PDB Short entry for 3CY3 HEADER TRANSFERASE 25-APR-08 3CY3 TITLE CRYSTAL STRUCTURE OF HUMAN PROTO-ONCOGENE SERINE THREONINE KINASE TITLE 2 (PIM1) IN COMPLEX WITH A CONSENSUS PEPTIDE AND THE JNK INHIBITOR V COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE/THREONINE-PROTEIN KINASE PIM-1; COMPND 3 CHAIN: A; COMPND 4 EC: 2.7.11.1; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: 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_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PIM1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)-R3; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PNIC28-BSA4; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630 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,A.C.W.PIKE,F.VON DELFT, AUTHOR 2 C.H.ARROWSMITH,A.M.EDWARDS,C.BOUNTRA,S.KNAPP,STRUCTURAL GENOMICS AUTHOR 3 CONSORTIUM (SGC) REVDAT 7 30-AUG-23 3CY3 1 REMARK REVDAT 6 16-FEB-22 3CY3 1 COMPND SOURCE DBREF REVDAT 5 20-OCT-21 3CY3 1 REMARK SEQADV LINK REVDAT 4 25-OCT-17 3CY3 1 REMARK REVDAT 3 13-JUL-11 3CY3 1 VERSN REVDAT 2 24-FEB-09 3CY3 1 VERSN REVDAT 1 15-JUL-08 3CY3 0 JRNL AUTH P.FILIPPAKOPOULOS,A.BULLOCK,O.FEDOROV,A.C.W.PIKE, JRNL AUTH 2 F.VON DELFT,C.H.ARROWSMITH,A.M.EDWARDS,C.BOUNTRA,S.KNAPP JRNL TITL PROTO-ONCOGENE SERINE THREONINE KINASE (PIM1) IN COMPLEX JRNL TITL 2 WITH A CONSENSUS PEPTIDE AND THE JNK INHIBITOR V. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.15 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) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.19 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 24159 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) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1208 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) : 2.15 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.21 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1680 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2440 REMARK 3 BIN FREE R VALUE SET COUNT : 78 REMARK 3 BIN FREE R VALUE : 0.3110 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2260 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 31 REMARK 3 SOLVENT ATOMS : 218 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) : 28.53 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.18000 REMARK 3 B22 (A**2) : 0.18000 REMARK 3 B33 (A**2) : -0.28000 REMARK 3 B12 (A**2) : 0.09000 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): 0.158 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.149 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.104 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.223 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.941 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2353 ; 0.015 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 1637 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3188 ; 1.464 ; 1.962 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3920 ; 1.001 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 276 ; 6.150 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 117 ;32.524 ;22.821 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 383 ;12.729 ;15.039 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 23 ;15.981 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 335 ; 0.090 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2602 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 507 ; 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): 1388 ; 2.506 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 563 ; 0.788 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2242 ; 3.672 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 965 ; 6.267 ; 8.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 946 ; 7.909 ;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 119 REMARK 3 ORIGIN FOR THE GROUP (A): -20.4430 30.7830 8.8450 REMARK 3 T TENSOR REMARK 3 T11: -0.0478 T22: 0.0286 REMARK 3 T33: -0.1102 T12: -0.1224 REMARK 3 T13: 0.0206 T23: 0.0490 REMARK 3 L TENSOR REMARK 3 L11: 4.1476 L22: 4.9808 REMARK 3 L33: 3.8823 L12: 2.1117 REMARK 3 L13: 1.6615 L23: 1.7474 REMARK 3 S TENSOR REMARK 3 S11: 0.2052 S12: -0.4878 S13: -0.1040 REMARK 3 S21: 0.4639 S22: -0.2434 S23: 0.3712 REMARK 3 S31: 0.3709 S32: -0.4669 S33: 0.0382 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 120 A 305 REMARK 3 ORIGIN FOR THE GROUP (A): -2.9560 44.7820 -1.7270 REMARK 3 T TENSOR REMARK 3 T11: -0.1681 T22: -0.1503 REMARK 3 T33: -0.2504 T12: 0.0055 REMARK 3 T13: -0.0186 T23: -0.0104 REMARK 3 L TENSOR REMARK 3 L11: 0.9602 L22: 1.5764 REMARK 3 L33: 2.0846 L12: 0.0322 REMARK 3 L13: 0.0749 L23: -0.3111 REMARK 3 S TENSOR REMARK 3 S11: 0.0356 S12: 0.0146 S13: -0.0160 REMARK 3 S21: -0.0868 S22: 0.0105 S23: 0.0100 REMARK 3 S31: 0.0731 S32: -0.0155 S33: -0.0461 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 3CY3 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_1000047354. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-SEP-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) : 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 : 24190 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 31.189 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : 0.10300 REMARK 200 R SYM (I) : 0.10300 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.27 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : 0.74700 REMARK 200 R SYM FOR SHELL (I) : 0.74700 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.000 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 (%): 59.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 9 % PEG 10000, 7.2 % ETHYLENE GLYCOL, REMARK 280 0.09 M HEPES PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 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 53.81533 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 26.90767 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 40.36150 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 13.45383 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 67.26917 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: 1100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13120 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 2.8 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 GLY B 10 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 CG CD OE1 OE2 REMARK 470 SER A 36 OG REMARK 470 GLU A 79 CG CD OE1 OE2 REMARK 470 LEU A 80 CG CD1 CD2 REMARK 470 THR A 84 OG1 CG2 REMARK 470 LYS A 94 NZ REMARK 470 ARG A 179 NH1 NH2 REMARK 470 ASP A 202 OD1 OD2 REMARK 470 ARG A 274 CZ NH1 NH2 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 588 O HOH A 625 2.19 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 170 CB - CG - OD1 ANGL. DEV. = 6.7 DEGREES REMARK 500 ARG B 5 NE - CZ - NH1 ANGL. DEV. = 3.1 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 167 50.18 -148.45 REMARK 500 ASP A 186 74.92 56.83 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 EDO A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE JN5 A 501 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: 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 DBREF 3CY3 A 1 313 UNP P11309 PIM1_HUMAN 1 313 DBREF 3CY3 B 1 14 PDB 3CY3 3CY3 1 14 SEQADV 3CY3 SER A 0 UNP P11309 EXPRESSION TAG SEQADV 3CY3 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 SEP 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 MODRES 3CY3 SEP A 261 SER MODIFIED RESIDUE HET SEP A 261 10 HET EDO A 401 4 HET JN5 A 501 27 HETNAM SEP PHOSPHOSERINE HETNAM EDO 1,2-ETHANEDIOL HETNAM JN5 (2S)-1,3-BENZOTHIAZOL-2-YL{2-[(2-PYRIDIN-3-YLETHYL) HETNAM 2 JN5 AMINO]PYRIMIDIN-4-YL}ETHANENITRILE HETSYN SEP PHOSPHONOSERINE HETSYN EDO ETHYLENE GLYCOL FORMUL 1 SEP C3 H8 N O6 P FORMUL 3 EDO C2 H6 O2 FORMUL 4 JN5 C20 H16 N6 S FORMUL 5 HOH *218(H2 O) HELIX 1 1 PRO A 33 SER A 36 5 4 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 ASN A 286 1 7 HELIX 14 14 HIS A 287 GLN A 291 5 5 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 ILE A 66 N TYR A 53 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 LINK C SER A 260 N SEP A 261 1555 1555 1.32 LINK C SEP A 261 N GLU A 262 1555 1555 1.34 CISPEP 1 GLU A 124 PRO A 125 0 -2.64 SITE 1 AC1 5 GLU A 89 LEU A 93 ILE A 104 ASP A 186 SITE 2 AC1 5 PHE A 187 SITE 1 AC2 7 PHE A 49 ALA A 65 LYS A 67 GLU A 121 SITE 2 AC2 7 LEU A 174 ILE A 185 ASP A 186 CRYST1 98.239 98.239 80.723 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 0.010179 0.005877 0.000000 0.00000 SCALE2 0.000000 0.011754 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012388 0.00000