HEADER GENE REGULATION 04-FEB-20 6XZH TITLE STRUCTURE OF ZVDR LBD-CALCITRIOL IN COMPLEX WITH CHIMERA 10 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: ARG-HIS-LYS-ILE-URL-URK-URL-LEU-GLN; 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; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630 KEYWDS NUCLEAR RECEPTOR, FOLDAMER, HELIX MIMICRY, PROTEIN-PROTEIN KEYWDS 2 INTERACTION, GENE REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR J.BURATTO,A.Y.BELORUSOVA,N.ROCHEL,G.GUICHARD REVDAT 4 24-JAN-24 6XZH 1 REMARK REVDAT 3 15-NOV-23 6XZH 1 LINK ATOM REVDAT 2 01-SEP-21 6XZH 1 JRNL REVDAT 1 17-FEB-21 6XZH 0 JRNL AUTH L.CUSSOL,L.MAURAN-AMBROSINO,J.BURATTO,A.Y.BELORUSOVA, JRNL AUTH 2 M.NEUVILLE,J.OSZ,S.FRIBOURG,J.FREMAUX,C.DOLAIN,S.R.GOUDREAU, JRNL AUTH 3 N.ROCHEL,G.GUICHARD JRNL TITL STRUCTURAL BASIS FOR ALPHA-HELIX MIMICRY AND INHIBITION OF JRNL TITL 2 PROTEIN-PROTEIN INTERACTIONS WITH OLIGOUREA FOLDAMERS. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 60 2296 2021 JRNL REFN ESSN 1521-3773 JRNL PMID 32935897 JRNL DOI 10.1002/ANIE.202008992 REMARK 2 REMARK 2 RESOLUTION. 2.37 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1_2155 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) : 2.37 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.53 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 14411 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.225 REMARK 3 R VALUE (WORKING SET) : 0.222 REMARK 3 FREE R VALUE : 0.282 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 722 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 20.5270 - 4.0470 1.00 2965 156 0.1797 0.2303 REMARK 3 2 4.0470 - 3.2162 1.00 2752 145 0.2264 0.2985 REMARK 3 3 3.2162 - 2.8108 1.00 2711 142 0.2945 0.3519 REMARK 3 4 2.8108 - 2.5543 1.00 2656 141 0.3278 0.4230 REMARK 3 5 2.5543 - 2.3720 0.98 2605 138 0.3683 0.4383 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) : 0.400 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 34.750 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.009 1985 REMARK 3 ANGLE : 1.197 2686 REMARK 3 CHIRALITY : 0.060 312 REMARK 3 PLANARITY : 0.007 339 REMARK 3 DIHEDRAL : 15.742 1199 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 154 THROUGH 306 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.5231 42.9881 38.7899 REMARK 3 T TENSOR REMARK 3 T11: 0.6041 T22: 0.6147 REMARK 3 T33: 0.4814 T12: 0.1339 REMARK 3 T13: 0.0002 T23: 0.0345 REMARK 3 L TENSOR REMARK 3 L11: 4.3142 L22: 5.2752 REMARK 3 L33: 9.3744 L12: 1.8911 REMARK 3 L13: 3.4263 L23: 5.5168 REMARK 3 S TENSOR REMARK 3 S11: -0.2996 S12: -0.4176 S13: 0.4223 REMARK 3 S21: 0.0369 S22: 0.0709 S23: 0.1650 REMARK 3 S31: -0.4679 S32: -0.0137 S33: 0.2267 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 307 THROUGH 452 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.3791 34.9782 44.6452 REMARK 3 T TENSOR REMARK 3 T11: 0.7285 T22: 0.6503 REMARK 3 T33: 0.4764 T12: 0.1771 REMARK 3 T13: 0.0060 T23: -0.0136 REMARK 3 L TENSOR REMARK 3 L11: 1.8008 L22: 4.7078 REMARK 3 L33: 7.2470 L12: 0.5696 REMARK 3 L13: -0.3734 L23: 2.7236 REMARK 3 S TENSOR REMARK 3 S11: -0.0575 S12: -0.3770 S13: 0.0010 REMARK 3 S21: 1.0584 S22: 0.0683 S23: 0.0586 REMARK 3 S31: 0.6582 S32: -0.0579 S33: -0.0108 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 8 ) REMARK 3 ORIGIN FOR THE GROUP (A): 20.2371 40.0385 27.2289 REMARK 3 T TENSOR REMARK 3 T11: 0.7267 T22: 0.8448 REMARK 3 T33: 0.6827 T12: 0.0437 REMARK 3 T13: -0.0061 T23: -0.1086 REMARK 3 L TENSOR REMARK 3 L11: 2.2796 L22: 2.1040 REMARK 3 L33: 2.3181 L12: 0.6953 REMARK 3 L13: 2.0331 L23: -0.2364 REMARK 3 S TENSOR REMARK 3 S11: -0.4787 S12: 0.2968 S13: 0.1958 REMARK 3 S21: -0.1485 S22: 0.9721 S23: -1.0280 REMARK 3 S31: -0.4701 S32: 1.8383 S33: -0.7888 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 6XZH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-FEB-20. REMARK 100 THE DEPOSITION ID IS D_1292106523. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-SEP-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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) : 0.98 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 : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14448 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.370 REMARK 200 RESOLUTION RANGE LOW (A) : 20.527 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.2900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.37 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.46 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.880 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 (%): 47.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM ACETATE 2.5 M, HEPES 100 MM, PH REMARK 280 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 290K 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 173.42667 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 86.71333 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 130.07000 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 43.35667 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 216.78333 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 173.42667 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 86.71333 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 43.35667 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 130.07000 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 216.78333 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 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 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 152 REMARK 465 SER A 153 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 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 LEU A 156 CD1 CD2 REMARK 470 ASP A 158 CG OD1 OD2 REMARK 470 LYS A 173 CE NZ REMARK 470 ARG A 184 CD NE CZ NH1 NH2 REMARK 470 ARG A 251 NE CZ NH1 NH2 REMARK 470 LYS A 274 CD CE NZ REMARK 470 ARG A 280 NE CZ NH1 NH2 REMARK 470 GLU A 310 CG CD OE1 OE2 REMARK 470 ASP A 320 CG OD1 OD2 REMARK 470 LYS A 322 CD CE NZ REMARK 470 GLU A 336 CG CD OE1 OE2 REMARK 470 LYS A 343 CG CD CE NZ REMARK 470 LYS A 349 CD CE NZ REMARK 470 VAL A 374 CG1 CG2 REMARK 470 GLN A 375 CG CD OE1 NE2 REMARK 470 VAL A 378 CG1 CG2 REMARK 470 ARG A 386 CZ NH1 NH2 REMARK 470 ARG A 403 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 404 CG CD1 CD2 REMARK 470 LYS A 408 CG CD CE NZ REMARK 470 LYS A 425 CE NZ REMARK 470 GLU A 451 CG CD OE1 OE2 REMARK 470 VAL A 452 CG1 CG2 REMARK 470 ARG B 0 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 2 CE NZ REMARK 470 OUK B 5 CD CE NZ REMARK 470 GLN B 8 CG CD OE1 NE2 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 URL B 4 CA - C - N ANGL. DEV. = 30.1 DEGREES REMARK 500 OUK B 5 CA - C - N ANGL. DEV. = 25.8 DEGREES REMARK 500 URL B 6 CA - C - N ANGL. DEV. = 17.8 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 LEU A 252 47.58 70.48 REMARK 500 PRO A 277 109.88 -50.94 REMARK 500 CYS A 316 65.13 -108.38 REMARK 500 ASP A 370 51.83 -91.08 REMARK 500 GLN A 375 -76.06 -97.41 REMARK 500 ASP A 376 71.37 -65.24 REMARK 500 HIS B 1 116.07 73.77 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 URL B 4 OUK B 5 132.52 REMARK 500 OUK B 5 URL B 6 126.16 REMARK 500 URL B 6 LEU B 7 137.02 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 URL B 4 -28.21 REMARK 500 OUK B 5 -22.72 REMARK 500 URL B 6 -27.04 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 VDX A 4001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues URL B 4 and OUK B 5 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues OUK B 5 and URL B 6 DBREF 6XZH A 156 453 UNP Q9PTN2 VDRA_DANRE 156 453 DBREF 6XZH B 0 8 PDB 6XZH 6XZH 0 8 SEQADV 6XZH GLY A 152 UNP Q9PTN2 EXPRESSION TAG SEQADV 6XZH SER A 153 UNP Q9PTN2 EXPRESSION TAG SEQADV 6XZH HIS A 154 UNP Q9PTN2 EXPRESSION TAG SEQADV 6XZH MET A 155 UNP Q9PTN2 EXPRESSION TAG SEQRES 1 A 302 GLY SER HIS MET LEU SER ASP GLU GLN MET GLN ILE ILE SEQRES 2 A 302 ASN SER LEU VAL GLU ALA HIS HIS LYS THR TYR ASP ASP SEQRES 3 A 302 SER TYR SER ASP PHE VAL ARG PHE ARG PRO PRO VAL ARG SEQRES 4 A 302 GLU GLY PRO VAL THR ARG SER ALA SER ARG ALA ALA SER SEQRES 5 A 302 LEU HIS SER LEU SER ASP ALA SER SER ASP SER PHE ASN SEQRES 6 A 302 HIS SER PRO GLU SER VAL ASP THR LYS LEU ASN PHE SER SEQRES 7 A 302 ASN LEU LEU MET MET TYR GLN ASP SER GLY SER PRO ASP SEQRES 8 A 302 SER SER GLU GLU ASP GLN GLN SER ARG LEU SER MET LEU SEQRES 9 A 302 PRO HIS LEU ALA ASP LEU VAL SER TYR SER ILE GLN LYS SEQRES 10 A 302 VAL ILE GLY PHE ALA LYS MET ILE PRO GLY PHE ARG ASP SEQRES 11 A 302 LEU THR ALA GLU ASP GLN ILE ALA LEU LEU LYS SER SER SEQRES 12 A 302 ALA ILE GLU ILE ILE MET LEU ARG SER ASN GLN SER PHE SEQRES 13 A 302 SER LEU GLU ASP MET SER TRP SER CYS GLY GLY PRO ASP SEQRES 14 A 302 PHE LYS TYR CYS ILE ASN ASP VAL THR LYS ALA GLY HIS SEQRES 15 A 302 THR LEU GLU LEU LEU GLU PRO LEU VAL LYS PHE GLN VAL SEQRES 16 A 302 GLY LEU LYS LYS LEU LYS LEU HIS GLU GLU GLU HIS VAL SEQRES 17 A 302 LEU LEU MET ALA ILE CYS LEU LEU SER PRO ASP ARG PRO SEQRES 18 A 302 GLY VAL GLN ASP HIS VAL ARG ILE GLU ALA LEU GLN ASP SEQRES 19 A 302 ARG LEU CYS ASP VAL LEU GLN ALA TYR ILE ARG ILE GLN SEQRES 20 A 302 HIS PRO GLY GLY ARG LEU LEU TYR ALA LYS MET ILE GLN SEQRES 21 A 302 LYS LEU ALA ASP LEU ARG SER LEU ASN GLU GLU HIS SER SEQRES 22 A 302 LYS GLN TYR ARG SER LEU SER PHE GLN PRO GLU HIS SER SEQRES 23 A 302 MET GLN LEU THR PRO LEU VAL LEU GLU VAL PHE GLY SER SEQRES 24 A 302 GLU VAL SER SEQRES 1 B 9 ARG HIS LYS ILE URL OUK URL LEU GLN HET URL B 4 10 HET OUK B 5 8 HET URL B 6 10 HET VDX A4001 30 HETNAM URL [(2~{S})-2-AZANYL-4-METHYL-PENTYL]CARBAMIC ACID HETNAM OUK [(5~{S})-5-AZANYL-6-(CARBOXYAMINO)HEXYL]AZANIUM HETNAM VDX 5-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL- HETNAM 2 VDX OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE- HETNAM 3 VDX CYCLOHEXANE-1,3-DIOL HETSYN VDX 1,25 DIHYDROXY VITAMIN D3 FORMUL 2 URL 2(C7 H16 N2 O2) FORMUL 2 OUK C7 H18 N3 O2 1+ FORMUL 3 VDX C27 H44 O3 FORMUL 4 HOH *5(H2 O) HELIX 1 AA1 SER A 157 THR A 174 1 18 HELIX 2 AA2 TYR A 179 PHE A 185 5 7 HELIX 3 AA3 MET A 254 ILE A 276 1 23 HELIX 4 AA4 GLY A 278 LEU A 282 5 5 HELIX 5 AA5 THR A 283 SER A 303 1 21 HELIX 6 AA6 GLY A 318 ASP A 320 5 3 HELIX 7 AA7 CYS A 324 LYS A 330 1 7 HELIX 8 AA8 THR A 334 LEU A 351 1 18 HELIX 9 AA9 HIS A 354 LEU A 367 1 14 HELIX 10 AB1 ASP A 376 HIS A 399 1 24 HELIX 11 AB2 LEU A 404 PHE A 432 1 29 HELIX 12 AB3 GLN A 433 MET A 438 1 6 HELIX 13 AB4 THR A 441 PHE A 448 1 8 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 LINK C ILE B 3 N URL B 4 1555 1555 1.36 LINK C URL B 4 N OUK B 5 1555 1555 1.34 LINK C OUK B 5 N URL B 6 1555 1555 1.35 LINK C URL B 6 N LEU B 7 1555 1555 1.32 SITE 1 AC1 11 TYR A 175 SER A 265 ILE A 299 ARG A 302 SITE 2 AC1 11 SER A 303 SER A 306 CYS A 316 VAL A 328 SITE 3 AC1 11 HIS A 333 HIS A 423 TYR A 427 SITE 1 AC2 8 HIS A 154 ILE A 270 GLU A 446 LYS B 2 SITE 2 AC2 8 ILE B 3 URL B 6 LEU B 7 GLN B 8 SITE 1 AC3 6 HIS A 154 GLU A 435 ILE B 3 URL B 4 SITE 2 AC3 6 LEU B 7 GLN B 8 CRYST1 66.090 66.090 260.140 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 0.015131 0.008736 0.000000 0.00000 SCALE2 0.000000 0.017472 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003844 0.00000