10 20 30 40 50 60 70 80 3D5X - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER TRANSFERASE 17-MAY-08 3D5X
TITLE CRYSTAL STRUCTURE OF AN ACTIVATED (THR->ASP) POLO-LIKE TITLE 2 KINASE 1 (PLK1) CATALYTIC DOMAIN IN COMPLEX WITH TITLE 3 WORTMANNIN.
COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLO-LIKE KINASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN; COMPND 5 EC: 2.7.11.21; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DANIO RERIO; SOURCE 3 ORGANISM_COMMON: LEOPARD DANIO,ZEBRA DANIO,ZEBRA FISH; SOURCE 4 ORGANISM_TAXID: 7955; SOURCE 5 GENE: PLK1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) STAR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX6P-1
KEYWDS POLO-LIKE KINASE 1, PLK1, CATALYTIC DOMAIN, SMALL-MOLECULE KEYWDS 2 INHIBITOR, KINASE, TRANSFERASE
EXPDTA X-RAY DIFFRACTION
AUTHOR R.A.ELLING,R.V.FUCINI,M.J.ROMANOWSKI
REVDAT 3 24-FEB-09 3D5X 1 VERSN REVDAT 2 09-SEP-08 3D5X 1 LINK REVDAT 1 26-AUG-08 3D5X 0
JRNL AUTH R.A.ELLING,R.V.FUCINI,M.J.ROMANOWSKI JRNL TITL STRUCTURES OF THE WILD-TYPE AND ACTIVATED JRNL TITL 2 CATALYTIC DOMAINS OF BRACHYDANIO RERIO POLO-LIKE JRNL TITL 3 KINASE 1 (PLK1): CHANGES IN THE ACTIVE-SITE JRNL TITL 4 CONFORMATION AND INTERACTIONS WITH LIGANDS. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 64 909 2008 JRNL REFN ISSN 0907-4449 JRNL PMID 18703838 JRNL DOI 10.1107/S0907444908019513
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 9568 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) : 0.263 REMARK 3 R VALUE (WORKING SET) : 0.260 REMARK 3 FREE R VALUE : 0.299 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.000 REMARK 3 FREE R VALUE TEST SET COUNT : 720 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 15 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.90 REMARK 3 REFLECTION IN BIN (WORKING SET) : 928 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.50 REMARK 3 BIN R VALUE (WORKING SET) : 0.3270 REMARK 3 BIN FREE R VALUE SET COUNT : 64 REMARK 3 BIN FREE R VALUE : 0.3370 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2196 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 31 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 56.50 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 1.376 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.415 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.315 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 15.364 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.902 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.857 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2280 ; 0.006 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3095 ; 1.026 ; 1.992 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 276 ; 3.862 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 100 ;35.648 ;23.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 382 ;14.396 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;11.381 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 347 ; 0.061 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1719 ; 0.002 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 955 ; 0.178 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1578 ; 0.296 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 56 ; 0.117 ; 0.200 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): 30 ; 0.117 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 2 ; 0.066 ; 0.200 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): 1433 ; 1.240 ; 2.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2255 ; 2.146 ; 5.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 965 ; 0.908 ; 2.500 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 840 ; 1.486 ; 5.000 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 : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 3D5X COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-MAY-08. REMARK 100 THE RCSB ID CODE IS RCSB047632.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-APR-07 REMARK 200 TEMPERATURE (KELVIN) : 180 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-1 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 : SIDE-SCATTERING CUBE ROOT I- REMARK 200 BEAM BENT SINGLE CRYSTAL; REMARK 200 ASYMMETRIC CUT 12.2 DEGS. REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTALCLEAR REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12803 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 2.900 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.44200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.100 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: 3D5U REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HANGING-DROP VAPOR DIFFUSION AT 4 REMARK 280 C (277K); PROTEIN AND WORTMANNIN AT A 1:1 MOLAR RATIO; PROTEIN REMARK 280 AT 7 MG/ML IN 50 MM TRIS-HCL PH 7.5, 200 MM NACL AND 3 MM DTT; REMARK 280 CRYSTALLIZATION CONDITION: 0.1 M HEPES PH 7.5, 0.2 M (NH4) REMARK 280 2SO4, 22.5% PEG 3350 AND 15% GLYCEROL; CRYOPROTECTANT: 15% REMARK 280 ETHYLENE GLYCOL, VAPOR DIFFUSION, HANGING DROP
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 3 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,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 Z,X,Y REMARK 290 6555 Z,-X,-Y REMARK 290 7555 -Z,-X,Y REMARK 290 8555 -Z,X,-Y REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z,-X REMARK 290 11555 Y,-Z,-X REMARK 290 12555 -Y,-Z,X REMARK 290 13555 X+1/2,Y+1/2,Z+1/2 REMARK 290 14555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 15555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 16555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 17555 Z+1/2,X+1/2,Y+1/2 REMARK 290 18555 Z+1/2,-X+1/2,-Y+1/2 REMARK 290 19555 -Z+1/2,-X+1/2,Y+1/2 REMARK 290 20555 -Z+1/2,X+1/2,-Y+1/2 REMARK 290 21555 Y+1/2,Z+1/2,X+1/2 REMARK 290 22555 -Y+1/2,Z+1/2,-X+1/2 REMARK 290 23555 Y+1/2,-Z+1/2,-X+1/2 REMARK 290 24555 -Y+1/2,-Z+1/2,X+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 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 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 0.00000 REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 67.77100 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 67.77100 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 67.77100 REMARK 290 SMTRY1 14 -1.000000 0.000000 0.000000 67.77100 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 67.77100 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 67.77100 REMARK 290 SMTRY1 15 -1.000000 0.000000 0.000000 67.77100 REMARK 290 SMTRY2 15 0.000000 1.000000 0.000000 67.77100 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 67.77100 REMARK 290 SMTRY1 16 1.000000 0.000000 0.000000 67.77100 REMARK 290 SMTRY2 16 0.000000 -1.000000 0.000000 67.77100 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 67.77100 REMARK 290 SMTRY1 17 0.000000 0.000000 1.000000 67.77100 REMARK 290 SMTRY2 17 1.000000 0.000000 0.000000 67.77100 REMARK 290 SMTRY3 17 0.000000 1.000000 0.000000 67.77100 REMARK 290 SMTRY1 18 0.000000 0.000000 1.000000 67.77100 REMARK 290 SMTRY2 18 -1.000000 0.000000 0.000000 67.77100 REMARK 290 SMTRY3 18 0.000000 -1.000000 0.000000 67.77100 REMARK 290 SMTRY1 19 0.000000 0.000000 -1.000000 67.77100 REMARK 290 SMTRY2 19 -1.000000 0.000000 0.000000 67.77100 REMARK 290 SMTRY3 19 0.000000 1.000000 0.000000 67.77100 REMARK 290 SMTRY1 20 0.000000 0.000000 -1.000000 67.77100 REMARK 290 SMTRY2 20 1.000000 0.000000 0.000000 67.77100 REMARK 290 SMTRY3 20 0.000000 -1.000000 0.000000 67.77100 REMARK 290 SMTRY1 21 0.000000 1.000000 0.000000 67.77100 REMARK 290 SMTRY2 21 0.000000 0.000000 1.000000 67.77100 REMARK 290 SMTRY3 21 1.000000 0.000000 0.000000 67.77100 REMARK 290 SMTRY1 22 0.000000 -1.000000 0.000000 67.77100 REMARK 290 SMTRY2 22 0.000000 0.000000 1.000000 67.77100 REMARK 290 SMTRY3 22 -1.000000 0.000000 0.000000 67.77100 REMARK 290 SMTRY1 23 0.000000 1.000000 0.000000 67.77100 REMARK 290 SMTRY2 23 0.000000 0.000000 -1.000000 67.77100 REMARK 290 SMTRY3 23 -1.000000 0.000000 0.000000 67.77100 REMARK 290 SMTRY1 24 0.000000 -1.000000 0.000000 67.77100 REMARK 290 SMTRY2 24 0.000000 0.000000 -1.000000 67.77100 REMARK 290 SMTRY3 24 1.000000 0.000000 0.000000 67.77100 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 12 REMARK 465 PRO A 13 REMARK 465 LEU A 14 REMARK 465 GLY A 15 REMARK 465 SER A 16 REMARK 465 ASP A 17 REMARK 465 PRO A 18 REMARK 465 LYS A 19 REMARK 465 SER A 20 REMARK 465 ALA A 21 REMARK 465 PRO A 22 REMARK 465 LEU A 23 REMARK 465 LEU A 197 REMARK 465 CYS A 198 REMARK 465 GLY A 199 REMARK 465 THR A 200 REMARK 465 PRO A 201 REMARK 465 ASN A 202 REMARK 465 TYR A 203 REMARK 465 ARG A 310 REMARK 465 PHE A 311 REMARK 465 SER A 312
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 ARG A 34 CG CD NE CZ NH1 NH2 REMARK 470 PHE A 50 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 52 CD CE NZ REMARK 470 MET A 74 CG SD CE REMARK 470 LYS A 77 CD CE NZ REMARK 470 LYS A 83 N CG CD CE NZ REMARK 470 LYS A 92 CD CE NZ REMARK 470 LYS A 129 CD CE NZ REMARK 470 LYS A 132 CE NZ REMARK 470 LYS A 195 CG CD CE NZ REMARK 470 LYS A 211 CE NZ REMARK 470 LYS A 212 CG CD CE NZ REMARK 470 LYS A 243 CG CD CE NZ REMARK 470 LYS A 250 CD CE NZ REMARK 470 LYS A 251 CG CD CE NZ REMARK 470 ARG A 258 CG CD NE CZ NH1 NH2
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 ARG A 34 -76.53 -68.95 REMARK 500 LEU A 75 59.39 -108.00 REMARK 500 ARG A 122 -150.07 53.36 REMARK 500 LYS A 132 -141.44 59.49 REMARK 500 ARG A 161 -11.18 73.11 REMARK 500 ASP A 180 84.09 59.65 REMARK 500 SER A 215 -127.14 -137.78 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 KWT A 1
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3D5U RELATED DB: PDB REMARK 900 RELATED ID: 3D5V RELATED DB: PDB REMARK 900 RELATED ID: 3D5W RELATED DB: PDB
DBREF 3D5X A 17 312 UNP Q4KMI8 Q4KMI8_DANRE 17 312
SEQADV 3D5X GLY A 12 UNP Q4KMI8 EXPRESSION TAG SEQADV 3D5X PRO A 13 UNP Q4KMI8 EXPRESSION TAG SEQADV 3D5X LEU A 14 UNP Q4KMI8 EXPRESSION TAG SEQADV 3D5X GLY A 15 UNP Q4KMI8 EXPRESSION TAG SEQADV 3D5X SER A 16 UNP Q4KMI8 EXPRESSION TAG SEQADV 3D5X ASP A 196 UNP Q4KMI8 THR 196 ENGINEERED
SEQRES 1 A 301 GLY PRO LEU GLY SER ASP PRO LYS SER ALA PRO LEU LYS SEQRES 2 A 301 GLU ILE PRO ASP VAL LEU VAL ASP PRO ARG THR MET LYS SEQRES 3 A 301 ARG TYR MET ARG GLY ARG PHE LEU GLY LYS GLY GLY PHE SEQRES 4 A 301 ALA LYS CYS TYR GLU ILE THR ASP MET ASP THR LYS GLU SEQRES 5 A 301 VAL PHE ALA GLY LYS VAL VAL PRO LYS SER MET LEU LEU SEQRES 6 A 301 LYS PRO HIS GLN LYS GLU LYS MET SER THR GLU ILE ALA SEQRES 7 A 301 ILE HIS LYS SER LEU ASP ASN PRO HIS VAL VAL GLY PHE SEQRES 8 A 301 HIS GLY PHE PHE GLU ASP ASP ASP PHE VAL TYR VAL VAL SEQRES 9 A 301 LEU GLU ILE CYS ARG ARG ARG SER LEU LEU GLU LEU HIS SEQRES 10 A 301 LYS ARG ARG LYS ALA VAL THR GLU PRO GLU ALA ARG TYR SEQRES 11 A 301 PHE MET ARG GLN THR ILE GLN GLY VAL GLN TYR LEU HIS SEQRES 12 A 301 ASN ASN ARG VAL ILE HIS ARG ASP LEU LYS LEU GLY ASN SEQRES 13 A 301 LEU PHE LEU ASN ASP ASP MET ASP VAL LYS ILE GLY ASP SEQRES 14 A 301 PHE GLY LEU ALA THR LYS ILE GLU PHE ASP GLY GLU ARG SEQRES 15 A 301 LYS LYS ASP LEU CYS GLY THR PRO ASN TYR ILE ALA PRO SEQRES 16 A 301 GLU VAL LEU CYS LYS LYS GLY HIS SER PHE GLU VAL ASP SEQRES 17 A 301 ILE TRP SER LEU GLY CYS ILE LEU TYR THR LEU LEU VAL SEQRES 18 A 301 GLY LYS PRO PRO PHE GLU THR SER CYS LEU LYS GLU THR SEQRES 19 A 301 TYR ILE ARG ILE LYS LYS ASN GLU TYR SER VAL PRO ARG SEQRES 20 A 301 HIS ILE ASN PRO VAL ALA SER ALA LEU ILE ARG ARG MET SEQRES 21 A 301 LEU HIS ALA ASP PRO THR LEU ARG PRO SER VAL ALA GLU SEQRES 22 A 301 LEU LEU THR ASP GLU PHE PHE THR SER GLY TYR ALA PRO SEQRES 23 A 301 MET ARG LEU PRO THR SER CYS LEU THR VAL PRO PRO ARG SEQRES 24 A 301 PHE SER
HET KWT A 1 31
HETNAM KWT (1S,6BR,9AS,11R,11BR)-9A,11B-DIMETHYL-1-[(METHYLOXY) HETNAM 2 KWT METHYL]-3,6,9-TRIOXO-1,6,6B,7,8,9,9A,10,11,11B- HETNAM 3 KWT DECAHYDRO-3H-FURO[4,3,2-DE]INDENO[4,5-H][2]BENZOPYRAN- HETNAM 4 KWT 11-YL ACETATE
HETSYN KWT [1S-(1A,6BA,9AB,11A,11BB)]-11-(ACETYLOXY)-1,6B,7,8,9A, HETSYN 2 KWT 10,11,11B-OCTAHYDRO-1-(METHOXYMETHLY) -9A,11B- HETSYN 3 KWT DIMETHYL-3H-FURO[4,3,2-DE]INDENL[4,5-H]-2-BENZOPYRAN- HETSYN 4 KWT 3,6,9,TRIONE; WORTMANNIN
FORMUL 2 KWT C23 H24 O8
HELIX 1 1 LYS A 77 GLU A 82 1 6 HELIX 2 2 LYS A 83 LEU A 94 1 12 HELIX 3 3 SER A 123 LYS A 132 1 10 HELIX 4 4 THR A 135 ASN A 156 1 22 HELIX 5 5 ALA A 205 CYS A 210 1 6 HELIX 6 6 PHE A 216 GLY A 233 1 18 HELIX 7 7 CYS A 241 LYS A 251 1 11 HELIX 8 8 ASN A 261 LEU A 272 1 12 HELIX 9 9 SER A 281 LEU A 286 1 6 HELIX 10 10 GLU A 289 GLY A 294 1 6 HELIX 11 11 PRO A 301 THR A 306 5 6
SHEET 1 A 6 VAL A 29 VAL A 31 0 SHEET 2 A 6 ARG A 38 GLY A 48 -1 O TYR A 39 N LEU A 30 SHEET 3 A 6 ALA A 51 ASP A 58 -1 O THR A 57 N MET A 40 SHEET 4 A 6 VAL A 64 PRO A 71 -1 O GLY A 67 N TYR A 54 SHEET 5 A 6 PHE A 111 LEU A 116 -1 O VAL A 114 N LYS A 68 SHEET 6 A 6 PHE A 102 GLU A 107 -1 N GLY A 104 O VAL A 115 SHEET 1 B 2 VAL A 158 ILE A 159 0 SHEET 2 B 2 THR A 185 LYS A 186 -1 O THR A 185 N ILE A 159 SHEET 1 C 2 LEU A 168 LEU A 170 0 SHEET 2 C 2 VAL A 176 ILE A 178 -1 O LYS A 177 N PHE A 169
LINK NZ LYS A 68 C19 KWT A 1 1555 1555 1.43
SITE 1 AC1 10 LYS A 47 GLY A 48 ALA A 51 CYS A 53 SITE 2 AC1 10 ALA A 66 LYS A 68 LEU A 116 GLU A 117 SITE 3 AC1 10 CYS A 119 PHE A 169
CRYST1 135.542 135.542 135.542 90.00 90.00 90.00 I 2 3 24
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 0.007378 0.000000 0.000000 0.00000
SCALE2 0.000000 0.007378 0.000000 0.00000
SCALE3 0.000000 0.000000 0.007378 0.00000