PDB Short entry for 3CXW HEADER TRANSFERASE 25-APR-08 3CXW TITLE CRYSTAL STRUCTURE OF HUMAN PROTO-ONCOGENE SERINE THREONINE KINASE TITLE 2 (PIM1) IN COMPLEX WITH A CONSENSUS PEPTIDE AND A BETA CARBOLINE TITLE 3 LIGAND I COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTO-ONCOGENE SERINE/THREONINE-PROTEIN KINASE PIM-1, COMPND 3 ISOFORM 2; COMPND 4 CHAIN: A; COMPND 5 EC: 2.7.11.1; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: PIMTIDE PEPTIDE; COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 GENE: PIM1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)-R3; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PNIC28-BSA4; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 OTHER_DETAILS: SYNTHETIC PEPTIDE KEYWDS ONCOGENE, KINASE, SERINE-THREONINE, PIM1, STRUCTURAL GENOMICS KEYWDS 2 CONSORTIUM, SGC, ALTERNATIVE INITIATION, ATP-BINDING, MANGANESE, KEYWDS 3 MEMBRANE, METAL-BINDING, NUCLEOTIDE-BINDING, NUCLEUS, KEYWDS 4 PHOSPHOPROTEIN, PROTO-ONCOGENE, SERINE/THREONINE-PROTEIN KINASE, KEYWDS 5 TRANSFERASE, HOST-VIRUS INTERACTION, VIRAL IMMUNOEVASION, VIRION, KEYWDS 6 VIRULENCE EXPDTA X-RAY DIFFRACTION AUTHOR P.FILIPPAKOPOULOS,A.BULLOCK,O.FEDOROV,K.HUBER,F.BRACHER,A.C.W.PIKE, AUTHOR 2 A.ROOS,F.VON DELFT,C.H.ARROWSMITH,A.M.EDWARDS,C.BOUNTRA,S.KNAPP, AUTHOR 3 STRUCTURAL GENOMICS CONSORTIUM (SGC) REVDAT 9 30-AUG-23 3CXW 1 REMARK REVDAT 8 20-OCT-21 3CXW 1 REMARK SEQADV REVDAT 7 25-OCT-17 3CXW 1 REMARK REVDAT 6 19-JUN-13 3CXW 1 JRNL REVDAT 5 18-JAN-12 3CXW 1 JRNL REVDAT 4 13-JUL-11 3CXW 1 VERSN REVDAT 3 11-AUG-09 3CXW 1 ATOM COMPND HET HETNAM REVDAT 3 2 1 HETSYN SITE REVDAT 2 24-FEB-09 3CXW 1 VERSN REVDAT 1 15-JUL-08 3CXW 0 JRNL AUTH K.HUBER,L.BRAULT,O.FEDOROV,C.GASSER,P.FILIPPAKOPOULOS, JRNL AUTH 2 A.N.BULLOCK,D.FABBRO,J.TRAPPE,J.SCHWALLER,S.KNAPP,F.BRACHER JRNL TITL 7,8-DICHLORO-1-OXO-BETA-CARBOLINES AS A VERSATILE SCAFFOLD JRNL TITL 2 FOR THE DEVELOPMENT OF POTENT AND SELECTIVE KINASE JRNL TITL 3 INHIBITORS WITH UNUSUAL BINDING MODES JRNL REF J.MED.CHEM. V. 55 403 2012 JRNL REFN ISSN 0022-2623 JRNL PMID 22136433 JRNL DOI 10.1021/JM201286Z REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.71 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 26168 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) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1330 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1805 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.95 REMARK 3 BIN R VALUE (WORKING SET) : 0.2290 REMARK 3 BIN FREE R VALUE SET COUNT : 97 REMARK 3 BIN FREE R VALUE : 0.2980 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2263 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 217 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.43 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.12000 REMARK 3 B22 (A**2) : 0.12000 REMARK 3 B33 (A**2) : -0.18000 REMARK 3 B12 (A**2) : 0.06000 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): 0.145 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.141 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.102 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.081 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.938 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2369 ; 0.016 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 1639 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3216 ; 1.477 ; 1.961 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3942 ; 1.653 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 279 ; 6.494 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 118 ;32.886 ;22.881 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 389 ;14.065 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;17.488 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 340 ; 0.089 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2617 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 510 ; 0.001 ; 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): 1402 ; 2.196 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 570 ; 0.638 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2266 ; 3.400 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 967 ; 5.510 ; 8.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 950 ; 7.364 ;11.000 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 33 A 86 REMARK 3 ORIGIN FOR THE GROUP (A): 26.5336 55.0336 7.2290 REMARK 3 T TENSOR REMARK 3 T11: -0.0021 T22: 0.0891 REMARK 3 T33: -0.0581 T12: 0.1375 REMARK 3 T13: 0.0365 T23: -0.0066 REMARK 3 L TENSOR REMARK 3 L11: 7.1991 L22: 8.0440 REMARK 3 L33: 5.5420 L12: 1.3385 REMARK 3 L13: -1.7602 L23: -0.6169 REMARK 3 S TENSOR REMARK 3 S11: -0.0729 S12: 0.6532 S13: 0.3287 REMARK 3 S21: -0.6558 S22: 0.0999 S23: 0.3187 REMARK 3 S31: -0.5789 S32: -0.4082 S33: -0.0270 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 87 A 305 REMARK 3 ORIGIN FOR THE GROUP (A): 44.1172 41.9918 13.7399 REMARK 3 T TENSOR REMARK 3 T11: -0.1744 T22: -0.1478 REMARK 3 T33: -0.1852 T12: 0.0088 REMARK 3 T13: 0.0232 T23: -0.0159 REMARK 3 L TENSOR REMARK 3 L11: 1.4127 L22: 2.0274 REMARK 3 L33: 1.9425 L12: -0.4677 REMARK 3 L13: 0.0053 L23: -0.4453 REMARK 3 S TENSOR REMARK 3 S11: 0.0399 S12: 0.0273 S13: 0.0656 REMARK 3 S21: -0.0097 S22: -0.0105 S23: 0.0781 REMARK 3 S31: -0.1242 S32: -0.1029 S33: -0.0295 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: NULL REMARK 4 REMARK 4 3CXW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-MAY-08. REMARK 100 THE DEPOSITION ID IS D_1000047347. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-DEC-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97912 REMARK 200 MONOCHROMATOR : SI(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, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26203 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.12600 REMARK 200 R SYM (I) : 0.12600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.72400 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: PDB ENTRY 2C3I REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.14 M SODIUM MALONATE, 0.07 M BIS REMARK 280 -TRIS-PROPANE PH 7.5, 14 % PEG 3350, 7 % ETHYLENE GLYCOL, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.22133 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 27.11067 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 40.66600 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 13.55533 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 67.77667 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 300 REMARK: AUTHORS STATE THAT BY GEL FILTRATION THE PROTEIN APPEARS TO REMARK 300 BE MONOMERIC. THE BIOLOGICAL ASSEMBLY SHOWN IN REMARK 350 IS A REMARK 300 MONOMERIC COMPLEX BETWEEN THE PROTEIN AND THE CONSENSUS PEPTIDE. 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: 1140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12910 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 2.3 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 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 SER A 0 REMARK 465 MET A 1 REMARK 465 LEU A 2 REMARK 465 LEU A 3 REMARK 465 SER A 4 REMARK 465 LYS A 5 REMARK 465 ILE A 6 REMARK 465 ASN A 7 REMARK 465 SER A 8 REMARK 465 LEU A 9 REMARK 465 ALA A 10 REMARK 465 HIS A 11 REMARK 465 LEU A 12 REMARK 465 ARG A 13 REMARK 465 ALA A 14 REMARK 465 ALA A 15 REMARK 465 PRO A 16 REMARK 465 CYS A 17 REMARK 465 ASN A 18 REMARK 465 ASP A 19 REMARK 465 LEU A 20 REMARK 465 HIS A 21 REMARK 465 ALA A 22 REMARK 465 THR A 23 REMARK 465 LYS A 24 REMARK 465 LEU A 25 REMARK 465 ALA A 26 REMARK 465 PRO A 27 REMARK 465 GLY A 28 REMARK 465 LYS A 29 REMARK 465 GLU A 30 REMARK 465 LYS A 31 REMARK 465 GLU A 32 REMARK 465 ASN A 82 REMARK 465 GLY A 83 REMARK 465 LEU A 307 REMARK 465 SER A 308 REMARK 465 PRO A 309 REMARK 465 GLY A 310 REMARK 465 PRO A 311 REMARK 465 SER A 312 REMARK 465 LYS A 313 REMARK 465 PRO B 11 REMARK 465 PRO B 12 REMARK 465 THR B 13 REMARK 465 ALA B 14 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 GLU A 35 CD OE1 OE2 REMARK 470 SER A 36 OG REMARK 470 GLN A 39 CD OE1 NE2 REMARK 470 ASP A 72 OD1 OD2 REMARK 470 ARG A 73 CD NE CZ NH1 NH2 REMARK 470 GLU A 79 CG CD OE1 OE2 REMARK 470 THR A 84 OG1 CG2 REMARK 470 ARG A 105 CZ NH1 NH2 REMARK 470 ARG A 274 CG CD NE CZ NH1 NH2 REMARK 470 SER A 306 OG REMARK 470 LYS B 3 CD CE NZ 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 O HOH A 718 O HOH A 754 5565 1.99 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 ARG A 145 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 145 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG A 258 NE - CZ - NH1 ANGL. DEV. = -3.0 DEGREES REMARK 500 ARG A 258 NE - CZ - NH2 ANGL. DEV. = 4.3 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 ASP A 60 15.94 -148.86 REMARK 500 SER A 98 -178.89 -179.03 REMARK 500 ASP A 167 46.30 -151.16 REMARK 500 ASP A 186 77.59 66.30 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 CL A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 7CP A 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3CY2 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN PROTO-ONCOGENE SERINE THREONINE KINASE REMARK 900 (PIM1) IN COMPLEX WITH A CONSENSUS PEPTIDE AND A BETA CARBOLINE REMARK 900 LIGAND II REMARK 900 RELATED ID: 3CY3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN PROTO-ONCOGENE SERINE THREONINE KINASE REMARK 900 (PIM1) IN COMPLEX WITH A CONSENSUS PEPTIDE AND THE JNK INHIBITOR V DBREF 3CXW A 1 313 UNP P11309 PIM1_HUMAN 1 313 DBREF 3CXW B 1 14 PDB 3CXW 3CXW 1 14 SEQADV 3CXW SER A 0 UNP P11309 EXPRESSION TAG SEQADV 3CXW GLY A 250 UNP P11309 ARG 250 ENGINEERED MUTATION SEQRES 1 A 314 SER MET LEU LEU SER LYS ILE ASN SER LEU ALA HIS LEU SEQRES 2 A 314 ARG ALA ALA PRO CYS ASN ASP LEU HIS ALA THR LYS LEU SEQRES 3 A 314 ALA PRO GLY LYS GLU LYS GLU PRO LEU GLU SER GLN TYR SEQRES 4 A 314 GLN VAL GLY PRO LEU LEU GLY SER GLY GLY PHE GLY SER SEQRES 5 A 314 VAL TYR SER GLY ILE ARG VAL SER ASP ASN LEU PRO VAL SEQRES 6 A 314 ALA ILE LYS HIS VAL GLU LYS ASP ARG ILE SER ASP TRP SEQRES 7 A 314 GLY GLU LEU PRO ASN GLY THR ARG VAL PRO MET GLU VAL SEQRES 8 A 314 VAL LEU LEU LYS LYS VAL SER SER GLY PHE SER GLY VAL SEQRES 9 A 314 ILE ARG LEU LEU ASP TRP PHE GLU ARG PRO ASP SER PHE SEQRES 10 A 314 VAL LEU ILE LEU GLU ARG PRO GLU PRO VAL GLN ASP LEU SEQRES 11 A 314 PHE ASP PHE ILE THR GLU ARG GLY ALA LEU GLN GLU GLU SEQRES 12 A 314 LEU ALA ARG SER PHE PHE TRP GLN VAL LEU GLU ALA VAL SEQRES 13 A 314 ARG HIS CYS HIS ASN CYS GLY VAL LEU HIS ARG ASP ILE SEQRES 14 A 314 LYS ASP GLU ASN ILE LEU ILE ASP LEU ASN ARG GLY GLU SEQRES 15 A 314 LEU LYS LEU ILE ASP PHE GLY SER GLY ALA LEU LEU LYS SEQRES 16 A 314 ASP THR VAL TYR THR ASP PHE ASP GLY THR ARG VAL TYR SEQRES 17 A 314 SER PRO PRO GLU TRP ILE ARG TYR HIS ARG TYR HIS GLY SEQRES 18 A 314 ARG SER ALA ALA VAL TRP SER LEU GLY ILE LEU LEU TYR SEQRES 19 A 314 ASP MET VAL CYS GLY ASP ILE PRO PHE GLU HIS ASP GLU SEQRES 20 A 314 GLU ILE ILE GLY GLY GLN VAL PHE PHE ARG GLN ARG VAL SEQRES 21 A 314 SER SER GLU CYS GLN HIS LEU ILE ARG TRP CYS LEU ALA SEQRES 22 A 314 LEU ARG PRO SER ASP ARG PRO THR PHE GLU GLU ILE GLN SEQRES 23 A 314 ASN HIS PRO TRP MET GLN ASP VAL LEU LEU PRO GLN GLU SEQRES 24 A 314 THR ALA GLU ILE HIS LEU HIS SER LEU SER PRO GLY PRO SEQRES 25 A 314 SER LYS SEQRES 1 B 14 ALA ARG LYS ARG ARG ARG HIS PRO SER GLY PRO PRO THR SEQRES 2 B 14 ALA HET CL A 401 1 HET 7CP A 501 25 HETNAM CL CHLORIDE ION HETNAM 7CP (4R)-7,8-DICHLORO-1',9-DIMETHYL-1-OXO-1,2,4,9- HETNAM 2 7CP TETRAHYDROSPIRO[BETA-CARBOLINE-3,4'-PIPERIDINE]-4- HETNAM 3 7CP CARBONITRILE FORMUL 3 CL CL 1- FORMUL 4 7CP C18 H18 CL2 N4 O FORMUL 5 HOH *217(H2 O) HELIX 1 1 PRO A 33 GLN A 37 1 5 HELIX 2 2 ASP A 72 ILE A 74 5 3 HELIX 3 3 MET A 88 SER A 97 1 10 HELIX 4 4 LEU A 129 GLY A 137 1 9 HELIX 5 5 GLN A 140 CYS A 161 1 22 HELIX 6 6 LYS A 169 GLU A 171 5 3 HELIX 7 7 THR A 204 SER A 208 5 5 HELIX 8 8 PRO A 209 HIS A 216 1 8 HELIX 9 9 HIS A 219 GLY A 238 1 20 HELIX 10 10 HIS A 244 GLY A 251 1 8 HELIX 11 11 SER A 260 LEU A 271 1 12 HELIX 12 12 ARG A 274 ARG A 278 5 5 HELIX 13 13 THR A 280 HIS A 287 1 8 HELIX 14 14 PRO A 288 GLN A 291 5 4 HELIX 15 15 LEU A 295 LEU A 304 1 10 SHEET 1 A 5 TYR A 38 GLY A 47 0 SHEET 2 A 5 GLY A 50 ARG A 57 -1 O SER A 54 N GLY A 41 SHEET 3 A 5 PRO A 63 GLU A 70 -1 O HIS A 68 N SER A 51 SHEET 4 A 5 SER A 115 GLU A 121 -1 O LEU A 118 N LYS A 67 SHEET 5 A 5 LEU A 106 GLU A 111 -1 N ASP A 108 O ILE A 119 SHEET 1 B 2 TRP A 77 GLU A 79 0 SHEET 2 B 2 ARG A 85 PRO A 87 -1 O VAL A 86 N GLY A 78 SHEET 1 C 3 VAL A 126 ASP A 128 0 SHEET 2 C 3 ILE A 173 ASP A 176 -1 O ILE A 175 N GLN A 127 SHEET 3 C 3 GLU A 181 LEU A 184 -1 O GLU A 181 N ASP A 176 SHEET 1 D 2 VAL A 163 LEU A 164 0 SHEET 2 D 2 ALA A 191 LEU A 192 -1 O ALA A 191 N LEU A 164 CISPEP 1 GLU A 124 PRO A 125 0 -9.05 SITE 1 AC1 2 LYS A 67 ASP A 186 SITE 1 AC2 11 LEU A 44 PHE A 49 ALA A 65 LYS A 67 SITE 2 AC2 11 ARG A 122 GLU A 171 ASN A 172 LEU A 174 SITE 3 AC2 11 ILE A 185 ASP A 186 SER B 9 CRYST1 98.371 98.371 81.332 90.00 90.00 120.00 P 65 6 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 0.010166 0.005869 0.000000 0.00000 SCALE2 0.000000 0.011738 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012295 0.00000