HEADER TRANSFERASE/TRANSFERASE INHIBITOR 04-MAY-14 4PH4
TITLE THE CRYSTAL STRUCTURE OF HUMAN VPS34 IN COMPLEX WITH PIK-III
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PHOSPHATIDYLINOSITOL 3-KINASE CATALYTIC SUBUNIT TYPE 3;
COMPND 3 CHAIN: B;
COMPND 4 FRAGMENT: UNP RESIDUES 293-887;
COMPND 5 SYNONYM: PTDINS-3-KINASE TYPE 3,PHOSPHATIDYLINOSITOL 3-KINASE P100
COMPND 6 SUBUNIT,PHOSPHOINOSITIDE-3-KINASE CLASS 3,HVPS34;
COMPND 7 EC: 2.7.1.137;
COMPND 8 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: PIK3C3, VPS34;
SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA;
SOURCE 7 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM;
SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108;
SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: SF9;
SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS
KEYWDS VPS34, AUTOPHAGY, CLASS III, PHOSPHATIDYLINOSITOL-3-KINASE, PIK3C3,
KEYWDS 2 TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR M.S.KNAPP,R.A.ELLING
REVDAT 4 27-DEC-23 4PH4 1 SOURCE KEYWDS REMARK
REVDAT 3 12-NOV-14 4PH4 1 JRNL
REVDAT 2 05-NOV-14 4PH4 1 JRNL
REVDAT 1 29-OCT-14 4PH4 0
JRNL AUTH W.E.DOWDLE,B.NYFELER,J.NAGEL,R.A.ELLING,S.LIU,
JRNL AUTH 2 E.TRIANTAFELLOW,S.MENON,Z.WANG,A.HONDA,G.PARDEE,J.CANTWELL,
JRNL AUTH 3 C.LUU,I.CORNELLA-TARACIDO,E.HARRINGTON,P.FEKKES,H.LEI,
JRNL AUTH 4 Q.FANG,M.E.DIGAN,D.BURDICK,A.F.POWERS,S.B.HELLIWELL,
JRNL AUTH 5 S.D'AQUIN,J.BASTIEN,H.WANG,D.WIEDERSCHAIN,J.KUERTH,
JRNL AUTH 6 P.BERGMAN,D.SCHWALB,J.THOMAS,S.UGWONALI,F.HARBINSKI,
JRNL AUTH 7 J.TALLARICO,C.J.WILSON,V.E.MYER,J.A.PORTER,D.E.BUSSIERE,
JRNL AUTH 8 P.M.FINAN,M.A.LABOW,X.MAO,L.G.HAMANN,B.D.MANNING,R.A.VALDEZ,
JRNL AUTH 9 T.NICHOLSON,M.SCHIRLE,M.S.KNAPP,E.P.KEANEY,L.O.MURPHY
JRNL TITL SELECTIVE VPS34 INHIBITOR BLOCKS AUTOPHAGY AND UNCOVERS A
JRNL TITL 2 ROLE FOR NCOA4 IN FERRITIN DEGRADATION AND IRON HOMEOSTASIS
JRNL TITL 3 IN VIVO.
JRNL REF NAT.CELL BIOL. V. 16 1069 2014
JRNL REFN ISSN 1465-7392
JRNL PMID 25327288
JRNL DOI 10.1038/NCB3053
REMARK 2
REMARK 2 RESOLUTION. 2.80 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : BUSTER-TNT BUSTER 2.11.4
REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER,
REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN,
REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.34
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 3 NUMBER OF REFLECTIONS : 24604
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) : 0.195
REMARK 3 R VALUE (WORKING SET) : 0.194
REMARK 3 FREE R VALUE : 0.223
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030
REMARK 3 FREE R VALUE TEST SET COUNT : 1237
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 12
REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80
REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.92
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0
REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2938
REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2498
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2791
REMARK 3 BIN R VALUE (WORKING SET) : 0.2479
REMARK 3 BIN FREE R VALUE : 0.2792
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 147
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 4228
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 30
REMARK 3 SOLVENT ATOMS : 91
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 85.63
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 75.22
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -2.05580
REMARK 3 B22 (A**2) : -2.05580
REMARK 3 B33 (A**2) : 4.11150
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 COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL
REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.438
REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.262
REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.423
REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.263
REMARK 3
REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797
REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.947
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.929
REMARK 3
REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15
REMARK 3 TERM COUNT WEIGHT FUNCTION.
REMARK 3 BOND LENGTHS : 4365 ; 2.000 ; HARMONIC
REMARK 3 BOND ANGLES : 5912 ; 2.000 ; HARMONIC
REMARK 3 TORSION ANGLES : 1557 ; 2.000 ; SINUSOIDAL
REMARK 3 TRIGONAL CARBON PLANES : 121 ; 2.000 ; HARMONIC
REMARK 3 GENERAL PLANES : 639 ; 5.000 ; HARMONIC
REMARK 3 ISOTROPIC THERMAL FACTORS : 4365 ; 20.000 ; HARMONIC
REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL
REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL
REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL
REMARK 3 CHIRAL IMPROPER TORSION : 558 ; 5.000 ; SEMIHARMONIC
REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL
REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL
REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL
REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL
REMARK 3 IDEAL-DIST CONTACT TERM : 5143 ; 4.000 ; SEMIHARMONIC
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.009
REMARK 3 BOND ANGLES (DEGREES) : 1.07
REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.46
REMARK 3 OTHER TORSION ANGLES (DEGREES) : 19.35
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 1
REMARK 3
REMARK 3 TLS GROUP : 1
REMARK 3 SELECTION: { B|* }
REMARK 3 ORIGIN FOR THE GROUP (A): 9.3866 14.1087 -22.8495
REMARK 3 T TENSOR
REMARK 3 T11: 0.0000 T22: 0.0000
REMARK 3 T33: 0.0000 T12: 0.0000
REMARK 3 T13: 0.0000 T23: 0.0000
REMARK 3 L TENSOR
REMARK 3 L11: 0.0000 L22: 0.0000
REMARK 3 L33: 0.0000 L12: 0.0000
REMARK 3 L13: 0.0000 L23: 0.0000
REMARK 3 S TENSOR
REMARK 3 S11: 0.0000 S12: 0.0000 S13: 0.0000
REMARK 3 S21: 0.0000 S22: 0.0000 S23: 0.0000
REMARK 3 S31: 0.0000 S32: 0.0000 S33: 0.0000
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 4PH4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-MAY-14.
REMARK 100 THE DEPOSITION ID IS D_1000201373.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 21-JAN-09
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 : ALS
REMARK 200 BEAMLINE : 5.0.2
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.9774
REMARK 200 MONOCHROMATOR : DOUBLE-CRYSTAL, SI(111) LIQUID
REMARK 200 N2 COOLED
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : AIMLESS
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29404
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.980
REMARK 200 RESOLUTION RANGE LOW (A) : 48.750
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 200 DATA REDUNDANCY : 15.40
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.9000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL
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 (%): 65.84
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.60
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: VPS34 PROTEIN AND PIK-III WERE MIXED
REMARK 280 AND INCUBATED ON ICE FOR 1 HR (FINAL PIK-III CONCENTRATION WAS 1
REMARK 280 MM). PRIOR TO CRYSTALLIZATION, THE MIXTURE WAS PASSED THROUGH A
REMARK 280 0.2 UM FILTER. THE PROTEIN:LIGAND COMPLEX WAS CRYSTALLIZED USING
REMARK 280 THE HANGING DROP VAPOR DIFFUSION METHOD IN NEXTAL PLATES: 6 UL
REMARK 280 OF PROTEIN SOLUTION WAS MIXED WITH 4 UL OF PRECIPITANT, WHICH
REMARK 280 CONSISTED OF 20% (W/V) PEG 3350, 100 MM BIS-TRIS PROPANE, AND
REMARK 280 200 MM NA-K-PHOSPHATE. THE RESULTING DROP WAS SUSPENDED OVER A
REMARK 280 RESERVOIR OF 0.3 ML OF PRECIPITANT AND SEALED WITH A SCREW CAP.
REMARK 280 THE CRYSTALS GREW AT 30 DEGC IN APPROXIMATELY 12-24 HR., VAPOR
REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 303.15K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,-Y,Z+1/2
REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4
REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4
REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4
REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4
REMARK 290 7555 Y,X,-Z
REMARK 290 8555 -Y,-X,-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 73.12850
REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 57.26600
REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 57.26600
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 36.56425
REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 57.26600
REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 57.26600
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 109.69275
REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 57.26600
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 57.26600
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 36.56425
REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 57.26600
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 57.26600
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 109.69275
REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 73.12850
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: 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 MET B 263
REMARK 465 SER B 264
REMARK 465 TYR B 265
REMARK 465 TYR B 266
REMARK 465 HIS B 267
REMARK 465 HIS B 268
REMARK 465 HIS B 269
REMARK 465 HIS B 270
REMARK 465 HIS B 271
REMARK 465 HIS B 272
REMARK 465 ASP B 273
REMARK 465 TYR B 274
REMARK 465 ASP B 275
REMARK 465 ILE B 276
REMARK 465 PRO B 277
REMARK 465 THR B 278
REMARK 465 THR B 279
REMARK 465 GLU B 280
REMARK 465 ASN B 281
REMARK 465 LEU B 282
REMARK 465 TYR B 283
REMARK 465 PHE B 284
REMARK 465 GLN B 285
REMARK 465 GLY B 286
REMARK 465 ALA B 287
REMARK 465 MET B 288
REMARK 465 GLY B 289
REMARK 465 THR B 418
REMARK 465 LYS B 419
REMARK 465 LYS B 420
REMARK 465 ASP B 421
REMARK 465 SER B 422
REMARK 465 GLN B 423
REMARK 465 SER B 424
REMARK 465 SER B 425
REMARK 465 VAL B 426
REMARK 465 SER B 427
REMARK 465 GLU B 428
REMARK 465 ASN B 429
REMARK 465 VAL B 430
REMARK 465 SER B 431
REMARK 465 ASN B 432
REMARK 465 SER B 433
REMARK 465 GLY B 434
REMARK 465 ILE B 435
REMARK 465 ASN B 436
REMARK 465 SER B 437
REMARK 465 ALA B 438
REMARK 465 GLU B 439
REMARK 465 ILE B 440
REMARK 465 ASP B 441
REMARK 465 SER B 442
REMARK 465 SER B 443
REMARK 465 GLN B 444
REMARK 465 ILE B 445
REMARK 465 ILE B 446
REMARK 465 THR B 447
REMARK 465 SER B 448
REMARK 465 PRO B 449
REMARK 465 LEU B 450
REMARK 465 PRO B 451
REMARK 465 SER B 452
REMARK 465 VAL B 453
REMARK 465 SER B 454
REMARK 465 SER B 455
REMARK 465 PRO B 456
REMARK 465 PRO B 457
REMARK 465 PRO B 458
REMARK 465 ALA B 459
REMARK 465 SER B 460
REMARK 465 LYS B 461
REMARK 465 THR B 462
REMARK 465 LYS B 463
REMARK 465 GLU B 464
REMARK 465 VAL B 465
REMARK 465 PRO B 466
REMARK 465 ASP B 467
REMARK 465 GLY B 468
REMARK 465 GLU B 469
REMARK 465 ASN B 470
REMARK 465 ALA B 872
REMARK 465 ALA B 873
REMARK 465 VAL B 874
REMARK 465 VAL B 875
REMARK 465 GLU B 876
REMARK 465 GLN B 877
REMARK 465 ILE B 878
REMARK 465 HIS B 879
REMARK 465 LYS B 880
REMARK 465 PHE B 881
REMARK 465 ALA B 882
REMARK 465 GLN B 883
REMARK 465 TYR B 884
REMARK 465 TRP B 885
REMARK 465 ARG B 886
REMARK 465 LYS B 887
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 ILE B 292 CG1 CG2 CD1
REMARK 470 ARG B 293 CG CD NE CZ NH1 NH2
REMARK 470 GLN B 295 CG CD OE1 NE2
REMARK 470 LEU B 296 CG CD1 CD2
REMARK 470 LYS B 318 CG CD CE NZ
REMARK 470 TYR B 322 CG CD1 CD2 CE1 CE2 CZ OH
REMARK 470 LYS B 328 CG CD CE NZ
REMARK 470 LYS B 354 CG CD CE NZ
REMARK 470 LEU B 471 CG CD1 CD2
REMARK 470 ARG B 509 CG CD NE CZ NH1 NH2
REMARK 470 LYS B 530 CG CD CE NZ
REMARK 470 LYS B 771 CG CD CE NZ
REMARK 470 GLU B 785 CG CD OE1 OE2
REMARK 470 GLN B 791 CG CD OE1 NE2
REMARK 470 GLU B 797 CG CD OE1 OE2
REMARK 470 LYS B 800 CG CD CE NZ
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 ALA B 402 -8.84 -56.08
REMARK 500 GLU B 472 77.64 58.34
REMARK 500 ASP B 503 107.40 -51.27
REMARK 500 ASP B 510 74.96 -156.07
REMARK 500 ASP B 532 -178.33 -65.55
REMARK 500 LEU B 590 88.87 -54.04
REMARK 500 GLU B 596 89.39 -151.98
REMARK 500 ASP B 627 31.00 -94.78
REMARK 500 THR B 668 77.58 -118.22
REMARK 500 ASP B 761 87.44 62.04
REMARK 500 PHE B 762 55.79 -101.49
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 GOL B 901
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue 2UG B 902
DBREF 4PH4 B 293 887 UNP Q8NEB9 PK3C3_HUMAN 293 887
SEQADV 4PH4 MET B 263 UNP Q8NEB9 EXPRESSION TAG
SEQADV 4PH4 SER B 264 UNP Q8NEB9 EXPRESSION TAG
SEQADV 4PH4 TYR B 265 UNP Q8NEB9 EXPRESSION TAG
SEQADV 4PH4 TYR B 266 UNP Q8NEB9 EXPRESSION TAG
SEQADV 4PH4 HIS B 267 UNP Q8NEB9 EXPRESSION TAG
SEQADV 4PH4 HIS B 268 UNP Q8NEB9 EXPRESSION TAG
SEQADV 4PH4 HIS B 269 UNP Q8NEB9 EXPRESSION TAG
SEQADV 4PH4 HIS B 270 UNP Q8NEB9 EXPRESSION TAG
SEQADV 4PH4 HIS B 271 UNP Q8NEB9 EXPRESSION TAG
SEQADV 4PH4 HIS B 272 UNP Q8NEB9 EXPRESSION TAG
SEQADV 4PH4 ASP B 273 UNP Q8NEB9 EXPRESSION TAG
SEQADV 4PH4 TYR B 274 UNP Q8NEB9 EXPRESSION TAG
SEQADV 4PH4 ASP B 275 UNP Q8NEB9 EXPRESSION TAG
SEQADV 4PH4 ILE B 276 UNP Q8NEB9 EXPRESSION TAG
SEQADV 4PH4 PRO B 277 UNP Q8NEB9 EXPRESSION TAG
SEQADV 4PH4 THR B 278 UNP Q8NEB9 EXPRESSION TAG
SEQADV 4PH4 THR B 279 UNP Q8NEB9 EXPRESSION TAG
SEQADV 4PH4 GLU B 280 UNP Q8NEB9 EXPRESSION TAG
SEQADV 4PH4 ASN B 281 UNP Q8NEB9 EXPRESSION TAG
SEQADV 4PH4 LEU B 282 UNP Q8NEB9 EXPRESSION TAG
SEQADV 4PH4 TYR B 283 UNP Q8NEB9 EXPRESSION TAG
SEQADV 4PH4 PHE B 284 UNP Q8NEB9 EXPRESSION TAG
SEQADV 4PH4 GLN B 285 UNP Q8NEB9 EXPRESSION TAG
SEQADV 4PH4 GLY B 286 UNP Q8NEB9 EXPRESSION TAG
SEQADV 4PH4 ALA B 287 UNP Q8NEB9 EXPRESSION TAG
SEQADV 4PH4 MET B 288 UNP Q8NEB9 EXPRESSION TAG
SEQADV 4PH4 GLY B 289 UNP Q8NEB9 EXPRESSION TAG
SEQADV 4PH4 SER B 290 UNP Q8NEB9 EXPRESSION TAG
SEQADV 4PH4 GLY B 291 UNP Q8NEB9 EXPRESSION TAG
SEQADV 4PH4 ILE B 292 UNP Q8NEB9 EXPRESSION TAG
SEQRES 1 B 625 MET SER TYR TYR HIS HIS HIS HIS HIS HIS ASP TYR ASP
SEQRES 2 B 625 ILE PRO THR THR GLU ASN LEU TYR PHE GLN GLY ALA MET
SEQRES 3 B 625 GLY SER GLY ILE ARG ASP GLN LEU ASN ILE ILE VAL SER
SEQRES 4 B 625 TYR PRO PRO THR LYS GLN LEU THR TYR GLU GLU GLN ASP
SEQRES 5 B 625 LEU VAL TRP LYS PHE ARG TYR TYR LEU THR ASN GLN GLU
SEQRES 6 B 625 LYS ALA LEU THR LYS PHE LEU LYS CYS VAL ASN TRP ASP
SEQRES 7 B 625 LEU PRO GLN GLU ALA LYS GLN ALA LEU GLU LEU LEU GLY
SEQRES 8 B 625 LYS TRP LYS PRO MET ASP VAL GLU ASP SER LEU GLU LEU
SEQRES 9 B 625 LEU SER SER HIS TYR THR ASN PRO THR VAL ARG ARG TYR
SEQRES 10 B 625 ALA VAL ALA ARG LEU ARG GLN ALA ASP ASP GLU ASP LEU
SEQRES 11 B 625 LEU MET TYR LEU LEU GLN LEU VAL GLN ALA LEU LYS TYR
SEQRES 12 B 625 GLU ASN PHE ASP ASP ILE LYS ASN GLY LEU GLU PRO THR
SEQRES 13 B 625 LYS LYS ASP SER GLN SER SER VAL SER GLU ASN VAL SER
SEQRES 14 B 625 ASN SER GLY ILE ASN SER ALA GLU ILE ASP SER SER GLN
SEQRES 15 B 625 ILE ILE THR SER PRO LEU PRO SER VAL SER SER PRO PRO
SEQRES 16 B 625 PRO ALA SER LYS THR LYS GLU VAL PRO ASP GLY GLU ASN
SEQRES 17 B 625 LEU GLU GLN ASP LEU CYS THR PHE LEU ILE SER ARG ALA
SEQRES 18 B 625 CYS LYS ASN SER THR LEU ALA ASN TYR LEU TYR TRP TYR
SEQRES 19 B 625 VAL ILE VAL GLU CYS GLU ASP GLN ASP THR GLN GLN ARG
SEQRES 20 B 625 ASP PRO LYS THR HIS GLU MET TYR LEU ASN VAL MET ARG
SEQRES 21 B 625 ARG PHE SER GLN ALA LEU LEU LYS GLY ASP LYS SER VAL
SEQRES 22 B 625 ARG VAL MET ARG SER LEU LEU ALA ALA GLN GLN THR PHE
SEQRES 23 B 625 VAL ASP ARG LEU VAL HIS LEU MET LYS ALA VAL GLN ARG
SEQRES 24 B 625 GLU SER GLY ASN ARG LYS LYS LYS ASN GLU ARG LEU GLN
SEQRES 25 B 625 ALA LEU LEU GLY ASP ASN GLU LYS MET ASN LEU SER ASP
SEQRES 26 B 625 VAL GLU LEU ILE PRO LEU PRO LEU GLU PRO GLN VAL LYS
SEQRES 27 B 625 ILE ARG GLY ILE ILE PRO GLU THR ALA THR LEU PHE LYS
SEQRES 28 B 625 SER ALA LEU MET PRO ALA GLN LEU PHE PHE LYS THR GLU
SEQRES 29 B 625 ASP GLY GLY LYS TYR PRO VAL ILE PHE LYS HIS GLY ASP
SEQRES 30 B 625 ASP LEU ARG GLN ASP GLN LEU ILE LEU GLN ILE ILE SER
SEQRES 31 B 625 LEU MET ASP LYS LEU LEU ARG LYS GLU ASN LEU ASP LEU
SEQRES 32 B 625 LYS LEU THR PRO TYR LYS VAL LEU ALA THR SER THR LYS
SEQRES 33 B 625 HIS GLY PHE MET GLN PHE ILE GLN SER VAL PRO VAL ALA
SEQRES 34 B 625 GLU VAL LEU ASP THR GLU GLY SER ILE GLN ASN PHE PHE
SEQRES 35 B 625 ARG LYS TYR ALA PRO SER GLU ASN GLY PRO ASN GLY ILE
SEQRES 36 B 625 SER ALA GLU VAL MET ASP THR TYR VAL LYS SER CYS ALA
SEQRES 37 B 625 GLY TYR CYS VAL ILE THR TYR ILE LEU GLY VAL GLY ASP
SEQRES 38 B 625 ARG HIS LEU ASP ASN LEU LEU LEU THR LYS THR GLY LYS
SEQRES 39 B 625 LEU PHE HIS ILE ASP PHE GLY TYR ILE LEU GLY ARG ASP
SEQRES 40 B 625 PRO LYS PRO LEU PRO PRO PRO MET LYS LEU ASN LYS GLU
SEQRES 41 B 625 MET VAL GLU GLY MET GLY GLY THR GLN SER GLU GLN TYR
SEQRES 42 B 625 GLN GLU PHE ARG LYS GLN CYS TYR THR ALA PHE LEU HIS
SEQRES 43 B 625 LEU ARG ARG TYR SER ASN LEU ILE LEU ASN LEU PHE SER
SEQRES 44 B 625 LEU MET VAL ASP ALA ASN ILE PRO ASP ILE ALA LEU GLU
SEQRES 45 B 625 PRO ASP LYS THR VAL LYS LYS VAL GLN ASP LYS PHE ARG
SEQRES 46 B 625 LEU ASP LEU SER ASP GLU GLU ALA VAL HIS TYR MET GLN
SEQRES 47 B 625 SER LEU ILE ASP GLU SER VAL HIS ALA LEU PHE ALA ALA
SEQRES 48 B 625 VAL VAL GLU GLN ILE HIS LYS PHE ALA GLN TYR TRP ARG
SEQRES 49 B 625 LYS
HET GOL B 901 6
HET 2UG B 902 24
HETNAM GOL GLYCEROL
HETNAM 2UG 4'-(CYCLOPROPYLMETHYL)-N~2~-(PYRIDIN-4-YL)-4,5'-
HETNAM 2 2UG BIPYRIMIDINE-2,2'-DIAMINE
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 2 GOL C3 H8 O3
FORMUL 3 2UG C17 H17 N7
FORMUL 4 HOH *91(H2 O)
HELIX 1 AA1 GLY B 291 TYR B 302 1 12
HELIX 2 AA2 THR B 309 PHE B 319 1 11
HELIX 3 AA3 TYR B 321 LYS B 328 5 8
HELIX 4 AA4 ALA B 329 LYS B 335 1 7
HELIX 5 AA5 LEU B 341 TRP B 355 1 15
HELIX 6 AA6 ASP B 359 LEU B 364 1 6
HELIX 7 AA7 GLU B 365 SER B 368 5 4
HELIX 8 AA8 ASN B 373 ARG B 385 1 13
HELIX 9 AA9 ASP B 388 ALA B 402 1 15
HELIX 10 AB1 LEU B 403 GLU B 406 5 4
HELIX 11 AB2 ASN B 407 GLY B 414 1 8
HELIX 12 AB3 ASP B 474 LYS B 485 1 12
HELIX 13 AB4 ASN B 486 ASP B 503 1 18
HELIX 14 AB5 ASP B 503 ASP B 510 1 8
HELIX 15 AB6 ASP B 510 GLY B 531 1 22
HELIX 16 AB7 ASP B 532 GLN B 560 1 29
HELIX 17 AB8 ASN B 565 ASP B 579 1 15
HELIX 18 AB9 LEU B 641 GLU B 661 1 21
HELIX 19 AC1 VAL B 690 GLY B 698 1 9
HELIX 20 AC2 SER B 699 ALA B 708 1 10
HELIX 21 AC3 GLY B 713 ILE B 717 5 5
HELIX 22 AC4 SER B 718 GLY B 740 1 23
HELIX 23 AC5 ASN B 780 MET B 787 1 8
HELIX 24 AC6 SER B 792 ARG B 811 1 20
HELIX 25 AC7 TYR B 812 LEU B 822 1 11
HELIX 26 AC8 ILE B 828 LEU B 833 1 6
HELIX 27 AC9 GLU B 834 ASP B 836 5 3
HELIX 28 AD1 LYS B 837 ARG B 847 1 11
HELIX 29 AD2 SER B 851 LEU B 870 1 20
SHEET 1 AA1 4 ILE B 591 LEU B 593 0
SHEET 2 AA1 4 GLU B 596 ILE B 604 -1 O VAL B 599 N LEU B 593
SHEET 3 AA1 4 ALA B 619 THR B 625 -1 O LYS B 624 N GLY B 603
SHEET 4 AA1 4 THR B 610 LEU B 611 -1 N THR B 610 O GLN B 620
SHEET 1 AA2 6 ILE B 591 LEU B 593 0
SHEET 2 AA2 6 GLU B 596 ILE B 604 -1 O VAL B 599 N LEU B 593
SHEET 3 AA2 6 ALA B 619 THR B 625 -1 O LYS B 624 N GLY B 603
SHEET 4 AA2 6 LYS B 630 HIS B 637 -1 O PHE B 635 N ALA B 619
SHEET 5 AA2 6 HIS B 679 GLN B 683 -1 O MET B 682 N ILE B 634
SHEET 6 AA2 6 VAL B 672 ALA B 674 -1 N LEU B 673 O PHE B 681
SHEET 1 AA3 3 VAL B 688 PRO B 689 0
SHEET 2 AA3 3 LEU B 749 LEU B 751 -1 O LEU B 751 N VAL B 688
SHEET 3 AA3 3 LEU B 757 HIS B 759 -1 O PHE B 758 N LEU B 750
SITE 1 AC1 4 GLN B 686 VAL B 688 THR B 752 LYS B 753
SITE 1 AC2 14 ILE B 634 LYS B 636 TYR B 670 MET B 682
SITE 2 AC2 14 GLN B 683 PHE B 684 ILE B 685 SER B 687
SITE 3 AC2 14 LEU B 750 ILE B 760 ASP B 761 HOH B1015
SITE 4 AC2 14 HOH B1024 HOH B1050
CRYST1 114.532 114.532 146.257 90.00 90.00 90.00 P 41 21 2 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 0.008731 0.000000 0.000000 0.00000
SCALE2 0.000000 0.008731 0.000000 0.00000
SCALE3 0.000000 0.000000 0.006837 0.00000