HEADER TRANSCRIPTION 23-JUN-16 5GID TITLE CRYSTAL STRUCTURE OF VDR IN COMPLEX WITH DLAM-4 (C2 FORM) COMPND MOL_ID: 1; COMPND 2 MOLECULE: VITAMIN D3 RECEPTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 124-164,UNP RESIDUES 212-419; COMPND 5 SYNONYM: VDR,1,25-DIHYDROXYVITAMIN D3 RECEPTOR,NUCLEAR RECEPTOR COMPND 6 SUBFAMILY 1 GROUP I MEMBER 1; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: SRC1; COMPND 10 CHAIN: C; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 GENE: VDR, NR1I1; 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_TAXID: 9606 KEYWDS NUCLEAR RECEPTOR, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR L.ASANO,T.SHIMIZU REVDAT 3 20-MAR-24 5GID 1 REMARK REVDAT 2 26-FEB-20 5GID 1 JRNL REMARK REVDAT 1 07-DEC-16 5GID 0 JRNL AUTH L.ASANO,T.WAKU,R.ABE,N.KUWABARA,I.ITO,J.YANAGISAWA, JRNL AUTH 2 K.NAGASAWA,T.SHIMIZU JRNL TITL REGULATION OF THE VITAMIN D RECEPTOR BY VITAMIN D LACTAM JRNL TITL 2 DERIVATIVES. JRNL REF FEBS LETT. V. 590 3270 2016 JRNL REFN ISSN 0014-5793 JRNL PMID 27500498 JRNL DOI 10.1002/1873-3468.12348 REMARK 2 REMARK 2 RESOLUTION. 2.15 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) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.82 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 14860 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.030 REMARK 3 FREE R VALUE TEST SET COUNT : 2817 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 40.8282 - 5.8339 0.90 1169 136 0.1621 0.1720 REMARK 3 2 5.8339 - 4.6326 0.95 1247 133 0.1477 0.1833 REMARK 3 3 4.6326 - 4.0476 0.95 1242 143 0.1298 0.1709 REMARK 3 4 4.0476 - 3.6778 0.95 1244 138 0.1627 0.1895 REMARK 3 5 3.6778 - 3.4143 0.97 1259 140 0.1793 0.2209 REMARK 3 6 3.4143 - 3.2131 0.97 1245 140 0.2169 0.2549 REMARK 3 7 3.2131 - 3.0523 0.98 1258 136 0.2368 0.2767 REMARK 3 8 3.0523 - 2.9194 0.98 1314 149 0.2278 0.2991 REMARK 3 9 2.9194 - 2.8071 0.98 1251 140 0.2217 0.3014 REMARK 3 10 2.8071 - 2.7102 0.99 1286 143 0.2430 0.2683 REMARK 3 11 2.7102 - 2.6255 0.99 1257 140 0.2334 0.3169 REMARK 3 12 2.6255 - 2.5505 0.99 1324 153 0.2355 0.2779 REMARK 3 13 2.5505 - 2.4833 0.99 1263 138 0.2515 0.2089 REMARK 3 14 2.4833 - 2.4227 0.99 1312 144 0.2652 0.2821 REMARK 3 15 2.4227 - 2.3677 0.99 1277 139 0.2869 0.3302 REMARK 3 16 2.3677 - 2.3173 0.98 1298 143 0.2885 0.3316 REMARK 3 17 2.3173 - 2.2709 0.99 1286 142 0.3071 0.3693 REMARK 3 18 2.2709 - 2.2281 0.98 1236 133 0.3206 0.2980 REMARK 3 19 2.2281 - 2.1883 0.99 1340 155 0.3375 0.3550 REMARK 3 20 2.1883 - 2.1512 0.93 1174 132 0.3693 0.4065 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) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.550 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 : 0.003 1996 REMARK 3 ANGLE : 0.879 2716 REMARK 3 CHIRALITY : 0.042 316 REMARK 3 PLANARITY : 0.004 343 REMARK 3 DIHEDRAL : 15.351 1222 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 124 THROUGH 152 ) REMARK 3 ORIGIN FOR THE GROUP (A): -23.0019 6.5165 13.6059 REMARK 3 T TENSOR REMARK 3 T11: 0.4169 T22: 0.4381 REMARK 3 T33: 0.3487 T12: 0.0745 REMARK 3 T13: -0.0256 T23: -0.0953 REMARK 3 L TENSOR REMARK 3 L11: 6.9644 L22: 1.7373 REMARK 3 L33: 2.8914 L12: 0.1247 REMARK 3 L13: -0.4951 L23: -0.4985 REMARK 3 S TENSOR REMARK 3 S11: -0.0405 S12: -1.2053 S13: 0.6433 REMARK 3 S21: 0.5456 S22: 0.0098 S23: -0.1198 REMARK 3 S31: -0.6184 S32: -0.4370 S33: -0.0466 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 153 THROUGH 222 ) REMARK 3 ORIGIN FOR THE GROUP (A): -5.1127 10.9202 -8.3285 REMARK 3 T TENSOR REMARK 3 T11: 0.5896 T22: 0.7235 REMARK 3 T33: 0.8475 T12: -0.0495 REMARK 3 T13: 0.0691 T23: 0.2421 REMARK 3 L TENSOR REMARK 3 L11: 7.1116 L22: 3.3192 REMARK 3 L33: 2.9178 L12: -0.7763 REMARK 3 L13: 0.5110 L23: -0.3260 REMARK 3 S TENSOR REMARK 3 S11: 0.3520 S12: 1.5273 S13: 1.5942 REMARK 3 S21: -0.4657 S22: -0.3636 S23: -0.3039 REMARK 3 S31: -0.3702 S32: 0.7699 S33: 0.1277 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 223 THROUGH 283 ) REMARK 3 ORIGIN FOR THE GROUP (A): -17.7823 0.9447 3.6163 REMARK 3 T TENSOR REMARK 3 T11: 0.3296 T22: 0.3229 REMARK 3 T33: 0.2977 T12: 0.0311 REMARK 3 T13: -0.0148 T23: -0.0419 REMARK 3 L TENSOR REMARK 3 L11: 7.6202 L22: 1.7913 REMARK 3 L33: 3.4083 L12: -0.1226 REMARK 3 L13: 0.0257 L23: -0.1665 REMARK 3 S TENSOR REMARK 3 S11: 0.0140 S12: -0.0723 S13: -0.3205 REMARK 3 S21: 0.0188 S22: -0.0177 S23: 0.0130 REMARK 3 S31: -0.0831 S32: -0.0084 S33: 0.0353 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 284 THROUGH 301 ) REMARK 3 ORIGIN FOR THE GROUP (A): -13.5609 11.4953 -9.8189 REMARK 3 T TENSOR REMARK 3 T11: 0.7022 T22: 0.7079 REMARK 3 T33: 0.8290 T12: -0.0783 REMARK 3 T13: 0.0293 T23: 0.0683 REMARK 3 L TENSOR REMARK 3 L11: 4.8192 L22: 0.6750 REMARK 3 L33: 1.5311 L12: -0.7982 REMARK 3 L13: -0.3188 L23: -0.8562 REMARK 3 S TENSOR REMARK 3 S11: 0.1648 S12: 1.3333 S13: 0.6475 REMARK 3 S21: -0.6178 S22: 0.6819 S23: -0.9784 REMARK 3 S31: -1.1134 S32: 0.8085 S33: 0.0405 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 302 THROUGH 334 ) REMARK 3 ORIGIN FOR THE GROUP (A): -27.6364 4.1880 -1.8685 REMARK 3 T TENSOR REMARK 3 T11: 0.4257 T22: 0.3834 REMARK 3 T33: 0.3809 T12: 0.0521 REMARK 3 T13: -0.0178 T23: 0.0121 REMARK 3 L TENSOR REMARK 3 L11: 6.1987 L22: 1.9458 REMARK 3 L33: 3.7345 L12: -0.3557 REMARK 3 L13: 0.0948 L23: -1.2548 REMARK 3 S TENSOR REMARK 3 S11: -0.0551 S12: 0.3698 S13: 0.2987 REMARK 3 S21: -0.1919 S22: 0.0336 S23: 0.1127 REMARK 3 S31: -0.3144 S32: -0.2068 S33: -0.0375 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 335 THROUGH 402 ) REMARK 3 ORIGIN FOR THE GROUP (A): -29.4728 -4.8808 2.0374 REMARK 3 T TENSOR REMARK 3 T11: 0.3036 T22: 0.3766 REMARK 3 T33: 0.4554 T12: 0.0138 REMARK 3 T13: -0.0291 T23: -0.0340 REMARK 3 L TENSOR REMARK 3 L11: 6.4593 L22: 1.6926 REMARK 3 L33: 3.0963 L12: -0.7746 REMARK 3 L13: 0.4274 L23: 0.3502 REMARK 3 S TENSOR REMARK 3 S11: 0.0969 S12: 0.1320 S13: -0.9801 REMARK 3 S21: 0.0117 S22: -0.0303 S23: 0.2716 REMARK 3 S31: 0.1093 S32: -0.3204 S33: 0.0234 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 403 THROUGH 419 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.8542 -3.6921 -4.3385 REMARK 3 T TENSOR REMARK 3 T11: 0.4284 T22: 0.6579 REMARK 3 T33: 0.4815 T12: 0.0362 REMARK 3 T13: -0.0201 T23: 0.0285 REMARK 3 L TENSOR REMARK 3 L11: 7.9879 L22: 2.8524 REMARK 3 L33: 5.3087 L12: -0.3618 REMARK 3 L13: -0.8322 L23: -0.1879 REMARK 3 S TENSOR REMARK 3 S11: -0.0264 S12: 0.9780 S13: -0.5380 REMARK 3 S21: -0.5359 S22: -0.3051 S23: -0.2094 REMARK 3 S31: 0.6404 S32: 0.8940 S33: 0.2026 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 626 THROUGH 634 ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.6102 -9.2414 9.8947 REMARK 3 T TENSOR REMARK 3 T11: 0.5747 T22: 0.8405 REMARK 3 T33: 0.8481 T12: 0.0698 REMARK 3 T13: 0.0052 T23: 0.1460 REMARK 3 L TENSOR REMARK 3 L11: 8.1645 L22: 3.4134 REMARK 3 L33: 4.2853 L12: 0.8034 REMARK 3 L13: 0.8773 L23: -0.1993 REMARK 3 S TENSOR REMARK 3 S11: 0.2458 S12: -0.3046 S13: -2.5948 REMARK 3 S21: -0.1181 S22: -0.7151 S23: -0.0554 REMARK 3 S31: 0.5948 S32: 0.5896 S33: 0.1344 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE ENTRY CONTAINS FRIEDEL PAIRS IN REMARK 3 I_PLUS/MINUS COLUMNS REMARK 4 REMARK 4 5GID COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-JUN-16. REMARK 100 THE DEPOSITION ID IS D_1300000826. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JUN-14 REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 130 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14860 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 41.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.3300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: NULL REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS-HCL, PEG 8000, NACL, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 77.25500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.17250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 77.25500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 21.17250 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1000 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 ASP A 160 REMARK 465 GLY A 161 REMARK 465 SER A 162 REMARK 465 THR A 163 REMARK 465 GLY A 164 REMARK 465 SER A 212 REMARK 465 VAL A 213 REMARK 465 THR A 214 REMARK 465 LEU A 215 REMARK 465 ASP A 216 REMARK 465 LEU A 217 REMARK 465 SER A 218 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 126 CG CD OE1 OE2 REMARK 470 ARG A 151 CG CD NE CZ NH1 NH2 REMARK 470 MET A 159 CG SD CE REMARK 470 ARG A 248 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 249 CG OD1 OD2 REMARK 470 GLN A 287 CG CD OE1 NE2 REMARK 470 ASP A 288 CG OD1 OD2 REMARK 470 LYS A 290 CG CD CE NZ REMARK 470 LYS A 298 CG CD CE NZ REMARK 470 GLN A 343 CG CD OE1 NE2 REMARK 470 LYS A 346 CG CD CE NZ REMARK 470 GLU A 349 CG CD OE1 OE2 REMARK 470 ARG A 364 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 398 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 403 CG CD OE1 NE2 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 GLN A 343 -87.62 -79.94 REMARK 500 PHE A 418 40.19 -80.24 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 VDP A 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5GIC RELATED DB: PDB REMARK 900 RELATED ID: 5GIE RELATED DB: PDB DBREF 5GID A 124 164 UNP P13053 VDR_RAT 124 164 DBREF 5GID A 212 419 UNP P13053 VDR_RAT 212 419 DBREF 5GID C 626 634 PDB 5GID 5GID 626 634 SEQRES 1 A 249 LEU SER GLU GLU GLN GLN HIS ILE ILE ALA ILE LEU LEU SEQRES 2 A 249 ASP ALA HIS HIS LYS THR TYR ASP PRO THR TYR ALA ASP SEQRES 3 A 249 PHE ARG ASP PHE ARG PRO PRO VAL ARG MET ASP GLY SER SEQRES 4 A 249 THR GLY SER VAL THR LEU ASP LEU SER PRO LEU SER MET SEQRES 5 A 249 LEU PRO HIS LEU ALA ASP LEU VAL SER TYR SER ILE GLN SEQRES 6 A 249 LYS VAL ILE GLY PHE ALA LYS MET ILE PRO GLY PHE ARG SEQRES 7 A 249 ASP LEU THR SER ASP ASP GLN ILE VAL LEU LEU LYS SER SEQRES 8 A 249 SER ALA ILE GLU VAL ILE MET LEU ARG SER ASN GLN SER SEQRES 9 A 249 PHE THR MET ASP ASP MET SER TRP ASP CYS GLY SER GLN SEQRES 10 A 249 ASP TYR LYS TYR ASP VAL THR ASP VAL SER LYS ALA GLY SEQRES 11 A 249 HIS THR LEU GLU LEU ILE GLU PRO LEU ILE LYS PHE GLN SEQRES 12 A 249 VAL GLY LEU LYS LYS LEU ASN LEU HIS GLU GLU GLU HIS SEQRES 13 A 249 VAL LEU LEU MET ALA ILE CYS ILE VAL SER PRO ASP ARG SEQRES 14 A 249 PRO GLY VAL GLN ASP ALA LYS LEU VAL GLU ALA ILE GLN SEQRES 15 A 249 ASP ARG LEU SER ASN THR LEU GLN THR TYR ILE ARG CYS SEQRES 16 A 249 ARG HIS PRO PRO PRO GLY SER HIS GLN LEU TYR ALA LYS SEQRES 17 A 249 MET ILE GLN LYS LEU ALA ASP LEU ARG SER LEU ASN GLU SEQRES 18 A 249 GLU HIS SER LYS GLN TYR ARG SER LEU SER PHE GLN PRO SEQRES 19 A 249 GLU ASN SER MET LYS LEU THR PRO LEU VAL LEU GLU VAL SEQRES 20 A 249 PHE GLY SEQRES 1 C 9 ASN HIS PRO MET LEU MET ASN LEU LEU HET VDP A 501 42 HETNAM VDP (3R,5S)-5-[(2R)-2-[(1R,3AS,4E,7AR)-7A-METHYL-4-[(2Z)-2- HETNAM 2 VDP [(3S,5R)-2-METHYLIDENE-3,5-BIS(OXIDANYL) HETNAM 3 VDP CYCLOHEXYLIDENE]ETHYLIDENE]-2,3,3A,5,6,7-HEXAHYDRO-1H- HETNAM 4 VDP INDEN-1-YL]PROPYL]-3-METHYL-3-OXIDANYL-1-(4- HETNAM 5 VDP PHENYLBUTYL)PYRROLIDIN-2-ONE FORMUL 3 VDP C37 H53 N O4 FORMUL 4 HOH *36(H2 O) HELIX 1 AA1 SER A 125 TYR A 143 1 19 HELIX 2 AA2 TYR A 147 PHE A 153 5 7 HELIX 3 AA3 MET A 222 MET A 243 1 22 HELIX 4 AA4 THR A 251 SER A 271 1 21 HELIX 5 AA5 ASP A 292 SER A 297 1 6 HELIX 6 AA6 THR A 302 LYS A 318 1 17 HELIX 7 AA7 HIS A 322 VAL A 335 1 14 HELIX 8 AA8 ALA A 345 HIS A 367 1 23 HELIX 9 AA9 GLN A 374 PHE A 402 1 29 HELIX 10 AB1 GLN A 403 MET A 408 1 6 HELIX 11 AB2 THR A 411 PHE A 418 1 8 HELIX 12 AB3 HIS C 627 LEU C 634 1 8 SHEET 1 AA1 3 PHE A 275 THR A 276 0 SHEET 2 AA1 3 SER A 281 ASP A 283 -1 O SER A 281 N THR A 276 SHEET 3 AA1 3 LYS A 290 TYR A 291 -1 O TYR A 291 N TRP A 282 CISPEP 1 PRO A 369 PRO A 370 0 2.71 SITE 1 AC1 12 TYR A 143 LEU A 220 SER A 233 ILE A 267 SITE 2 AC1 12 ARG A 270 SER A 271 SER A 274 TRP A 282 SITE 3 AC1 12 THR A 302 HIS A 393 TYR A 397 PHE A 418 CRYST1 154.510 42.345 42.320 90.00 96.46 90.00 C 1 2 1 4 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 0.006472 0.000000 0.000732 0.00000 SCALE2 0.000000 0.023616 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023780 0.00000