HEADER TRANSCRIPTION/TRANSFERASE 16-FEB-12 4DQM
TITLE REVEALING A MARINE NATURAL PRODUCT AS A NOVEL AGONIST FOR RETINOIC
TITLE 2 ACID RECEPTORS WITH A UNIQUE BINDING MODE AND ANTITUMOR ACTIVITY
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: RETINOIC ACID RECEPTOR ALPHA;
COMPND 3 CHAIN: A, C;
COMPND 4 FRAGMENT: LIGAND BINDING DOMAIN, UNP RESIDUES 182-415;
COMPND 5 SYNONYM: RAR-ALPHA, NUCLEAR RECEPTOR SUBFAMILY 1 GROUP B MEMBER 1;
COMPND 6 ENGINEERED: YES;
COMPND 7 MOL_ID: 2;
COMPND 8 MOLECULE: NUCLEAR RECEPTOR COACTIVATOR 1;
COMPND 9 CHAIN: B, D;
COMPND 10 FRAGMENT: LXXLL MOTIF 7, UNP RESIDUES 1432-1441;
COMPND 11 SYNONYM: NCOA-1, CLASS E BASIC HELIX-LOOP-HELIX PROTEIN 74, BHLHE74,
COMPND 12 PROTEIN HIN-2, RIP160, RENAL CARCINOMA ANTIGEN NY-REN-52, STEROID
COMPND 13 RECEPTOR COACTIVATOR 1, SRC-1;
COMPND 14 EC: 2.3.1.48;
COMPND 15 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 GENE: NR1B1, RARA;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET24A;
SOURCE 11 MOL_ID: 2;
SOURCE 12 SYNTHETIC: YES;
SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 14 ORGANISM_COMMON: HUMAN;
SOURCE 15 ORGANISM_TAXID: 9606;
SOURCE 16 OTHER_DETAILS: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED.
KEYWDS NUCLEAR RECEPTOR TRANSCRIPTION FACTOR, LIGAND BINDING DOMAIN,
KEYWDS 2 TRANSCRIPTION REGULATION, NUCLEUS, TRANSCRIPTION-TRANSFERASE COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR S.WANG,Z.WANG,S.LIN,W.ZHENG,R.WANG,S.JIN,J.CHEN,L.JIN,Y.LI
REVDAT 3 15-NOV-17 4DQM 1 REMARK
REVDAT 2 16-APR-14 4DQM 1 REMARK
REVDAT 1 03-OCT-12 4DQM 0
JRNL AUTH S.WANG,Z.WANG,S.LIN,W.ZHENG,R.WANG,S.JIN,J.CHEN,L.JIN,Y.LI
JRNL TITL REVEALING A NATURAL MARINE PRODUCT AS A NOVEL AGONIST FOR
JRNL TITL 2 RETINOIC ACID RECEPTORS WITH A UNIQUE BINDING MODE AND
JRNL TITL 3 INHIBITORY EFFECTS ON CANCER CELLS.
JRNL REF BIOCHEM.J. V. 446 79 2012
JRNL REFN ISSN 0264-6021
JRNL PMID 22642567
JRNL DOI 10.1042/BJ20120726
REMARK 2
REMARK 2 RESOLUTION. 2.75 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC
REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.75
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.46
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 84.9
REMARK 3 NUMBER OF REFLECTIONS : 16995
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) : 0.216
REMARK 3 R VALUE (WORKING SET) : 0.213
REMARK 3 FREE R VALUE : 0.259
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 922
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) : 2.55
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.62
REMARK 3 REFLECTION IN BIN (WORKING SET) : 1139
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 82.04
REMARK 3 BIN R VALUE (WORKING SET) : 0.3210
REMARK 3 BIN FREE R VALUE SET COUNT : 62
REMARK 3 BIN FREE R VALUE : 0.3350
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 3855
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 54
REMARK 3 SOLVENT ATOMS : 31
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 62.50
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.10000
REMARK 3 B22 (A**2) : 0.15000
REMARK 3 B33 (A**2) : -0.05000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.00000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.885
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.337
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.263
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.510
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.943
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.931
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3968 ; 0.014 ; 0.020
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5360 ; 1.750 ; 2.018
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 484 ; 6.145 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 162 ;39.109 ;24.815
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 763 ;19.768 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;23.147 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 636 ; 0.102 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2863 ; 0.007 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
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): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL
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 : MASK
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 USED IF PRESENT IN
REMARK 3 THE INPUT U VALUES: REFINED INDIVIDUALLY
REMARK 4
REMARK 4 4DQM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-FEB-12.
REMARK 100 THE DEPOSITION ID IS D_1000070660.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 29-JUL-10
REMARK 200 TEMPERATURE (KELVIN) : 200
REMARK 200 PH : 7.0
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : APS
REMARK 200 BEAMLINE : 21-ID-F
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.5619
REMARK 200 MONOCHROMATOR : DIAMOND [111]
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17478
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.550
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5
REMARK 200 DATA REDUNDANCY : 7.400
REMARK 200 R MERGE (I) : 0.09200
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.5000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.75
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.80
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8
REMARK 200 DATA REDUNDANCY IN SHELL : 7.70
REMARK 200 R MERGE FOR SHELL (I) : 0.64800
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: MOLREP
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 57.58
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.90
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 2% V/V TACSIMATE PH7.0, 5% 2-PROPANOL,
REMARK 280 0.1M IMADAZOLE , 8% PEG 3350, VAPOR DIFFUSION, HANGING DROP,
REMARK 280 TEMPERATURE 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21
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,Y+1/2,-Z+1/2
REMARK 290 4555 -X,-Y+1/2,Z+1/2
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 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 52.23000
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 56.74000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 52.23000
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 56.74000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1, 2
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: 950 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 11290 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 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 350
REMARK 350 BIOMOLECULE: 2
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: 900 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 11220 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D
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 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 ASP C 282 N
REMARK 480
REMARK 480 ZERO OCCUPANCY ATOM
REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO
REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS
REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME;
REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 480 M RES C SSEQI ATOMS
REMARK 480 CYS A 333 SG
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 N SER A 287 O3 LUF A 501 1.68
REMARK 500 SG CYS A 235 C23 LUF A 501 1.79
REMARK 500 N SER C 287 O3 LUF C 501 1.87
REMARK 500 SG CYS C 235 C23 LUF C 501 1.91
REMARK 500 OE2 GLU C 412 O SER D 1433 1.96
REMARK 500 NH2 ARG C 364 O HOH C 610 2.12
REMARK 500 CA PHE C 286 O3 LUF C 501 2.14
REMARK 500 CA PHE A 286 O3 LUF A 501 2.16
REMARK 500 C PHE A 286 O3 LUF A 501 2.19
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS
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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3)
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 RES CSSEQI ATM2 DEVIATION
REMARK 500 CYS A 333 CB CYS A 333 SG -0.344
REMARK 500 HIS A 372 CG HIS A 372 CD2 0.054
REMARK 500 TRP C 225 CE2 TRP C 225 CD2 0.079
REMARK 500 HIS C 372 CG HIS C 372 CD2 0.056
REMARK 500 GLU D1441 CD GLU D1441 OE2 0.068
REMARK 500
REMARK 500 REMARK: NULL
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 CYS A 333 CA - CB - SG ANGL. DEV. = 17.3 DEGREES
REMARK 500 LEU C 378 CB - CG - CD1 ANGL. DEV. = -10.4 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 TYR A 208 126.90 -174.44
REMARK 500 SER A 213 42.22 23.62
REMARK 500 GLU A 215 -64.30 -99.12
REMARK 500 ASP A 322 -165.84 -106.32
REMARK 500 LYS A 390 6.73 -69.97
REMARK 500 PRO A 403 -73.66 -75.75
REMARK 500 LEU B1434 -53.40 -22.43
REMARK 500 PHE C 199 86.37 -154.71
REMARK 500 THR C 209 -151.51 -127.03
REMARK 500 THR C 210 157.08 179.70
REMARK 500 SER C 213 49.27 28.91
REMARK 500 LEU C 220 112.86 -161.87
REMARK 500 ASP C 341 18.69 86.53
REMARK 500 PRO C 403 -81.80 -71.65
REMARK 500 SER D1433 3.16 -53.47
REMARK 500 LEU D1434 -53.64 107.17
REMARK 500 THR D1440 44.80 -93.34
REMARK 500
REMARK 500 REMARK: NULL
REMARK 610
REMARK 610 MISSING HETEROATOM
REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 610 I=INSERTION CODE):
REMARK 610 M RES C SSEQI
REMARK 610 LUF C 501
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LUF A 501
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LUF C 501
DBREF 4DQM A 182 415 UNP P10276 RARA_HUMAN 182 415
DBREF 4DQM B 1432 1441 UNP Q15788 NCOA1_HUMAN 1432 1441
DBREF 4DQM C 182 415 UNP P10276 RARA_HUMAN 182 415
DBREF 4DQM D 1432 1441 UNP Q15788 NCOA1_HUMAN 1432 1441
SEQRES 1 A 234 PRO GLU VAL GLY GLU LEU ILE GLU LYS VAL ARG LYS ALA
SEQRES 2 A 234 HIS GLN GLU THR PHE PRO ALA LEU CYS GLN LEU GLY LYS
SEQRES 3 A 234 TYR THR THR ASN ASN SER SER GLU GLN ARG VAL SER LEU
SEQRES 4 A 234 ASP ILE ASP LEU TRP ASP LYS PHE SER GLU LEU SER THR
SEQRES 5 A 234 LYS CYS ILE ILE LYS THR VAL GLU PHE ALA LYS GLN LEU
SEQRES 6 A 234 PRO GLY PHE THR THR LEU THR ILE ALA ASP GLN ILE THR
SEQRES 7 A 234 LEU LEU LYS ALA ALA CYS LEU ASP ILE LEU ILE LEU ARG
SEQRES 8 A 234 ILE CYS THR ARG TYR THR PRO GLU GLN ASP THR MET THR
SEQRES 9 A 234 PHE SER ASP GLY LEU THR LEU ASN ARG THR GLN MET HIS
SEQRES 10 A 234 ASN ALA GLY PHE GLY PRO LEU THR ASP LEU VAL PHE ALA
SEQRES 11 A 234 PHE ALA ASN GLN LEU LEU PRO LEU GLU MET ASP ASP ALA
SEQRES 12 A 234 GLU THR GLY LEU LEU SER ALA ILE CYS LEU ILE CYS GLY
SEQRES 13 A 234 ASP ARG GLN ASP LEU GLU GLN PRO ASP ARG VAL ASP MET
SEQRES 14 A 234 LEU GLN GLU PRO LEU LEU GLU ALA LEU LYS VAL TYR VAL
SEQRES 15 A 234 ARG LYS ARG ARG PRO SER ARG PRO HIS MET PHE PRO LYS
SEQRES 16 A 234 MET LEU MET LYS ILE THR ASP LEU ARG SER ILE SER ALA
SEQRES 17 A 234 LYS GLY ALA GLU ARG VAL ILE THR LEU LYS MET GLU ILE
SEQRES 18 A 234 PRO GLY SER MET PRO PRO LEU ILE GLN GLU MET LEU GLU
SEQRES 1 B 10 LYS SER LEU LEU GLN GLN LEU LEU THR GLU
SEQRES 1 C 234 PRO GLU VAL GLY GLU LEU ILE GLU LYS VAL ARG LYS ALA
SEQRES 2 C 234 HIS GLN GLU THR PHE PRO ALA LEU CYS GLN LEU GLY LYS
SEQRES 3 C 234 TYR THR THR ASN ASN SER SER GLU GLN ARG VAL SER LEU
SEQRES 4 C 234 ASP ILE ASP LEU TRP ASP LYS PHE SER GLU LEU SER THR
SEQRES 5 C 234 LYS CYS ILE ILE LYS THR VAL GLU PHE ALA LYS GLN LEU
SEQRES 6 C 234 PRO GLY PHE THR THR LEU THR ILE ALA ASP GLN ILE THR
SEQRES 7 C 234 LEU LEU LYS ALA ALA CYS LEU ASP ILE LEU ILE LEU ARG
SEQRES 8 C 234 ILE CYS THR ARG TYR THR PRO GLU GLN ASP THR MET THR
SEQRES 9 C 234 PHE SER ASP GLY LEU THR LEU ASN ARG THR GLN MET HIS
SEQRES 10 C 234 ASN ALA GLY PHE GLY PRO LEU THR ASP LEU VAL PHE ALA
SEQRES 11 C 234 PHE ALA ASN GLN LEU LEU PRO LEU GLU MET ASP ASP ALA
SEQRES 12 C 234 GLU THR GLY LEU LEU SER ALA ILE CYS LEU ILE CYS GLY
SEQRES 13 C 234 ASP ARG GLN ASP LEU GLU GLN PRO ASP ARG VAL ASP MET
SEQRES 14 C 234 LEU GLN GLU PRO LEU LEU GLU ALA LEU LYS VAL TYR VAL
SEQRES 15 C 234 ARG LYS ARG ARG PRO SER ARG PRO HIS MET PHE PRO LYS
SEQRES 16 C 234 MET LEU MET LYS ILE THR ASP LEU ARG SER ILE SER ALA
SEQRES 17 C 234 LYS GLY ALA GLU ARG VAL ILE THR LEU LYS MET GLU ILE
SEQRES 18 C 234 PRO GLY SER MET PRO PRO LEU ILE GLN GLU MET LEU GLU
SEQRES 1 D 10 LYS SER LEU LEU GLN GLN LEU LEU THR GLU
HET LUF A 501 28
HET LUF C 501 26
HETNAM LUF (5S)-4-[(3E,7E)-4,8-DIMETHYL-10-(2,6,6-
HETNAM 2 LUF TRIMETHYLCYCLOHEX-1-EN-1-YL)DECA-3,7-DIEN-1-YL]-5-
HETNAM 3 LUF HYDROXYFURAN-2(5H)-ONE
HETSYN LUF LUFFARIELLOLIDE
FORMUL 5 LUF 2(C25 H38 O3)
FORMUL 7 HOH *31(H2 O)
HELIX 1 1 PRO A 182 PHE A 199 1 18
HELIX 2 2 ALA A 201 LEU A 205 5 5
HELIX 3 3 ASP A 221 GLN A 245 1 25
HELIX 4 4 GLY A 248 LEU A 252 5 5
HELIX 5 5 THR A 253 THR A 275 1 23
HELIX 6 6 ARG A 294 ALA A 300 1 7
HELIX 7 7 GLY A 301 PRO A 304 5 4
HELIX 8 8 LEU A 305 LEU A 317 1 13
HELIX 9 9 PRO A 318 GLU A 320 5 3
HELIX 10 10 ASP A 322 ILE A 335 1 14
HELIX 11 11 GLN A 344 ARG A 367 1 24
HELIX 12 12 HIS A 372 MET A 379 1 8
HELIX 13 13 MET A 379 LYS A 390 1 12
HELIX 14 14 LYS A 390 ILE A 402 1 13
HELIX 15 15 PRO A 407 GLU A 415 1 9
HELIX 16 16 SER B 1433 GLU B 1441 1 9
HELIX 17 17 GLU C 183 PHE C 199 1 17
HELIX 18 18 ALA C 201 LEU C 205 5 5
HELIX 19 19 ASP C 221 GLN C 245 1 25
HELIX 20 20 GLY C 248 LEU C 252 5 5
HELIX 21 21 THR C 253 THR C 275 1 23
HELIX 22 22 ARG C 294 ALA C 300 1 7
HELIX 23 23 GLY C 301 GLY C 303 5 3
HELIX 24 24 PRO C 304 LEU C 316 1 13
HELIX 25 25 ASP C 322 ILE C 335 1 14
HELIX 26 26 GLN C 344 ARG C 367 1 24
HELIX 27 27 HIS C 372 LYS C 390 1 19
HELIX 28 28 LYS C 390 MET C 400 1 11
HELIX 29 29 PRO C 407 GLU C 415 1 9
HELIX 30 30 LEU D 1435 THR D 1440 1 6
SHEET 1 A 3 TYR A 277 THR A 278 0
SHEET 2 A 3 THR A 283 THR A 285 -1 O THR A 283 N THR A 278
SHEET 3 A 3 THR A 291 ASN A 293 -1 O LEU A 292 N MET A 284
SHEET 1 B 3 TYR C 277 THR C 278 0
SHEET 2 B 3 THR C 283 THR C 285 -1 O THR C 283 N THR C 278
SHEET 3 B 3 THR C 291 ASN C 293 -1 O LEU C 292 N MET C 284
LINK SG CYS A 235 O2 LUF A 501 1555 1555 0.72
LINK SG CYS C 235 O2 LUF C 501 1555 1555 1.55
SITE 1 AC1 13 PHE A 228 LEU A 231 SER A 232 CYS A 235
SITE 2 AC1 13 LEU A 266 LEU A 269 ILE A 273 ARG A 276
SITE 3 AC1 13 PHE A 286 SER A 287 GLY A 301 VAL A 395
SITE 4 AC1 13 LEU A 414
SITE 1 AC2 13 PHE C 228 LEU C 231 SER C 232 CYS C 235
SITE 2 AC2 13 LEU C 266 LEU C 269 ILE C 273 ARG C 276
SITE 3 AC2 13 PHE C 286 SER C 287 PHE C 302 VAL C 395
SITE 4 AC2 13 HOH C 605
CRYST1 54.120 104.460 113.480 90.00 90.00 90.00 P 2 21 21 8
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 0.018477 0.000000 0.000000 0.00000
SCALE2 0.000000 0.009573 0.000000 0.00000
SCALE3 0.000000 0.000000 0.008812 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
