HEADER HORMONE 15-MAY-18 5ZWH TITLE COVALENT BOND FORMATION BETWEEN HISTIDINE OF VITAMIN D RECEPTOR (VDR) TITLE 2 AND A FULL AGONIST HAVING AN ENE-YNONE GROUP VIA CONJUGATE ADDITION TITLE 3 REACTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: VITAMIN D3 RECEPTOR; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: VDR,1,25-DIHYDROXYVITAMIN D3 RECEPTOR,NUCLEAR RECEPTOR COMPND 5 SUBFAMILY 1 GROUP I MEMBER 1; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: 13-MERIC PEPTIDE FROM DRIP205 NR2 BOX PEPTIDE; 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 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 EXPRESSION_SYSTEM: SYNTHETIC CONSTRUCT; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 32630 KEYWDS HORMONE COVALENT MODIFIER TRANSCRIPTION FACTOR VITAMIND3 ENONE KEYWDS 2 MICHAEL ADDITION ELECTROPHILE, HORMONE EXPDTA X-RAY DIFFRACTION AUTHOR M.YOSHIZAWA,T.ITOH,Y.ANAMI,A.KATO,N.YOSHIMOTO,K.YAMAMOTO REVDAT 3 23-OCT-24 5ZWH 1 REMARK REVDAT 2 08-AUG-18 5ZWH 1 JRNL REVDAT 1 18-JUL-18 5ZWH 0 JRNL AUTH M.YOSHIZAWA,T.ITOH,T.HORI,A.KATO,Y.ANAMI,N.YOSHIMOTO, JRNL AUTH 2 K.YAMAMOTO JRNL TITL IDENTIFICATION OF THE HISTIDINE RESIDUE IN VITAMIN D JRNL TITL 2 RECEPTOR THAT COVALENTLY BINDS TO ELECTROPHILIC LIGANDS JRNL REF J. MED. CHEM. V. 61 6339 2018 JRNL REFN ISSN 1520-4804 JRNL PMID 29936834 JRNL DOI 10.1021/ACS.JMEDCHEM.8B00774 REMARK 2 REMARK 2 RESOLUTION. 2.38 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0103 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.38 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.70 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.9 REMARK 3 NUMBER OF REFLECTIONS : 10001 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) : 0.237 REMARK 3 R VALUE (WORKING SET) : 0.235 REMARK 3 FREE R VALUE : 0.279 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 522 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) : 2.38 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.44 REMARK 3 REFLECTION IN BIN (WORKING SET) : 729 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.12 REMARK 3 BIN R VALUE (WORKING SET) : 0.3170 REMARK 3 BIN FREE R VALUE SET COUNT : 39 REMARK 3 BIN FREE R VALUE : 0.4160 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1927 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 60 REMARK 3 SOLVENT ATOMS : 14 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.61 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -4.50000 REMARK 3 B22 (A**2) : 4.79000 REMARK 3 B33 (A**2) : -0.02000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.36000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.579 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.307 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.278 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.279 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.932 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.902 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2031 ; 0.014 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1947 ; 0.007 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2760 ; 1.616 ; 2.012 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4488 ; 1.309 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 245 ; 5.006 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 83 ;35.376 ;25.060 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 341 ;16.137 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 7 ; 8.756 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 324 ; 0.086 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2231 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 435 ; 0.012 ; 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): 989 ; 2.465 ; 4.146 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 988 ; 2.459 ; 4.143 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1231 ; 3.619 ; 6.208 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1232 ; 3.618 ; 6.210 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1042 ; 2.418 ; 4.226 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1042 ; 2.417 ; 4.226 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1530 ; 3.580 ; 6.285 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 8610 ; 5.657 ;38.661 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 8606 ; 5.657 ;38.666 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 : NULL 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 5ZWH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-JUN-18. REMARK 100 THE DEPOSITION ID IS D_1300007785. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-JUN-16 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 : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NE3A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 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 : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10580 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.380 REMARK 200 RESOLUTION RANGE LOW (A) : 32.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.38 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.47 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: REFMAC REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MOPS-NA, NA-FORMATE, PEG 4000, REMARK 280 ETHYLENEGLYCOL, VAPOR 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 77.15000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.26000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 77.15000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 21.26000 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: 1070 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 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 GLY A 106 REMARK 465 SER A 107 REMARK 465 HIS A 108 REMARK 465 MET A 109 REMARK 465 GLY A 110 REMARK 465 SER A 111 REMARK 465 PRO A 112 REMARK 465 ASN A 113 REMARK 465 SER A 114 REMARK 465 PRO A 115 REMARK 465 LEU A 116 REMARK 465 LYS A 117 REMARK 465 ASP A 118 REMARK 465 SER A 119 REMARK 465 LEU A 120 REMARK 465 ARG A 121 REMARK 465 PRO A 122 REMARK 465 MET A 206 REMARK 465 ASP A 207 REMARK 465 GLY A 208 REMARK 465 SER A 209 REMARK 465 THR A 210 REMARK 465 GLY A 211 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 465 PRO A 219 REMARK 465 GLU A 421 REMARK 465 ILE A 422 REMARK 465 SER A 423 REMARK 465 ASP C 636 REMARK 465 ASN C 637 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 LYS A 123 CG CD CE NZ REMARK 470 ARG A 151 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 279 CG OD1 OD2 REMARK 470 LYS A 298 CG CD CE NZ REMARK 470 LYS A 311 CG CD CE NZ REMARK 470 LYS A 346 CG CD CE NZ REMARK 470 ARG A 364 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 366 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 395 CG CD CE NZ REMARK 470 ARG A 398 CG CD NE CZ NH1 NH2 REMARK 470 PHE A 402 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLN A 403 CG CD OE1 NE2 REMARK 470 ASN A 420 CG OD1 ND2 REMARK 470 LYS C 625 CG CD CE NZ REMARK 470 ASN C 626 CG OD1 ND2 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 NE2 HIS A 301 C24 9KX A 501 2.10 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 ALA A 299 59.49 -118.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 9N9 AND 9KX ARE IN ALTERNATE CONFORMATIONS OF EACH OTHER. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 9KX A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 9N9 A 502 DBREF 5ZWH A 116 423 UNP P13053 VDR_RAT 116 423 DBREF 5ZWH C 625 637 PDB 5ZWH 5ZWH 625 637 SEQADV 5ZWH GLY A 106 UNP P13053 EXPRESSION TAG SEQADV 5ZWH SER A 107 UNP P13053 EXPRESSION TAG SEQADV 5ZWH HIS A 108 UNP P13053 EXPRESSION TAG SEQADV 5ZWH MET A 109 UNP P13053 EXPRESSION TAG SEQADV 5ZWH GLY A 110 UNP P13053 EXPRESSION TAG SEQADV 5ZWH SER A 111 UNP P13053 EXPRESSION TAG SEQADV 5ZWH PRO A 112 UNP P13053 EXPRESSION TAG SEQADV 5ZWH ASN A 113 UNP P13053 EXPRESSION TAG SEQADV 5ZWH SER A 114 UNP P13053 EXPRESSION TAG SEQADV 5ZWH PRO A 115 UNP P13053 EXPRESSION TAG SEQADV 5ZWH A UNP P13053 SER 165 DELETION SEQADV 5ZWH A UNP P13053 TYR 166 DELETION SEQADV 5ZWH A UNP P13053 SER 167 DELETION SEQADV 5ZWH A UNP P13053 PRO 168 DELETION SEQADV 5ZWH A UNP P13053 ARG 169 DELETION SEQADV 5ZWH A UNP P13053 PRO 170 DELETION SEQADV 5ZWH A UNP P13053 THR 171 DELETION SEQADV 5ZWH A UNP P13053 LEU 172 DELETION SEQADV 5ZWH A UNP P13053 SER 173 DELETION SEQADV 5ZWH A UNP P13053 PHE 174 DELETION SEQADV 5ZWH A UNP P13053 SER 175 DELETION SEQADV 5ZWH A UNP P13053 GLY 176 DELETION SEQADV 5ZWH A UNP P13053 ASN 177 DELETION SEQADV 5ZWH A UNP P13053 SER 178 DELETION SEQADV 5ZWH A UNP P13053 SER 179 DELETION SEQADV 5ZWH A UNP P13053 SER 180 DELETION SEQADV 5ZWH A UNP P13053 SER 181 DELETION SEQADV 5ZWH A UNP P13053 SER 182 DELETION SEQADV 5ZWH A UNP P13053 SER 183 DELETION SEQADV 5ZWH A UNP P13053 ASP 184 DELETION SEQADV 5ZWH A UNP P13053 LEU 185 DELETION SEQADV 5ZWH A UNP P13053 TYR 186 DELETION SEQADV 5ZWH A UNP P13053 THR 187 DELETION SEQADV 5ZWH A UNP P13053 THR 188 DELETION SEQADV 5ZWH A UNP P13053 SER 189 DELETION SEQADV 5ZWH A UNP P13053 LEU 190 DELETION SEQADV 5ZWH A UNP P13053 ASP 191 DELETION SEQADV 5ZWH A UNP P13053 MET 192 DELETION SEQADV 5ZWH A UNP P13053 MET 193 DELETION SEQADV 5ZWH A UNP P13053 GLU 194 DELETION SEQADV 5ZWH A UNP P13053 PRO 195 DELETION SEQADV 5ZWH A UNP P13053 SER 196 DELETION SEQADV 5ZWH A UNP P13053 GLY 197 DELETION SEQADV 5ZWH A UNP P13053 PHE 198 DELETION SEQADV 5ZWH A UNP P13053 SER 199 DELETION SEQADV 5ZWH A UNP P13053 ASN 200 DELETION SEQADV 5ZWH A UNP P13053 LEU 201 DELETION SEQADV 5ZWH A UNP P13053 ASP 202 DELETION SEQADV 5ZWH A UNP P13053 LEU 203 DELETION SEQADV 5ZWH A UNP P13053 ASN 204 DELETION SEQADV 5ZWH A UNP P13053 GLY 205 DELETION SEQADV 5ZWH A UNP P13053 GLU 206 DELETION SEQADV 5ZWH A UNP P13053 ASP 207 DELETION SEQADV 5ZWH A UNP P13053 SER 208 DELETION SEQADV 5ZWH A UNP P13053 ASP 209 DELETION SEQADV 5ZWH A UNP P13053 ASP 210 DELETION SEQADV 5ZWH A UNP P13053 PRO 211 DELETION SEQRES 1 A 271 GLY SER HIS MET GLY SER PRO ASN SER PRO LEU LYS ASP SEQRES 2 A 271 SER LEU ARG PRO LYS LEU SER GLU GLU GLN GLN HIS ILE SEQRES 3 A 271 ILE ALA ILE LEU LEU ASP ALA HIS HIS LYS THR TYR ASP SEQRES 4 A 271 PRO THR TYR ALA ASP PHE ARG ASP PHE ARG PRO PRO VAL SEQRES 5 A 271 ARG MET ASP GLY SER THR GLY SER VAL THR LEU ASP LEU SEQRES 6 A 271 SER PRO LEU SER MET LEU PRO HIS LEU ALA ASP LEU VAL SEQRES 7 A 271 SER TYR SER ILE GLN LYS VAL ILE GLY PHE ALA LYS MET SEQRES 8 A 271 ILE PRO GLY PHE ARG ASP LEU THR SER ASP ASP GLN ILE SEQRES 9 A 271 VAL LEU LEU LYS SER SER ALA ILE GLU VAL ILE MET LEU SEQRES 10 A 271 ARG SER ASN GLN SER PHE THR MET ASP ASP MET SER TRP SEQRES 11 A 271 ASP CYS GLY SER GLN ASP TYR LYS TYR ASP VAL THR ASP SEQRES 12 A 271 VAL SER LYS ALA GLY HIS THR LEU GLU LEU ILE GLU PRO SEQRES 13 A 271 LEU ILE LYS PHE GLN VAL GLY LEU LYS LYS LEU ASN LEU SEQRES 14 A 271 HIS GLU GLU GLU HIS VAL LEU LEU MET ALA ILE CYS ILE SEQRES 15 A 271 VAL SER PRO ASP ARG PRO GLY VAL GLN ASP ALA LYS LEU SEQRES 16 A 271 VAL GLU ALA ILE GLN ASP ARG LEU SER ASN THR LEU GLN SEQRES 17 A 271 THR TYR ILE ARG CYS ARG HIS PRO PRO PRO GLY SER HIS SEQRES 18 A 271 GLN LEU TYR ALA LYS MET ILE GLN LYS LEU ALA ASP LEU SEQRES 19 A 271 ARG SER LEU ASN GLU GLU HIS SER LYS GLN TYR ARG SER SEQRES 20 A 271 LEU SER PHE GLN PRO GLU ASN SER MET LYS LEU THR PRO SEQRES 21 A 271 LEU VAL LEU GLU VAL PHE GLY ASN GLU ILE SER SEQRES 1 C 13 LYS ASN HIS PRO MET LEU MET ASN LEU LEU LYS ASP ASN HET 9KX A 501 30 HET 9N9 A 502 30 HETNAM 9KX (2S)-2-[(1R,3AS,4E,7AR)-7A-METHYL-4-[2-[(3R,5R)-4- HETNAM 2 9KX METHYLIDENE-3,5-BIS(OXIDANYL) HETNAM 3 9KX CYCLOHEXYLIDENE]ETHYLIDENE]-2,3,3A,5,6,7-HEXAHYDRO-1H- HETNAM 4 9KX INDEN-1-YL]OCT-4,6-DIENE-3-ONE HETNAM 9N9 (E,2S)-2-[(1R,3AS,4E,7AR)-7A-METHYL-4-[2-[(3R,5R)-4- HETNAM 2 9N9 METHYLIDENE-3,5-BIS(OXIDANYL) HETNAM 3 9N9 CYCLOHEXYLIDENE]ETHYLIDENE]-2,3,3A,5,6,7-HEXAHYDRO-1H- HETNAM 4 9N9 INDEN-1-YL]OCT-6-EN-4-YN-3-ONE FORMUL 3 9KX C27 H38 O3 FORMUL 4 9N9 C27 H36 O3 FORMUL 5 HOH *14(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 ILE A 244 1 23 HELIX 4 AA4 THR A 251 ASN A 272 1 22 HELIX 5 AA5 ASP A 292 ALA A 299 1 8 HELIX 6 AA6 THR A 302 ASN A 320 1 19 HELIX 7 AA7 HIS A 322 VAL A 335 1 14 HELIX 8 AA8 ASP A 344 HIS A 367 1 24 HELIX 9 AA9 GLN A 374 GLN A 403 1 30 HELIX 10 AB1 GLN A 403 LYS A 409 1 7 HELIX 11 AB2 THR A 411 PHE A 418 1 8 HELIX 12 AB3 HIS C 627 LYS C 635 1 9 SHEET 1 AA1 2 PHE A 275 THR A 276 0 SHEET 2 AA1 2 SER A 281 TRP A 282 -1 O SER A 281 N THR A 276 LINK NE2 HIS A 301 C23A9KX A 501 1555 1555 1.37 CISPEP 1 PRO A 369 PRO A 370 0 2.26 SITE 1 AC1 14 TYR A 143 VAL A 230 SER A 233 ILE A 264 SITE 2 AC1 14 ARG A 270 SER A 271 SER A 274 TRP A 282 SITE 3 AC1 14 VAL A 296 HIS A 301 HIS A 393 TYR A 397 SITE 4 AC1 14 9N9 A 502 HOH A 604 SITE 1 AC2 13 TYR A 143 LEU A 223 ALA A 227 VAL A 230 SITE 2 AC2 13 SER A 233 MET A 268 ARG A 270 SER A 271 SITE 3 AC2 13 SER A 274 TRP A 282 HIS A 301 LEU A 305 SITE 4 AC2 13 9KX A 501 CRYST1 154.300 42.520 41.960 90.00 95.72 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 0.006481 0.000000 0.000649 0.00000 SCALE2 0.000000 0.023518 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023951 0.00000