HEADER TRANSFERASE 25-APR-08 3CY2 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 II 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 F.VON DELFT,C.H.ARROWSMITH,A.M.EDWARDS,C.BOUNTRA,S.KNAPP,STRUCTURAL AUTHOR 3 GENOMICS CONSORTIUM (SGC) REVDAT 8 30-AUG-23 3CY2 1 REMARK REVDAT 7 20-OCT-21 3CY2 1 REMARK SEQADV REVDAT 6 25-OCT-17 3CY2 1 REMARK REVDAT 5 19-JUN-13 3CY2 1 JRNL REVDAT 4 18-JAN-12 3CY2 1 JRNL REVDAT 3 13-JUL-11 3CY2 1 VERSN REVDAT 2 24-FEB-09 3CY2 1 VERSN REVDAT 1 15-JUL-08 3CY2 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. 2.01 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) : 2.01 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.30 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 29927 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) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1553 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) : 2.01 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.06 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2096 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2780 REMARK 3 BIN FREE R VALUE SET COUNT : 114 REMARK 3 BIN FREE R VALUE : 0.3720 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2266 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 207 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) : 26.31 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.27000 REMARK 3 B22 (A**2) : 0.27000 REMARK 3 B33 (A**2) : -0.40000 REMARK 3 B12 (A**2) : 0.13000 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): 0.127 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.122 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.084 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.454 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.952 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2386 ; 0.015 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 1674 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3233 ; 1.371 ; 1.961 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4017 ; 1.609 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 277 ; 6.337 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 123 ;32.211 ;22.683 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 399 ;13.647 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;20.209 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 340 ; 0.085 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2625 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 520 ; 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): 1393 ; 2.280 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 566 ; 0.712 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2258 ; 3.382 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 993 ; 5.660 ; 8.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 975 ; 7.690 ;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 : 3 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 81 REMARK 3 ORIGIN FOR THE GROUP (A): -23.2550 31.0180 5.9130 REMARK 3 T TENSOR REMARK 3 T11: 0.1114 T22: 0.1512 REMARK 3 T33: -0.0110 T12: -0.1897 REMARK 3 T13: -0.0384 T23: 0.0307 REMARK 3 L TENSOR REMARK 3 L11: 8.9961 L22: 7.0279 REMARK 3 L33: 6.8020 L12: -0.9528 REMARK 3 L13: 1.6370 L23: 1.5283 REMARK 3 S TENSOR REMARK 3 S11: -0.0432 S12: -0.3664 S13: -0.3256 REMARK 3 S21: 0.8198 S22: 0.0652 S23: 0.3863 REMARK 3 S31: 0.9173 S32: -0.4977 S33: -0.0220 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 84 A 140 REMARK 3 ORIGIN FOR THE GROUP (A): -17.1180 37.6220 5.5120 REMARK 3 T TENSOR REMARK 3 T11: -0.0348 T22: 0.0536 REMARK 3 T33: -0.0266 T12: -0.0812 REMARK 3 T13: -0.0384 T23: 0.0054 REMARK 3 L TENSOR REMARK 3 L11: 1.5016 L22: 1.3242 REMARK 3 L33: 2.9587 L12: 0.8437 REMARK 3 L13: -0.4046 L23: -0.3991 REMARK 3 S TENSOR REMARK 3 S11: 0.1470 S12: -0.1414 S13: -0.0834 REMARK 3 S21: 0.0950 S22: -0.0426 S23: 0.2243 REMARK 3 S31: 0.4611 S32: -0.4561 S33: -0.1044 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 141 A 305 REMARK 3 ORIGIN FOR THE GROUP (A): -1.0590 45.0410 -1.1920 REMARK 3 T TENSOR REMARK 3 T11: -0.0769 T22: -0.0472 REMARK 3 T33: -0.0591 T12: 0.0000 REMARK 3 T13: -0.0266 T23: -0.0104 REMARK 3 L TENSOR REMARK 3 L11: 0.6165 L22: 1.3525 REMARK 3 L33: 1.6008 L12: 0.0457 REMARK 3 L13: -0.0453 L23: -0.2527 REMARK 3 S TENSOR REMARK 3 S11: 0.0346 S12: -0.0160 S13: 0.0076 REMARK 3 S21: -0.0250 S22: 0.0351 S23: -0.0575 REMARK 3 S31: 0.0606 S32: 0.0361 S33: -0.0697 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 3CY2 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_1000047353. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-SEP-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 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 FR-E+ SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.2.25 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29963 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.010 REMARK 200 RESOLUTION RANGE LOW (A) : 32.297 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : 0.07500 REMARK 200 FOR THE DATA SET : 8.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.01 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.10 REMARK 200 R MERGE FOR SHELL (I) : 0.70400 REMARK 200 R SYM FOR SHELL (I) : 0.70400 REMARK 200 FOR SHELL : 1.100 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 (%): 59.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.56 M NA SUCCINATE PH 7.0, 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 54.08600 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 27.04300 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 40.56450 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 13.52150 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 67.60750 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: 1120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 2.7 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 SER A 306 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 ALA B 1 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 SER A 36 OG REMARK 470 GLN A 39 CD OE1 NE2 REMARK 470 ASP A 72 OD1 OD2 REMARK 470 ARG A 73 NH1 NH2 REMARK 470 GLU A 79 CG CD OE1 OE2 REMARK 470 THR A 84 OG1 CG2 REMARK 470 LYS A 94 CE NZ REMARK 470 LYS B 3 CD CE NZ 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 HOH A 618 O HOH A 665 2.14 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 SER A 98 165.85 179.82 REMARK 500 ASP A 167 44.94 -147.79 REMARK 500 ASP A 176 99.41 -69.99 REMARK 500 ASP A 186 78.27 64.46 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 MB9 A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 551 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3CXW 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 I 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 3CY2 A 1 313 UNP P11309 PIM1_HUMAN 1 313 DBREF 3CY2 B 1 14 PDB 3CY2 3CY2 1 14 SEQADV 3CY2 SER A 0 UNP P11309 EXPRESSION TAG SEQADV 3CY2 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 MB9 A 501 23 HET EDO A 551 4 HETNAM CL CHLORIDE ION HETNAM MB9 (4R)-7-CHLORO-9-METHYL-1-OXO-1,2,4,9- HETNAM 2 MB9 TETRAHYDROSPIRO[BETA-CARBOLINE-3,4'-PIPERIDINE]-4- HETNAM 3 MB9 CARBONITRILE HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 CL CL 1- FORMUL 4 MB9 C17 H17 CL N4 O FORMUL 5 EDO C2 H6 O2 FORMUL 6 HOH *207(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 LEU A 107 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 -9.66 SITE 1 AC1 2 LYS A 67 ASP A 186 SITE 1 AC2 9 GLY A 45 PHE A 49 LYS A 67 ARG A 122 SITE 2 AC2 9 GLU A 171 ASN A 172 LEU A 174 ILE A 185 SITE 3 AC2 9 ASP A 186 SITE 1 AC3 3 HIS A 219 ARG A 221 SER A 222 CRYST1 98.668 98.668 81.129 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 0.010135 0.005851 0.000000 0.00000 SCALE2 0.000000 0.011703 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012326 0.00000 CONECT 2301 2302 2306 CONECT 2302 2301 2303 CONECT 2303 2302 2304 CONECT 2304 2303 2305 CONECT 2305 2304 2306 CONECT 2306 2301 2305 2307 2321 CONECT 2307 2306 2308 CONECT 2308 2307 2309 2310 CONECT 2309 2308 CONECT 2310 2308 2311 2320 CONECT 2311 2310 2312 2313 CONECT 2312 2311 CONECT 2313 2311 2314 2319 CONECT 2314 2313 2315 CONECT 2315 2314 2316 2317 CONECT 2316 2315 CONECT 2317 2315 2318 CONECT 2318 2317 2319 CONECT 2319 2313 2318 2320 CONECT 2320 2310 2319 2321 CONECT 2321 2306 2320 2322 CONECT 2322 2321 2323 CONECT 2323 2322 CONECT 2324 2325 2326 CONECT 2325 2324 CONECT 2326 2324 2327 CONECT 2327 2326 MASTER 426 0 3 15 12 0 5 6 2501 2 27 27 END