HEADER NUCLEAR PROTEIN 05-DEC-17 5YXJ
TITLE FXR LIGAND BINDING DOMAIN
CAVEAT 5YXJ RESIDUES LEU A 245 AND THR A 246 ARE NOT PROPERLY LINKED
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: BILE ACID RECEPTOR;
COMPND 3 CHAIN: A, B;
COMPND 4 SYNONYM: FARNESOID X-ACTIVATED RECEPTOR,FARNESOL RECEPTOR HRR-1,
COMPND 5 NUCLEAR RECEPTOR SUBFAMILY 1 GROUP H MEMBER 4,RETINOID X RECEPTOR-
COMPND 6 INTERACTING PROTEIN 14,RXR-INTERACTING PROTEIN 14;
COMPND 7 ENGINEERED: YES;
COMPND 8 MOL_ID: 2;
COMPND 9 MOLECULE: PEPTIDE FROM NUCLEAR RECEPTOR COACTIVATOR 2;
COMPND 10 CHAIN: C, D;
COMPND 11 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: NR1H4, BAR, FXR, HRR1, RIP14;
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_COMMON: HUMAN;
SOURCE 12 ORGANISM_TAXID: 9606
KEYWDS COMPLEX, NUCLEAR PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR L.YI,L.YONG
REVDAT 2 27-MAR-24 5YXJ 1 REMARK
REVDAT 1 13-MAR-19 5YXJ 0
JRNL AUTH L.YI,L.YONG
JRNL TITL A LIGAND OF DRUG BINDING TO FXR
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 2
REMARK 2 RESOLUTION. 2.62 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.8.0189
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) : 2.62
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 115.70
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 87.5
REMARK 3 NUMBER OF REFLECTIONS : 16902
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) : 0.209
REMARK 3 R VALUE (WORKING SET) : 0.207
REMARK 3 FREE R VALUE : 0.248
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 892
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) : 2.62
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.69
REMARK 3 REFLECTION IN BIN (WORKING SET) : 1323
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.19
REMARK 3 BIN R VALUE (WORKING SET) : 0.2740
REMARK 3 BIN FREE R VALUE SET COUNT : 64
REMARK 3 BIN FREE R VALUE : 0.3190
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 3842
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 70
REMARK 3 SOLVENT ATOMS : 115
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.42
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.82000
REMARK 3 B22 (A**2) : -3.21000
REMARK 3 B33 (A**2) : 2.80000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 1.94000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 1.296
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.337
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.232
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.153
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.937
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.914
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3991 ; 0.015 ; 0.019
REMARK 3 BOND LENGTHS OTHERS (A): 3722 ; 0.002 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5385 ; 1.812 ; 1.988
REMARK 3 BOND ANGLES OTHERS (DEGREES): 8660 ; 1.115 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 460 ; 6.711 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 197 ;39.403 ;25.025
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 745 ;19.055 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;14.141 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 600 ; 0.096 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4303 ; 0.007 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): 770 ; 0.002 ; 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): 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 : 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 U VALUES : REFINED INDIVIDUALLY
REMARK 4
REMARK 4 5YXJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-DEC-17.
REMARK 100 THE DEPOSITION ID IS D_1300006069.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 21-OCT-15
REMARK 200 TEMPERATURE (KELVIN) : 293
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SSRF
REMARK 200 BEAMLINE : BL17U1
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.05
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20327
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.620
REMARK 200 RESOLUTION RANGE LOW (A) : 115.700
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8
REMARK 200 DATA REDUNDANCY : 4.900
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.8000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.62
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 10.00
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: PHASER
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 58.79
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.98
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M LITHIUM SULFATE MONOHYDRATE, 0.1M
REMARK 280 TRIS PH 8.5, 25% W/V POLYETHYLENE GLYCOL 3350, VAPOR DIFFUSION,
REMARK 280 HANGING DROP, TEMPERATURE 298K
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 81.67550
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 17.48800
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 81.67550
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 17.48800
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
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: 1000 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 11990 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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: 980 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 12060 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 LYS A 339
REMARK 465 LEU A 340
REMARK 465 PRO A 341
REMARK 465 GLN A 472
REMARK 465 LYS B 339
REMARK 465 LEU B 340
REMARK 465 PRO B 341
REMARK 465 SER B 342
REMARK 465 GLY B 343
REMARK 465 VAL B 456
REMARK 465 ASN B 457
REMARK 465 ASP B 458
REMARK 465 GLN B 472
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 LEU A 245 CG CD1 CD2
REMARK 470 ARG B 455 CG CD NE CZ NH1 NH2
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 O THR A 462 O HOH A 601 1.51
REMARK 500 O HOH A 608 O HOH A 662 1.66
REMARK 500 O HOH A 666 O HOH A 678 1.78
REMARK 500 N TRP A 469 O HOH A 602 1.79
REMARK 500 C ILE A 335 O HOH A 604 1.80
REMARK 500 O PRO A 463 O HOH A 603 1.89
REMARK 500 O ILE A 335 O HOH A 604 1.97
REMARK 500 O PRO A 463 O HOH A 605 2.00
REMARK 500 SD MET A 257 O HOH A 663 2.06
REMARK 500 C PRO A 463 O HOH A 603 2.06
REMARK 500 N CYS A 466 O HOH A 601 2.06
REMARK 500 O CYS A 466 O HOH A 606 2.09
REMARK 500 C ILE A 468 O HOH A 602 2.09
REMARK 500 CG2 ILE A 468 O HOH A 602 2.10
REMARK 500 OE1 GLU A 276 O HOH A 607 2.11
REMARK 500 N ASP A 470 O HOH A 606 2.13
REMARK 500 N LEU A 464 O HOH A 608 2.14
REMARK 500 OH TYR A 260 OE2 GLU A 334 2.17
REMARK 500 OH TYR B 382 O HOH B 601 2.17
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC
REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15
REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A
REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375
REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE
REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS.
REMARK 500
REMARK 500 DISTANCE CUTOFF:
REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS
REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE
REMARK 500 CG GLN B 267 C ARG B 455 1565 2.18
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 LEU A 245 C THR A 246 N -0.206
REMARK 500 TRP B 454 CB TRP B 454 CG -0.131
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 LEU A 245 CB - CA - C ANGL. DEV. = 12.0 DEGREES
REMARK 500 LEU A 245 CA - C - N ANGL. DEV. = 13.8 DEGREES
REMARK 500 LEU A 245 O - C - N ANGL. DEV. = -21.1 DEGREES
REMARK 500 THR A 246 N - CA - CB ANGL. DEV. = 16.8 DEGREES
REMARK 500 THR A 246 N - CA - C ANGL. DEV. = -16.5 DEGREES
REMARK 500 ASP B 312 CB - CA - C ANGL. DEV. = 28.3 DEGREES
REMARK 500 ASP B 312 N - CA - C ANGL. DEV. = -20.4 DEGREES
REMARK 500 ARG B 351 NE - CZ - NH1 ANGL. DEV. = 3.3 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 245 131.81 113.61
REMARK 500 LEU A 391 45.26 -97.79
REMARK 500 GLU A 425 -37.34 -34.52
REMARK 500 VAL A 456 -33.64 -143.74
REMARK 500 LEU B 245 75.13 65.67
REMARK 500 ASP B 312 176.84 166.79
REMARK 500 LEU B 391 53.90 -101.88
REMARK 500 ILE B 421 -74.04 -66.16
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 LEU A 245 -20.53
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 93U A 501
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue 93U B 501
DBREF 5YXJ A 244 472 UNP Q96RI1 NR1H4_HUMAN 258 486
DBREF 5YXJ B 244 472 UNP Q96RI1 NR1H4_HUMAN 258 486
DBREF 5YXJ C 745 755 UNP E7EWM1 E7EWM1_HUMAN 741 751
DBREF 5YXJ D 745 755 UNP E7EWM1 E7EWM1_HUMAN 741 751
SEQRES 1 A 229 GLU LEU THR PRO ASP GLN GLN THR LEU LEU HIS PHE ILE
SEQRES 2 A 229 MET ASP SER TYR ASN LYS GLN ARG MET PRO GLN GLU ILE
SEQRES 3 A 229 THR ASN LYS ILE LEU LYS GLU GLU PHE SER ALA GLU GLU
SEQRES 4 A 229 ASN PHE LEU ILE LEU THR GLU MET ALA THR ASN HIS VAL
SEQRES 5 A 229 GLN VAL LEU VAL GLU PHE THR LYS LYS LEU PRO GLY PHE
SEQRES 6 A 229 GLN THR LEU ASP HIS GLU ASP GLN ILE ALA LEU LEU LYS
SEQRES 7 A 229 GLY SER ALA VAL GLU ALA MET PHE LEU ARG SER ALA GLU
SEQRES 8 A 229 ILE PHE ASN LYS LYS LEU PRO SER GLY HIS SER ASP LEU
SEQRES 9 A 229 LEU GLU GLU ARG ILE ARG ASN SER GLY ILE SER ASP GLU
SEQRES 10 A 229 TYR ILE THR PRO MET PHE SER PHE TYR LYS SER ILE GLY
SEQRES 11 A 229 GLU LEU LYS MET THR GLN GLU GLU TYR ALA LEU LEU THR
SEQRES 12 A 229 ALA ILE VAL ILE LEU SER PRO ASP ARG GLN TYR ILE LYS
SEQRES 13 A 229 ASP ARG GLU ALA VAL GLU LYS LEU GLN GLU PRO LEU LEU
SEQRES 14 A 229 ASP VAL LEU GLN LYS LEU CYS LYS ILE HIS GLN PRO GLU
SEQRES 15 A 229 ASN PRO GLN HIS PHE ALA CYS LEU LEU GLY ARG LEU THR
SEQRES 16 A 229 GLU LEU ARG THR PHE ASN HIS HIS HIS ALA GLU MET LEU
SEQRES 17 A 229 MET SER TRP ARG VAL ASN ASP HIS LYS PHE THR PRO LEU
SEQRES 18 A 229 LEU CYS GLU ILE TRP ASP VAL GLN
SEQRES 1 B 229 GLU LEU THR PRO ASP GLN GLN THR LEU LEU HIS PHE ILE
SEQRES 2 B 229 MET ASP SER TYR ASN LYS GLN ARG MET PRO GLN GLU ILE
SEQRES 3 B 229 THR ASN LYS ILE LEU LYS GLU GLU PHE SER ALA GLU GLU
SEQRES 4 B 229 ASN PHE LEU ILE LEU THR GLU MET ALA THR ASN HIS VAL
SEQRES 5 B 229 GLN VAL LEU VAL GLU PHE THR LYS LYS LEU PRO GLY PHE
SEQRES 6 B 229 GLN THR LEU ASP HIS GLU ASP GLN ILE ALA LEU LEU LYS
SEQRES 7 B 229 GLY SER ALA VAL GLU ALA MET PHE LEU ARG SER ALA GLU
SEQRES 8 B 229 ILE PHE ASN LYS LYS LEU PRO SER GLY HIS SER ASP LEU
SEQRES 9 B 229 LEU GLU GLU ARG ILE ARG ASN SER GLY ILE SER ASP GLU
SEQRES 10 B 229 TYR ILE THR PRO MET PHE SER PHE TYR LYS SER ILE GLY
SEQRES 11 B 229 GLU LEU LYS MET THR GLN GLU GLU TYR ALA LEU LEU THR
SEQRES 12 B 229 ALA ILE VAL ILE LEU SER PRO ASP ARG GLN TYR ILE LYS
SEQRES 13 B 229 ASP ARG GLU ALA VAL GLU LYS LEU GLN GLU PRO LEU LEU
SEQRES 14 B 229 ASP VAL LEU GLN LYS LEU CYS LYS ILE HIS GLN PRO GLU
SEQRES 15 B 229 ASN PRO GLN HIS PHE ALA CYS LEU LEU GLY ARG LEU THR
SEQRES 16 B 229 GLU LEU ARG THR PHE ASN HIS HIS HIS ALA GLU MET LEU
SEQRES 17 B 229 MET SER TRP ARG VAL ASN ASP HIS LYS PHE THR PRO LEU
SEQRES 18 B 229 LEU CYS GLU ILE TRP ASP VAL GLN
SEQRES 1 C 11 GLU ASN ALA LEU LEU ARG TYR LEU LEU ASP LYS
SEQRES 1 D 11 GLU ASN ALA LEU LEU ARG TYR LEU LEU ASP LYS
HET 93U A 501 35
HET 93U B 501 35
HETNAM 93U 2-[BENZYL(METHYL)AMINO]ETHYL METHYL 2,6-DIMETHYL-4-(3-
HETNAM 2 93U NITROPHENYL)PYRIDINE-3,5-DICARBOXYLATE
FORMUL 5 93U 2(C26 H27 N3 O6)
FORMUL 7 HOH *115(H2 O)
HELIX 1 AA1 THR A 246 GLN A 263 1 18
HELIX 2 AA2 PRO A 266 GLU A 276 1 11
HELIX 3 AA3 SER A 279 LEU A 305 1 27
HELIX 4 AA4 GLY A 307 LEU A 311 5 5
HELIX 5 AA5 ASP A 312 LYS A 338 1 27
HELIX 6 AA6 GLY A 343 ARG A 353 1 11
HELIX 7 AA7 SER A 358 GLU A 374 1 17
HELIX 8 AA8 THR A 378 LEU A 391 1 14
HELIX 9 AA9 ASP A 400 GLN A 423 1 24
HELIX 10 AB1 GLN A 428 THR A 442 1 15
HELIX 11 AB2 THR A 442 SER A 453 1 12
HELIX 12 AB3 SER A 453 ASP A 458 1 6
HELIX 13 AB4 THR A 462 TRP A 469 1 8
HELIX 14 AB5 THR B 246 ASN B 261 1 16
HELIX 15 AB6 PRO B 266 GLU B 276 1 11
HELIX 16 AB7 SER B 279 LYS B 303 1 25
HELIX 17 AB8 GLY B 307 LEU B 311 5 5
HELIX 18 AB9 HIS B 313 LYS B 338 1 26
HELIX 19 AC1 SER B 345 ASN B 354 1 10
HELIX 20 AC2 SER B 358 LEU B 375 1 18
HELIX 21 AC3 THR B 378 LEU B 391 1 14
HELIX 22 AC4 ASP B 400 GLN B 423 1 24
HELIX 23 AC5 GLN B 428 THR B 442 1 15
HELIX 24 AC6 THR B 442 ARG B 455 1 14
HELIX 25 AC7 THR B 462 ASP B 470 1 9
HELIX 26 AC8 ASN C 746 LYS C 755 1 10
HELIX 27 AC9 ASN D 746 LYS D 755 1 10
SITE 1 AC1 12 HIS A 294 MET A 328 PHE A 329 SER A 332
SITE 2 AC1 12 ILE A 357 ILE A 362 MET A 365 TYR A 369
SITE 3 AC1 12 HIS A 447 MET A 450 LEU A 451 TRP A 469
SITE 1 AC2 13 PHE B 284 LEU B 287 MET B 290 HIS B 294
SITE 2 AC2 13 MET B 328 PHE B 329 SER B 332 ILE B 357
SITE 3 AC2 13 TYR B 361 HIS B 447 MET B 450 TRP B 454
SITE 4 AC2 13 TRP B 469
CRYST1 163.351 34.976 118.926 90.00 103.38 90.00 C 1 2 1 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 0.006122 0.000000 0.001457 0.00000
SCALE2 0.000000 0.028591 0.000000 0.00000
SCALE3 0.000000 0.000000 0.008643 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
