HEADER TRANSFERASE 21-JUN-04 1W1G
TITLE CRYSTAL STRUCTURE OF THE PDK1 PLECKSTRIN HOMOLOGY (PH)
TITLE 2 DOMAIN BOUND TO DIC4-PHOSPHATIDYLINOSITOL (3,4,5)-
TITLE 3 TRISPHOSPHATE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 3-PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE-1;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: PLECKSTRIN HOMOLOGY DOMAIN, RESIDUES 409-556;
COMPND 5 SYNONYM: HPDK1;
COMPND 6 EC: 2.7.1.37;
COMPND 7 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693;
SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21;
SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PGEX
KEYWDS TRANSFERASE, PDK1, PHOSPHOINOSITIDE DEPENDENT PROTEIN
KEYWDS 2 KINASE 1, PKB, PLECKSTRIN HOMOLOGY DOMAIN, INOSITOL
KEYWDS 3 PHOSPHATE, PHOSPHOINOSITIDE, SIGNAL TRANSDUCTION,
KEYWDS 4 PI3-KINASE, PIP3 SERINE/THREONINE PROTEIN KINASE
EXPDTA X-RAY DIFFRACTION
AUTHOR D.KOMANDER,M.DEAK,D.R.ALESSI,D.M.F.VAN AALTEN
REVDAT 2 24-FEB-09 1W1G 1 VERSN
REVDAT 1 19-NOV-04 1W1G 0
JRNL AUTH D.KOMANDER,A.FAIRSERVICE,M.DEAK,G.S.KULAR,
JRNL AUTH 2 A.R.PRESCOTT,C.P.DOWNES,S.T.SAFRANY,D.R.ALESSI,
JRNL AUTH 3 D.M.F.VAN AALTEN
JRNL TITL STRUCTURAL INSIGHTS INTO THE REGULATION OF PDK1 BY
JRNL TITL 2 PHOSPHOINOSITIDES AND INOSITOL PHOSPHATES
JRNL REF EMBO J. V. 23 3918 2004
JRNL REFN ISSN 0261-4189
JRNL PMID 15457207
JRNL DOI 10.1038/SJ.EMBOJ.7600379
REMARK 2
REMARK 2 RESOLUTION. 1.45 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.2.0003
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) : 1.45
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7
REMARK 3 NUMBER OF REFLECTIONS : 25241
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) : 0.183
REMARK 3 R VALUE (WORKING SET) : 0.182
REMARK 3 FREE R VALUE : 0.236
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.100
REMARK 3 FREE R VALUE TEST SET COUNT : 545
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) : 1.45
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.49
REMARK 3 REFLECTION IN BIN (WORKING SET) : 1834
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.00
REMARK 3 BIN R VALUE (WORKING SET) : 0.3390
REMARK 3 BIN FREE R VALUE SET COUNT : 44
REMARK 3 BIN FREE R VALUE : 0.3080
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 1206
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 33
REMARK 3 SOLVENT ATOMS : 163
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.94
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 1.58000
REMARK 3 B22 (A**2) : -0.83000
REMARK 3 B33 (A**2) : -0.73000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.06000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.089
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.081
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.073
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.471
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.972
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.956
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1273 ; 0.016 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): 1115 ; 0.002 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1731 ; 1.703 ; 1.961
REMARK 3 BOND ANGLES OTHERS (DEGREES): 2588 ; 0.860 ; 3.001
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 142 ; 6.622 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 67 ;34.693 ;23.731
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 219 ;13.710 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;17.708 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 184 ; 0.109 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1363 ; 0.008 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): 263 ; 0.001 ; 0.020
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 267 ; 0.221 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1116 ; 0.200 ; 0.200
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 613 ; 0.181 ; 0.200
REMARK 3 NON-BONDED TORSION OTHERS (A): 672 ; 0.107 ; 0.200
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 117 ; 0.159 ; 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): 8 ; 0.166 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): 39 ; 0.240 ; 0.200
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 17 ; 0.274 ; 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): 746 ; 1.727 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 287 ; 0.745 ; 1.500
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1168 ; 2.305 ; 2.000
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 612 ; 3.614 ; 3.000
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 563 ; 4.923 ; 4.500
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 : 2
REMARK 3
REMARK 3 TLS GROUP : 1
REMARK 3 NUMBER OF COMPONENTS GROUP : 3
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 414 A 466
REMARK 3 RESIDUE RANGE : A 472 A 487
REMARK 3 RESIDUE RANGE : A 494 A 543
REMARK 3 ORIGIN FOR THE GROUP (A): 10.5388 27.1746 24.0723
REMARK 3 T TENSOR
REMARK 3 T11: -0.0377 T22: 0.0133
REMARK 3 T33: -0.0088 T12: -0.0001
REMARK 3 T13: -0.0004 T23: -0.0049
REMARK 3 L TENSOR
REMARK 3 L11: 0.1679 L22: 1.4071
REMARK 3 L33: 0.4956 L12: 0.1263
REMARK 3 L13: -0.1429 L23: -0.5604
REMARK 3 S TENSOR
REMARK 3 S11: -0.0012 S12: -0.0141 S13: 0.0265
REMARK 3 S21: -0.0763 S22: 0.0301 S23: -0.0092
REMARK 3 S31: 0.0443 S32: -0.0069 S33: -0.0288
REMARK 3
REMARK 3 TLS GROUP : 2
REMARK 3 NUMBER OF COMPONENTS GROUP : 4
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 408 A 413
REMARK 3 RESIDUE RANGE : A 466 A 471
REMARK 3 RESIDUE RANGE : A 544 A 549
REMARK 3 RESIDUE RANGE : A 488 A 493
REMARK 3 ORIGIN FOR THE GROUP (A): 9.5684 26.7739 22.8190
REMARK 3 T TENSOR
REMARK 3 T11: -0.0232 T22: -0.0096
REMARK 3 T33: -0.0304 T12: -0.0101
REMARK 3 T13: -0.0146 T23: -0.0199
REMARK 3 L TENSOR
REMARK 3 L11: 0.4742 L22: 1.4621
REMARK 3 L33: 0.4845 L12: 0.2713
REMARK 3 L13: -0.2195 L23: -0.8330
REMARK 3 S TENSOR
REMARK 3 S11: 0.0278 S12: 0.0203 S13: 0.0334
REMARK 3 S21: -0.0906 S22: 0.0671 S23: 0.0777
REMARK 3 S31: 0.0498 S32: 0.0051 S33: -0.0950
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : BABINET MODEL WITH 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 ADDED IN THE
REMARK 3 RIDING POSITIONS. THE SIDE CHAINS OF SOME DISORDERED RESIDUES
REMARK 3 WERE REFINED EITHER WITH THE OCCUPANCY SET TO 0.02, OR THE
REMARK 3 RESIDUE WAS MUTATED TO ALA. THE ACYL-CHAINS OF THE LIGAND WERE
REMARK 3 NOT MODELLED DUE TO DISORDER.
REMARK 4
REMARK 4 1W1G COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-JUN-04.
REMARK 100 THE PDBE ID CODE IS EBI-20199.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 15-SEP-03
REMARK 200 TEMPERATURE (KELVIN) : 100.0
REMARK 200 PH : 4.20
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : N
REMARK 200 RADIATION SOURCE : ROTATING ANODE
REMARK 200 BEAMLINE : NULL
REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : MIRRORS
REMARK 200
REMARK 200 DETECTOR TYPE : IMAGE PLATE (RAXIS 4)
REMARK 200 DETECTOR MANUFACTURER : RIGAKU
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTALCLEAR
REMARK 200 DATA SCALING SOFTWARE : D*TREK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25810
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450
REMARK 200 RESOLUTION RANGE LOW (A) : 30.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7
REMARK 200 DATA REDUNDANCY : 2.900
REMARK 200 R MERGE (I) : 0.05000
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.8000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.50
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : 2.70
REMARK 200 R MERGE FOR SHELL (I) : 0.37000
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.500
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: CNS
REMARK 200 STARTING MODEL: PDK1PH INSP4 MODEL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 0.41
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.1
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 25 % PEG 4000, 0.1 M SODIUM
REMARK 280 ACETATE [PH 4.2], 0.3 M AMMONIUM ACETATE
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,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 29.47150
REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000
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 GENERATING THE BIOMOLECULE
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: PQS
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 406
REMARK 465 PRO A 551
REMARK 465 ASP A 552
REMARK 465 ALA A 553
REMARK 465 ALA A 554
REMARK 465 VAL A 555
REMARK 465 GLN A 556
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 408 CG CD1 CD2
REMARK 470 GLU A 503 CG CD OE1 OE2
REMARK 470 LYS A 509 CG CD CE NZ
REMARK 470 HIS A 550 CA C O CB CG ND1 CD2 CE1 NE2
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 NE2 GLN A 429 - O HOH A 2041 2.13
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 ASP A 464 CB - CG - OD2 ANGL. DEV. = 7.5 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 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 ASN A 411 64.84 39.46
REMARK 500 PHE A 470 -137.16 -121.79
REMARK 500 ASN A 510 -154.91 -160.56
REMARK 500 GLN A 548 -163.18 -119.56
REMARK 500
REMARK 500 REMARK: NULL
REMARK 525
REMARK 525 SOLVENT
REMARK 525
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
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 4PT A 1550
REMARK 700
REMARK 700 SHEET
REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN
REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW,
REMARK 700 TWO SHEETS ARE DEFINED.
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 4PT A1550
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1H1W RELATED DB: PDB
REMARK 900 HIGH RESOLUTION CRYSTAL STRUCTURE OF THE
REMARK 900 HUMAN PDK1 CATALYTIC DOMAIN
REMARK 900 RELATED ID: 1OKY RELATED DB: PDB
REMARK 900 STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN
REMARK 900 COMPLEX WITH STAUROSPORINE
REMARK 900 RELATED ID: 1OKZ RELATED DB: PDB
REMARK 900 STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN
REMARK 900 COMPLEX WITH UCN-01
REMARK 900 RELATED ID: 1UU3 RELATED DB: PDB
REMARK 900 STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN
REMARK 900 COMPLEX WITH LY333531
REMARK 900 RELATED ID: 1UU7 RELATED DB: PDB
REMARK 900 STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN
REMARK 900 COMPLEX WITH BIM-2
REMARK 900 RELATED ID: 1UU8 RELATED DB: PDB
REMARK 900 STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN
REMARK 900 COMPLEX WITH BIM-1
REMARK 900 RELATED ID: 1UU9 RELATED DB: PDB
REMARK 900 STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN
REMARK 900 COMPLEX WITH BIM-3
REMARK 900 RELATED ID: 1UVR RELATED DB: PDB
REMARK 900 STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN
REMARK 900 COMPLEX WITH BIM-8
REMARK 900 RELATED ID: 1W1D RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF THE PDK1 PLECKSTRIN
REMARK 900 HOMOLOGY (PH) DOMAIN BOUND TO INOSITOL (1,
REMARK 900 3,4,5)-TETRAKISPHOSPHATE
REMARK 900 RELATED ID: 1W1H RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF THE PDK1 PLECKSTRIN
REMARK 900 HOMOLOGY (PH) DOMAIN
DBREF 1W1G A 406 408 PDB 1W1G 1W1G 406 408
DBREF 1W1G A 409 556 UNP O15530 PDPK_HUMAN 409 556
SEQRES 1 A 151 GLY PRO LEU GLY SER ASN ILE GLU GLN TYR ILE HIS ASP
SEQRES 2 A 151 LEU ASP SER ASN SER PHE GLU LEU ASP LEU GLN PHE SER
SEQRES 3 A 151 GLU ASP GLU LYS ARG LEU LEU LEU GLU LYS GLN ALA GLY
SEQRES 4 A 151 GLY ASN PRO TRP HIS GLN PHE VAL GLU ASN ASN LEU ILE
SEQRES 5 A 151 LEU LYS MET GLY PRO VAL ASP LYS ARG LYS GLY LEU PHE
SEQRES 6 A 151 ALA ARG ARG ARG GLN LEU LEU LEU THR GLU GLY PRO HIS
SEQRES 7 A 151 LEU TYR TYR VAL ASP PRO VAL ASN LYS VAL LEU LYS GLY
SEQRES 8 A 151 GLU ILE PRO TRP SER GLN GLU LEU ARG PRO GLU ALA LYS
SEQRES 9 A 151 ASN PHE LYS THR PHE PHE VAL HIS THR PRO ASN ARG THR
SEQRES 10 A 151 TYR TYR LEU MET ASP PRO SER GLY ASN ALA HIS LYS TRP
SEQRES 11 A 151 CYS ARG LYS ILE GLN GLU VAL TRP ARG GLN ARG TYR GLN
SEQRES 12 A 151 SER HIS PRO ASP ALA ALA VAL GLN
HET 4PT A1550 33
HETNAM 4PT (2R)-3-{[(S)-{[(2S,3R,5S,6S)-2,6-DIHYDROXY-3,
HETNAM 2 4PT 4,5-TRIS(PHOSPHONOOXY)CYCLOHEXYL]OXY}
HETNAM 3 4PT (HYDROXY)PHOSPHORYL]OXY}-2-(1-HYDROXYBUTOXY)PROPYL
HETNAM 4 4PT BUTYRATE
HETSYN 4PT DIC4-PHOSPHATIDYLINOSITOL(3,4,5)TRISPHOSPHATE
FORMUL 2 4PT C17 H36 O22 P4
FORMUL 3 HOH *163(H2 O1)
HELIX 1 1 ASN A 411 GLN A 414 5 4
HELIX 2 2 SER A 431 ASN A 446 1 16
HELIX 3 3 TRP A 448 VAL A 452 5 5
HELIX 4 4 ASN A 531 GLN A 548 1 18
SHEET 1 AA 6 ILE A 416 ASP A 420 0
SHEET 2 AA 6 SER A 423 LEU A 426 -1 O SER A 423 N LEU A 419
SHEET 3 AA 6 ILE A 457 LYS A 467 -1 O LEU A 458 N LEU A 426
SHEET 4 AA 6 PHE A 470 THR A 479 -1 O PHE A 470 N LYS A 467
SHEET 5 AA 6 HIS A 483 ASP A 488 -1 O HIS A 483 N THR A 479
SHEET 6 AA 6 VAL A 493 ILE A 498 -1 O VAL A 493 N ASP A 488
SHEET 1 AB 6 ILE A 416 ASP A 420 0
SHEET 2 AB 6 SER A 423 LEU A 426 -1 O SER A 423 N LEU A 419
SHEET 3 AB 6 ILE A 457 LYS A 467 -1 O LEU A 458 N LEU A 426
SHEET 4 AB 6 ARG A 521 MET A 526 -1 O TYR A 524 N ARG A 466
SHEET 5 AB 6 THR A 513 THR A 518 -1 O PHE A 514 N LEU A 525
SHEET 6 AB 6 ARG A 505 ALA A 508 -1 O ARG A 505 N HIS A 517
CISPEP 1 GLY A 481 PRO A 482 0 -0.22
SITE 1 AC1 14 HIS A 417 LEU A 419 LYS A 465 LYS A 467
SITE 2 AC1 14 ARG A 472 ARG A 474 TYR A 486 LYS A 495
SITE 3 AC1 14 ARG A 521 HOH A2029 HOH A2084 HOH A2155
SITE 4 AC1 14 HOH A2156 HOH A2157
CRYST1 35.264 58.943 36.440 90.00 102.33 90.00 P 1 21 1 2
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 0.028357 0.000000 0.006201 0.00000
SCALE2 0.000000 0.016966 0.000000 0.00000
SCALE3 0.000000 0.000000 0.028091 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
