HEADER GENE REGULATION 04-FEB-20 6XZK
TITLE STRUCTURE OF ZVDR LBD-CALCITRIOL IN COMPLEX WITH CHIMERA 13
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: GLU-ASN-ALA-UIA-URL-URY-URV-UZN-LYS;
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 5 06-NOV-24 6XZK 1 REMARK
REVDAT 4 24-JAN-24 6XZK 1 REMARK
REVDAT 3 15-NOV-23 6XZK 1 LINK ATOM
REVDAT 2 01-SEP-21 6XZK 1 JRNL
REVDAT 1 17-FEB-21 6XZK 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. 2.00 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) : 2.00
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.93
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340
REMARK 3 COMPLETENESS FOR RANGE (%) : 96.6
REMARK 3 NUMBER OF REFLECTIONS : 23167
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) : 0.201
REMARK 3 FREE R VALUE : 0.224
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.870
REMARK 3 FREE R VALUE TEST SET COUNT : 1128
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 14.9310 - 3.9781 0.98 3045 163 0.1740 0.1979
REMARK 3 2 3.9781 - 3.1674 0.99 2864 158 0.1946 0.2087
REMARK 3 3 3.1674 - 2.7699 1.00 2840 142 0.2239 0.2703
REMARK 3 4 2.7699 - 2.5180 1.00 2832 146 0.2236 0.2556
REMARK 3 5 2.5180 - 2.3382 1.00 2782 147 0.2230 0.2298
REMARK 3 6 2.3382 - 2.2008 0.99 2757 135 0.2287 0.2476
REMARK 3 7 2.2008 - 2.0909 0.96 2681 148 0.2449 0.2761
REMARK 3 8 2.0909 - 2.0001 0.80 2238 89 0.2573 0.2543
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) : 0.190
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.150
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.01
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 2027
REMARK 3 ANGLE : 0.708 2733
REMARK 3 CHIRALITY : 0.038 314
REMARK 3 PLANARITY : 0.005 348
REMARK 3 DIHEDRAL : 16.042 1231
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 5
REMARK 3 TLS GROUP : 1
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 154 THROUGH 305 )
REMARK 3 ORIGIN FOR THE GROUP (A): -33.3924 30.0256 -5.0982
REMARK 3 T TENSOR
REMARK 3 T11: 0.2382 T22: 0.4080
REMARK 3 T33: 0.3037 T12: -0.0389
REMARK 3 T13: 0.0129 T23: -0.0129
REMARK 3 L TENSOR
REMARK 3 L11: 1.8298 L22: 3.4009
REMARK 3 L33: 3.8304 L12: -0.8770
REMARK 3 L13: -1.1639 L23: 2.8947
REMARK 3 S TENSOR
REMARK 3 S11: -0.0091 S12: -0.2541 S13: 0.1088
REMARK 3 S21: -0.2035 S22: 0.0401 S23: 0.0390
REMARK 3 S31: -0.3074 S32: 0.1258 S33: -0.0045
REMARK 3 TLS GROUP : 2
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 306 THROUGH 351 )
REMARK 3 ORIGIN FOR THE GROUP (A): -32.7709 12.8711 -0.8425
REMARK 3 T TENSOR
REMARK 3 T11: 0.3871 T22: 0.3848
REMARK 3 T33: 0.4123 T12: -0.0192
REMARK 3 T13: 0.0853 T23: 0.0881
REMARK 3 L TENSOR
REMARK 3 L11: 4.3053 L22: 4.7311
REMARK 3 L33: 7.8515 L12: -0.3658
REMARK 3 L13: -2.2386 L23: 1.5370
REMARK 3 S TENSOR
REMARK 3 S11: -0.2725 S12: -0.4789 S13: -0.7812
REMARK 3 S21: 0.1722 S22: 0.0401 S23: 0.3148
REMARK 3 S31: 0.9201 S32: -0.0514 S33: 0.2656
REMARK 3 TLS GROUP : 3
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 352 THROUGH 404 )
REMARK 3 ORIGIN FOR THE GROUP (A): -29.6760 35.7362 8.6662
REMARK 3 T TENSOR
REMARK 3 T11: 0.3098 T22: 0.6887
REMARK 3 T33: 0.3493 T12: 0.0164
REMARK 3 T13: -0.0110 T23: -0.1379
REMARK 3 L TENSOR
REMARK 3 L11: 5.6662 L22: 5.0991
REMARK 3 L33: 4.5074 L12: 1.3811
REMARK 3 L13: -1.5932 L23: 0.3322
REMARK 3 S TENSOR
REMARK 3 S11: -0.0844 S12: -0.9042 S13: 0.2574
REMARK 3 S21: 0.1626 S22: 0.2630 S23: -0.2013
REMARK 3 S31: -0.3959 S32: 0.4657 S33: -0.1676
REMARK 3 TLS GROUP : 4
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 405 THROUGH 452 )
REMARK 3 ORIGIN FOR THE GROUP (A): -20.7662 21.9032 -5.6104
REMARK 3 T TENSOR
REMARK 3 T11: 0.1880 T22: 0.4085
REMARK 3 T33: 0.3430 T12: -0.0011
REMARK 3 T13: 0.0069 T23: -0.0261
REMARK 3 L TENSOR
REMARK 3 L11: 3.2704 L22: 1.8605
REMARK 3 L33: 7.2659 L12: -1.3700
REMARK 3 L13: -1.7228 L23: 1.7754
REMARK 3 S TENSOR
REMARK 3 S11: -0.1230 S12: -0.6501 S13: -0.0897
REMARK 3 S21: 0.0915 S22: 0.2321 S23: -0.0957
REMARK 3 S31: 0.1755 S32: 0.6984 S33: -0.1444
REMARK 3 TLS GROUP : 5
REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 9 )
REMARK 3 ORIGIN FOR THE GROUP (A): -24.3865 36.9803 -17.8869
REMARK 3 T TENSOR
REMARK 3 T11: 0.5600 T22: 0.3992
REMARK 3 T33: 0.4070 T12: -0.1203
REMARK 3 T13: 0.0409 T23: -0.0620
REMARK 3 L TENSOR
REMARK 3 L11: 7.4481 L22: 7.0718
REMARK 3 L33: 2.5701 L12: 3.4280
REMARK 3 L13: -2.0640 L23: 2.3611
REMARK 3 S TENSOR
REMARK 3 S11: 0.0953 S12: -0.4571 S13: 0.6761
REMARK 3 S21: -0.7341 S22: 0.0024 S23: 0.2808
REMARK 3 S31: -1.8663 S32: 1.0134 S33: -0.1005
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 6XZK 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_1292106567.
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 : 6
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 : 23222
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000
REMARK 200 RESOLUTION RANGE LOW (A) : 14.931
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 96.2
REMARK 200 DATA REDUNDANCY : 1.200
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.0400
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07
REMARK 200 COMPLETENESS FOR SHELL (%) : 78.6
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 <I/SIGMA(I)> FOR SHELL : 3.320
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 (%): 47.67
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: LITHIUM SULFATE 1.8 M, MES 100 MM, PH
REMARK 280 6, 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 174.99200
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 87.49600
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 131.24400
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 43.74800
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 218.74000
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 174.99200
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 87.49600
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 43.74800
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 131.24400
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 218.74000
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: 2240 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 11740 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 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 375
REMARK 375 SPECIAL POSITION
REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS
REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL
REMARK 375 POSITIONS.
REMARK 375
REMARK 375 ATOM RES CSSEQI
REMARK 375 HOH A 683 LIES ON A SPECIAL POSITION.
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 GLY A 402
REMARK 465 ARG A 403
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 MET A 155 CE
REMARK 470 GLU A 159 CD OE1 OE2
REMARK 470 LYS A 173 CD CE NZ
REMARK 470 ARG A 251 CD NE CZ NH1 NH2
REMARK 470 ARG A 280 CG CD NE CZ NH1 NH2
REMARK 470 GLU A 310 OE2
REMARK 470 GLN A 375 CG CD OE1 NE2
REMARK 470 HIS A 377 CG ND1 CD2 CE1 NE2
REMARK 470 GLY A 401 CA C O
REMARK 470 LEU A 404 CD1 CD2
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 5 CA - C - N ANGL. DEV. = 26.8 DEGREES
REMARK 500 MFH B 6 CA - C - N ANGL. DEV. = 26.7 DEGREES
REMARK 500 URV B 7 CA - C - N ANGL. DEV. = 24.3 DEGREES
REMARK 500 UZN B 8 CA - C - N ANGL. DEV. = 14.7 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 367 34.19 -88.00
REMARK 500 URV B 7 7.53 -61.30
REMARK 500 UZN B 8 23.78 -69.60
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 5 MFH B 6 131.24
REMARK 500 MFH B 6 URV B 7 128.64
REMARK 500 URV B 7 UZN B 8 134.95
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 5 -27.31
REMARK 500 MFH B 6 -29.64
REMARK 500 URV B 7 -25.41
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 501
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 502
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 503
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residues UIA B 4 and URL B 5
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residues URL B 5 and MFH B 6
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residues MFH B 6 and URV B 7
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residues URV B 7 and UZN B 8
DBREF 6XZK A 156 453 UNP Q9PTN2 VDRA_DANRE 156 453
DBREF 6XZK B 1 9 PDB 6XZK 6XZK 1 9
SEQADV 6XZK GLY A 152 UNP Q9PTN2 EXPRESSION TAG
SEQADV 6XZK SER A 153 UNP Q9PTN2 EXPRESSION TAG
SEQADV 6XZK HIS A 154 UNP Q9PTN2 EXPRESSION TAG
SEQADV 6XZK 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 GLU ASN ALA UIA URL MFH URV UZN LYS
HET UIA B 4 7
HET URL B 5 10
HET MFH B 6 14
HET URV B 7 9
HET UZN B 8 10
HET VDX A 501 30
HET ACT A 502 4
HET ACT A 503 4
HETNAM UIA [(2~{R})-1-AZANYLPROPAN-2-YL]CARBAMIC ACID
HETNAM URL [(2~{S})-2-AZANYL-4-METHYL-PENTYL]CARBAMIC ACID
HETNAM MFH [(2~{S})-2-AZANYL-3-(4-HYDROXYPHENYL)PROPYL]CARBAMIC
HETNAM 2 MFH ACID
HETNAM URV [(2~{S})-2-AZANYL-3-METHYL-BUTYL]CARBAMIC ACID
HETNAM UZN [(2~{S})-2-AZANYLHEXYL]CARBAMIC ACID
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
HETNAM ACT ACETATE ION
HETSYN VDX 1,25 DIHYDROXY VITAMIN D3
FORMUL 2 UIA C4 H10 N2 O2
FORMUL 2 URL C7 H16 N2 O2
FORMUL 2 MFH C10 H14 N2 O3
FORMUL 2 URV C6 H14 N2 O2
FORMUL 2 UZN C7 H16 N2 O2
FORMUL 3 VDX C27 H44 O3
FORMUL 4 ACT 2(C2 H3 O2 1-)
FORMUL 6 HOH *100(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 MET A 275 1 22
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 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 405 PHE A 432 1 28
HELIX 11 AB2 GLN A 433 MET A 438 1 6
HELIX 12 AB3 THR A 441 GLY A 449 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
LINK C ALA B 3 N UIA B 4 1555 1555 1.34
LINK C UIA B 4 N URL B 5 1555 1555 1.35
LINK C URL B 5 N MFH B 6 1555 1555 1.34
LINK C MFH B 6 N URV B 7 1555 1555 1.34
LINK C URV B 7 N UZN B 8 1555 1555 1.34
LINK C UZN B 8 N LYS B 9 1555 1555 1.34
SITE 1 AC1 10 TYR A 175 SER A 265 ARG A 302 SER A 303
SITE 2 AC1 10 SER A 306 TRP A 314 CYS A 316 VAL A 328
SITE 3 AC1 10 HIS A 333 HIS A 423
SITE 1 AC2 8 THR A 174 TYR A 175 ASP A 176 TYR A 179
SITE 2 AC2 8 TYR A 264 LYS A 268 ARG A 302 HOH A 663
SITE 1 AC3 7 GLN A 398 SER A 431 GLY A 449 SER A 450
SITE 2 AC3 7 HOH A 605 HOH A 623 GLU B 1
SITE 1 AC4 10 ILE A 288 LYS A 292 GLU A 446 VAL A 447
SITE 2 AC4 10 HOH A 646 ASN B 2 ALA B 3 MFH B 6
SITE 3 AC4 10 URV B 7 UZN B 8
SITE 1 AC5 13 HIS A 154 ALA A 284 ILE A 288 LYS A 292
SITE 2 AC5 13 PRO A 434 GLU A 446 VAL A 447 ALA B 3
SITE 3 AC5 13 UIA B 4 URV B 7 UZN B 8 LYS B 9
SITE 4 AC5 13 HOH B 101
SITE 1 AC6 11 HIS A 154 LYS A 274 ALA A 284 PRO A 434
SITE 2 AC6 11 MET A 438 ALA B 3 UIA B 4 URL B 5
SITE 3 AC6 11 UZN B 8 LYS B 9 HOH B 101
SITE 1 AC7 7 LYS A 274 GLN A 287 MET A 438 UIA B 4
SITE 2 AC7 7 URL B 5 MFH B 6 LYS B 9
CRYST1 66.112 66.112 262.488 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 0.015126 0.008733 0.000000 0.00000
SCALE2 0.000000 0.017466 0.000000 0.00000
SCALE3 0.000000 0.000000 0.003810 0.00000