HEADER GENE REGULATION 04-FEB-20 6XZJ
TITLE STRUCTURE OF ZVDR LBD-CALCITRIOL IN COMPLEX WITH CHIMERA 12
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-LEU-URR-UIL-URL-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 5 13-NOV-24 6XZJ 1 REMARK
REVDAT 4 24-JAN-24 6XZJ 1 REMARK
REVDAT 3 15-NOV-23 6XZJ 1 LINK ATOM
REVDAT 2 01-SEP-21 6XZJ 1 JRNL
REVDAT 1 17-FEB-21 6XZJ 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. 2.10 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) : 2.10
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.04
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350
REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2
REMARK 3 NUMBER OF REFLECTIONS : 19738
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.204
REMARK 3 R VALUE (WORKING SET) : 0.202
REMARK 3 FREE R VALUE : 0.247
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 986
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 38.0400 - 4.0158 0.99 2986 156 0.1798 0.2206
REMARK 3 2 4.0158 - 3.1880 0.98 2738 144 0.1928 0.2357
REMARK 3 3 3.1880 - 2.7852 0.98 2688 141 0.2275 0.2979
REMARK 3 4 2.7852 - 2.5306 0.98 2655 140 0.2342 0.2729
REMARK 3 5 2.5306 - 2.3492 0.98 2633 139 0.2445 0.3260
REMARK 3 6 2.3492 - 2.2107 0.97 2579 135 0.2711 0.2963
REMARK 3 7 2.2107 - 2.1000 0.92 2473 131 0.3166 0.3432
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) : 0.250
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.410
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 64.93
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 : 0.004 2009
REMARK 3 ANGLE : 0.736 2713
REMARK 3 CHIRALITY : 0.040 314
REMARK 3 PLANARITY : 0.005 339
REMARK 3 DIHEDRAL : 15.542 1217
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 1
REMARK 3 TLS GROUP : 1
REMARK 3 SELECTION: ALL
REMARK 3 ORIGIN FOR THE GROUP (A): -31.9537 26.3781 -1.5954
REMARK 3 T TENSOR
REMARK 3 T11: 0.4266 T22: 0.5566
REMARK 3 T33: 0.4684 T12: -0.0340
REMARK 3 T13: 0.0101 T23: -0.1017
REMARK 3 L TENSOR
REMARK 3 L11: 1.4053 L22: 0.7581
REMARK 3 L33: 1.1796 L12: -0.5085
REMARK 3 L13: -0.9589 L23: 0.2891
REMARK 3 S TENSOR
REMARK 3 S11: -0.0767 S12: -0.1876 S13: 0.0111
REMARK 3 S21: 0.0855 S22: 0.0905 S23: -0.0554
REMARK 3 S31: 0.0760 S32: 0.0580 S33: -0.0000
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 6XZJ 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_1292106565.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 06-MAY-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 : ESRF
REMARK 200 BEAMLINE : ID23-1
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 6M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : AIMLESS
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19740
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100
REMARK 200 RESOLUTION RANGE LOW (A) : 38.040
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2
REMARK 200 DATA REDUNDANCY : 14.00
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.7400
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18
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 <I/SIGMA(I)> 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 (%): 45.96
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: NAACETATE 3M, 0.1 M TRIS PH 7.5, VAPOR
REMARK 280 DIFFUSION, HANGING DROP, 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 169.48000
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 84.74000
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 127.11000
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 42.37000
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 211.85000
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 169.48000
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 84.74000
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 42.37000
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 127.11000
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 211.85000
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: 2440 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 11100 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 GLU A 159 CG CD OE1 OE2
REMARK 470 GLN A 162 CG CD OE1 NE2
REMARK 470 LYS A 173 CD CE NZ
REMARK 470 ARG A 184 CD NE CZ NH1 NH2
REMARK 470 ARG A 251 CD NE CZ NH1 NH2
REMARK 470 GLU A 285 CG CD OE1 OE2
REMARK 470 GLU A 310 CG CD OE1 OE2
REMARK 470 ASP A 311 OD1 OD2
REMARK 470 LYS A 322 CE NZ
REMARK 470 GLU A 336 CD OE1 OE2
REMARK 470 LYS A 343 CE NZ
REMARK 470 LYS A 350 CE NZ
REMARK 470 LYS A 352 CE NZ
REMARK 470 GLN A 375 CD OE1 NE2
REMARK 470 ARG A 403 CG CD NE CZ NH1 NH2
REMARK 470 GLN A 411 CG CD OE1 NE2
REMARK 470 GLU A 421 OE1 OE2
REMARK 470 GLU A 451 CG CD OE1 OE2
REMARK 470 ARG B 686 CB CG CD NE CZ NH1 NH2
REMARK 470 GLN B 694 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 OUR B 691 CA - C - N ANGL. DEV. = 19.9 DEGREES
REMARK 500 UIL B 692 CA - C - N ANGL. DEV. = 26.8 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 367 37.15 -97.09
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 OUR B 691 UIL B 692 136.31
REMARK 500 UIL B 692 URL B 693 126.46
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 OUR B 691 -20.46
REMARK 500 UIL B 692 -27.05
REMARK 500 URL B 693 -11.40
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 residues OUR B 691 and UIL B
REMARK 800 692
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residues UIL B 692 and URL B
REMARK 800 693
DBREF 6XZJ A 156 453 UNP Q9PTN2 VDRA_DANRE 156 453
DBREF 6XZJ B 686 694 PDB 6XZJ 6XZJ 686 694
SEQADV 6XZJ GLY A 152 UNP Q9PTN2 EXPRESSION TAG
SEQADV 6XZJ SER A 153 UNP Q9PTN2 EXPRESSION TAG
SEQADV 6XZJ HIS A 154 UNP Q9PTN2 EXPRESSION TAG
SEQADV 6XZJ 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 LEU OUR UIL URL GLN
HET OUR B 691 13
HET UIL B 692 10
HET URL B 693 10
HET VDX A 501 30
HET ACT A 502 4
HETNAM OUR [AZANYL-[[(4~{S})-4-AZANYL-5-(CARBOXYAMINO)
HETNAM 2 OUR PENTYL]AMINO]METHYLIDENE]AZANIUM
HETNAM UIL [(2~{R})-1-AZANYL-4-METHYL-PENTAN-2-YL]CARBAMIC ACID
HETNAM URL [(2~{S})-2-AZANYL-4-METHYL-PENTYL]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 OUR C7 H18 N5 O2 1+
FORMUL 2 UIL C7 H16 N2 O2
FORMUL 2 URL C7 H16 N2 O2
FORMUL 3 VDX C27 H44 O3
FORMUL 4 ACT C2 H3 O2 1-
FORMUL 5 HOH *25(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 THR A 283 SER A 303 1 21
HELIX 5 AA5 GLY A 318 ASP A 320 5 3
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 GLY A 402 PHE A 432 1 31
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 LEU B 690 N OUR B 691 1555 1555 1.35
LINK C OUR B 691 N UIL B 692 1555 1555 1.34
LINK C UIL B 692 N URL B 693 1555 1555 1.34
LINK C URL B 693 N GLN B 694 1555 1555 1.35
SITE 1 AC1 13 TYR A 175 VAL A 262 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 ACT A 502
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 VDX A 501
SITE 1 AC3 11 HIS A 154 LYS A 274 ILE A 288 PRO A 434
SITE 2 AC3 11 MET A 438 HIS B 687 LYS B 688 ILE B 689
SITE 3 AC3 11 LEU B 690 URL B 693 GLN B 694
SITE 1 AC4 9 LYS A 274 ARG A 280 GLN A 287 PRO A 434
SITE 2 AC4 9 MET A 438 ILE B 689 LEU B 690 OUR B 691
SITE 3 AC4 9 GLN B 694
CRYST1 66.200 66.200 254.220 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 0.015106 0.008721 0.000000 0.00000
SCALE2 0.000000 0.017443 0.000000 0.00000
SCALE3 0.000000 0.000000 0.003934 0.00000