GROUP I MEMBER 1-A; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: NUCLEAR RECEPTOR COACTIVATOR 1; COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DANIO RERIO; SOURCE 3 ORGANISM_COMMON: ZEBRAFISH; SOURCE 4 ORGANISM_TAXID: 7955; SOURCE 5 GENE: VDRA, NR1I1A, VDR; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 866768; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_TAXID: 9606 KEYWDS GENE REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR N.ROCHEL REVDAT 4 17-JAN-24 6FOD 1 REMARK REVDAT 3 24-FEB-21 6FOD 1 REMARK REVDAT 2 27-JUN-18 6FOD 1 JRNL REVDAT 1 16-MAY-18 6FOD 0 JRNL AUTH P.GOGOI,S.SEOANE,R.SIGUEIRO,T.GUIBERTEAU,M.A.MAESTRO, JRNL AUTH 2 R.PEREZ-FERNANDEZ,N.ROCHEL,A.MOURINO JRNL TITL AROMATIC-BASED DESIGN OF HIGHLY ACTIVE AND NONCALCEMIC JRNL TITL 2 VITAMIN D RECEPTOR AGONISTS. JRNL REF J. MED. CHEM. V. 61 4928 2018 JRNL REFN ISSN 1520-4804 JRNL PMID 29733645 JRNL DOI 10.1021/ACS.JMEDCHEM.8B00337 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.2 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.83 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 12605 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) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.920 REMARK 3 FREE R VALUE TEST SET COUNT : 620 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.74 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.97 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2922 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2162 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2775 REMARK 3 BIN R VALUE (WORKING SET) : 0.2140 REMARK 3 BIN FREE R VALUE : 0.2611 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.03 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 147 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1995 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 29 REMARK 3 SOLVENT ATOMS : 27 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 63.59 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 73.42 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -11.17320 REMARK 3 B22 (A**2) : -11.17320 REMARK 3 B33 (A**2) : 22.34630 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.308 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.375 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.255 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.326 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.247 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.935 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.921 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 2065 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 2784 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 751 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 49 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 303 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 2065 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 261 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 2489 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.10 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.80 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 19.19 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|* } REMARK 3 ORIGIN FOR THE GROUP (A): 8.6126 37.0113 42.4723 REMARK 3 T TENSOR REMARK 3 T11: -0.1305 T22: -0.0258 REMARK 3 T33: -0.2529 T12: 0.0750 REMARK 3 T13: -0.0619 T23: -0.0337 REMARK 3 L TENSOR REMARK 3 L11: 1.7434 L22: 3.2204 REMARK 3 L33: 5.0479 L12: -0.6593 REMARK 3 L13: 0.3058 L23: 2.2542 REMARK 3 S TENSOR REMARK 3 S11: -0.2005 S12: -0.4696 S13: 0.0085 REMARK 3 S21: 0.4045 S22: 0.1783 S23: -0.1179 REMARK 3 S31: 0.2786 S32: -0.1862 S33: 0.0222 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6FOD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-FEB-18. REMARK 100 THE DEPOSITION ID IS D_1200008673. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JAN-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0721 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12779 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09900 REMARK 200 FOR THE DATA SET : 23.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.39300 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: PHENIX REMARK 200 STARTING MODEL: 2HC4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: BISTRIS PH 6.5, 1.6 M LITHIUM SULFATE REMARK 280 AND 50 MM MAGNESIUM SULFATE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 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 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 176.13333 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 88.06667 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 132.10000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 44.03333 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 220.16667 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 176.13333 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 88.06667 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 44.03333 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 132.10000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 220.16667 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: 4000 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21910 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.0 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 0.500000 -0.866025 0.000000 32.96500 REMARK 350 BIOMT2 2 -0.866025 -0.500000 0.000000 57.09705 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 44.03333 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 191 REMARK 465 GLY A 192 REMARK 465 PRO A 193 REMARK 465 VAL A 194 REMARK 465 THR A 195 REMARK 465 ARG A 196 REMARK 465 SER A 197 REMARK 465 ALA A 198 REMARK 465 SER A 199 REMARK 465 ARG A 200 REMARK 465 ALA A 201 REMARK 465 ALA A 202 REMARK 465 SER A 203 REMARK 465 LEU A 204 REMARK 465 HIS A 205 REMARK 465 SER A 206 REMARK 465 LEU A 207 REMARK 465 SER A 208 REMARK 465 ASP A 209 REMARK 465 ALA A 210 REMARK 465 SER A 211 REMARK 465 SER A 212 REMARK 465 ASP A 213 REMARK 465 SER A 214 REMARK 465 PHE A 215 REMARK 465 ASN A 216 REMARK 465 HIS A 217 REMARK 465 SER A 218 REMARK 465 PRO A 219 REMARK 465 GLU A 220 REMARK 465 SER A 221 REMARK 465 VAL A 222 REMARK 465 ASP A 223 REMARK 465 THR A 224 REMARK 465 LYS A 225 REMARK 465 LEU A 226 REMARK 465 ASN A 227 REMARK 465 PHE A 228 REMARK 465 SER A 229 REMARK 465 ASN A 230 REMARK 465 LEU A 231 REMARK 465 LEU A 232 REMARK 465 MET A 233 REMARK 465 MET A 234 REMARK 465 TYR A 235 REMARK 465 GLN A 236 REMARK 465 ASP A 237 REMARK 465 SER A 238 REMARK 465 GLY A 239 REMARK 465 SER A 240 REMARK 465 PRO A 241 REMARK 465 ASP A 242 REMARK 465 SER A 243 REMARK 465 SER A 244 REMARK 465 GLU A 245 REMARK 465 GLU A 246 REMARK 465 ASP A 247 REMARK 465 GLN A 248 REMARK 465 GLN A 249 REMARK 465 SER A 250 REMARK 465 SER A 453 REMARK 465 GLU B 697 REMARK 465 GLY B 698 REMARK 465 SER B 699 REMARK 465 PRO B 700 REMARK 465 SER B 701 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 451 CG CD OE1 OE2 REMARK 470 VAL A 452 CG1 CG2 REMARK 470 ARG B 687 CB CG CD NE CZ NH1 NH2 REMARK 470 GLN B 696 CG CD OE1 NE2 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 LYS B 689 CG CD CE NZ 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 LEU A 252 56.22 72.57 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 E05 A 4000 DBREF 6FOD A 156 453 UNP Q9PTN2 VDRA_DANRE 156 453 DBREF 6FOD B 687 701 PDB 6FOD 6FOD 687 701 SEQADV 6FOD HIS A 154 UNP Q9PTN2 EXPRESSION TAG SEQADV 6FOD MET A 155 UNP Q9PTN2 EXPRESSION TAG SEQRES 1 A 300 HIS MET LEU SER ASP GLU GLN MET GLN ILE ILE ASN SER SEQRES 2 A 300 LEU VAL GLU ALA HIS HIS LYS THR TYR ASP ASP SER TYR SEQRES 3 A 300 SER ASP PHE VAL ARG PHE ARG PRO PRO VAL ARG GLU GLY SEQRES 4 A 300 PRO VAL THR ARG SER ALA SER ARG ALA ALA SER LEU HIS SEQRES 5 A 300 SER LEU SER ASP ALA SER SER ASP SER PHE ASN HIS SER SEQRES 6 A 300 PRO GLU SER VAL ASP THR LYS LEU ASN PHE SER ASN LEU SEQRES 7 A 300 LEU MET MET TYR GLN ASP SER GLY SER PRO ASP SER SER SEQRES 8 A 300 GLU GLU ASP GLN GLN SER ARG LEU SER MET LEU PRO HIS SEQRES 9 A 300 LEU ALA ASP LEU VAL SER TYR SER ILE GLN LYS VAL ILE SEQRES 10 A 300 GLY PHE ALA LYS MET ILE PRO GLY PHE ARG ASP LEU THR SEQRES 11 A 300 ALA GLU ASP GLN ILE ALA LEU LEU LYS SER SER ALA ILE SEQRES 12 A 300 GLU ILE ILE MET LEU ARG SER ASN GLN SER PHE SER LEU SEQRES 13 A 300 GLU ASP MET SER TRP SER CYS GLY GLY PRO ASP PHE LYS SEQRES 14 A 300 TYR CYS ILE ASN ASP VAL THR LYS ALA GLY HIS THR LEU SEQRES 15 A 300 GLU LEU LEU GLU PRO LEU VAL LYS PHE GLN VAL GLY LEU SEQRES 16 A 300 LYS LYS LEU LYS LEU HIS GLU GLU GLU HIS VAL LEU LEU SEQRES 17 A 300 MET ALA ILE CYS LEU LEU SER PRO ASP ARG PRO GLY VAL SEQRES 18 A 300 GLN ASP HIS VAL ARG ILE GLU ALA LEU GLN ASP ARG LEU SEQRES 19 A 300 CYS ASP VAL LEU GLN ALA TYR ILE ARG ILE GLN HIS PRO SEQRES 20 A 300 GLY GLY ARG LEU LEU TYR ALA LYS MET ILE GLN LYS LEU SEQRES 21 A 300 ALA ASP LEU ARG SER LEU ASN GLU GLU HIS SER LYS GLN SEQRES 22 A 300 TYR ARG SER LEU SER PHE GLN PRO GLU HIS SER MET GLN SEQRES 23 A 300 LEU THR PRO LEU VAL LEU GLU VAL PHE GLY SER GLU VAL SEQRES 24 A 300 SER SEQRES 1 B 15 ARG HIS LYS ILE LEU HIS ARG LEU LEU GLN GLU GLY SER SEQRES 2 B 15 PRO SER HET E05 A4000 29 HETNAM E05 (1~{R},3~{S},5~{Z})-4-METHYLIDENE-5-[(~{E})-3-[3-(6- HETNAM 2 E05 METHYL-6-OXIDANYL-HEPTYL)PHENYL]PENT-2- HETNAM 3 E05 ENYLIDENE]CYCLOHEXANE-1,3-DIOL FORMUL 3 E05 C26 H38 O3 FORMUL 4 HOH *27(H2 O) HELIX 1 AA1 SER A 157 TYR A 175 1 19 HELIX 2 AA2 TYR A 179 PHE A 185 5 7 HELIX 3 AA3 MET A 254 LYS A 274 1 21 HELIX 4 AA4 GLY A 278 LEU A 282 5 5 HELIX 5 AA5 THR A 283 ASN A 304 1 22 HELIX 6 AA6 CYS A 324 LYS A 330 1 7 HELIX 7 AA7 THR A 334 LEU A 351 1 18 HELIX 8 AA8 HIS A 354 LEU A 367 1 14 HELIX 9 AA9 ASP A 376 HIS A 399 1 24 HELIX 10 AB1 LEU A 404 PHE A 432 1 29 HELIX 11 AB2 GLN A 433 MET A 438 1 6 HELIX 12 AB3 THR A 441 PHE A 448 1 8 HELIX 13 AB4 HIS B 688 GLN B 696 1 9 SHEET 1 AA1 3 PHE A 307 SER A 308 0 SHEET 2 AA1 3 SER A 313 SER A 315 -1 O SER A 313 N SER A 308 SHEET 3 AA1 3 LYS A 322 TYR A 323 -1 O TYR A 323 N TRP A 314 SITE 1 AC1 13 TYR A 175 TYR A 179 SER A 265 ILE A 299 SITE 2 AC1 13 ARG A 302 SER A 303 SER A 306 TRP A 314 SITE 3 AC1 13 CYS A 316 VAL A 328 HIS A 333 HIS A 423 SITE 4 AC1 13 TYR A 427 CRYST1 65.930 65.930 264.200 90.00 90.00 120.00 P 65 2 2 12 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 0.015168 0.008757 0.000000 0.00000 SCALE2 0.000000 0.017514 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003785 0.00000