PDB Short entry for 2XIY HEADER TRANSFERASE 01-JUL-10 2XIY TITLE PROTEIN KINASE PIM-1 IN COMPLEX WITH FRAGMENT-2 FROM TITLE 2 CRYSTALLOGRAPHIC FRAGMENT SCREEN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTO-ONCOGENE SERINE/THREONINE PROTEIN KINASE PIM-1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: KINASE DOMAIN, RESIDUES 14-313; COMPND 5 EC: 2.7.1.37, 2.7.11.1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET30A, HIS-TEV-PIM-1(14-313) KEYWDS PHOSPHORYLATION, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.N.SCHULZ,J.FANGHANEL,M.SCHAFER,V.BADOCK,H.BRIEM,U.BOEMER,D.NGUYEN, AUTHOR 2 M.HUSEMANN,R.C.HILLIG REVDAT 2 16-MAR-11 2XIY 1 JRNL REVDAT 1 23-FEB-11 2XIY 0 JRNL AUTH M.N.SCHULZ,J.FANGHANEL,M.SCHAFER,V.BADOCK,H.BRIEM,U.BOEMER, JRNL AUTH 2 D.NGUYEN,M.HUSEMANN,R.C.HILLIG JRNL TITL CRYSTALLOGRAPHIC FRAGMENT SCREEN IDENTIFIES CINNAMIC ACID JRNL TITL 2 DERIVATIVES AS STARTING POINTS FOR POTENT PIM-1 INHIBITORS JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 67 156 2011 JRNL REFN ISSN 0907-4449 JRNL PMID 21358046 JRNL DOI 10.1107/S0907444910054144 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.62 REMARK 3 DATA CUTOFF (SIGMA(F)) : NONE REMARK 3 COMPLETENESS FOR RANGE (%) : 95.97 REMARK 3 NUMBER OF REFLECTIONS : 20074 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) : 0.17150 REMARK 3 R VALUE (WORKING SET) : 0.16994 REMARK 3 FREE R VALUE : 0.20075 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.0 REMARK 3 FREE R VALUE TEST SET COUNT : 1065 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) : 2.200 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.257 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1081 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 69.35 REMARK 3 BIN R VALUE (WORKING SET) : 0.218 REMARK 3 BIN FREE R VALUE SET COUNT : 46 REMARK 3 BIN FREE R VALUE : 0.288 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2277 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 32 REMARK 3 SOLVENT ATOMS : 132 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.238 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.50 REMARK 3 B22 (A**2) : -0.50 REMARK 3 B33 (A**2) : 0.75 REMARK 3 B12 (A**2) : -0.25 REMARK 3 B13 (A**2) : 0.00 REMARK 3 B23 (A**2) : 0.00 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.188 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.159 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.115 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.666 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.948 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2374 ; 0.010 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3230 ; 1.214 ; 1.959 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 286 ; 5.742 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 125 ;33.818 ;23.040 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 399 ;14.985 ;15.038 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;17.420 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 341 ; 0.080 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1852 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1079 ; 0.187 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1573 ; 0.304 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 128 ; 0.142 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 30 ; 0.151 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 10 ; 0.108 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1447 ; 1.904 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2267 ; 2.815 ; 3.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1076 ; 4.709 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 958 ; 6.381 ; 6.000 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 123 REMARK 3 ORIGIN FOR THE GROUP (A): -16.5260 -33.4810 7.5500 REMARK 3 T TENSOR REMARK 3 T11: 0.0158 T22: 0.1496 REMARK 3 T33: -0.2683 T12: 0.0744 REMARK 3 T13: -0.0698 T23: -0.0128 REMARK 3 L TENSOR REMARK 3 L11: 10.2918 L22: 3.5296 REMARK 3 L33: 5.4265 L12: -2.0364 REMARK 3 L13: -1.8852 L23: 1.5259 REMARK 3 S TENSOR REMARK 3 S11: -0.0070 S12: -0.7125 S13: -0.1320 REMARK 3 S21: 0.2466 S22: 0.0844 S23: -0.2451 REMARK 3 S31: 0.0819 S32: 0.5816 S33: -0.0773 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 124 A 306 REMARK 3 ORIGIN FOR THE GROUP (A): -37.0850 -24.5430 -3.4680 REMARK 3 T TENSOR REMARK 3 T11: -0.0929 T22: -0.0820 REMARK 3 T33: -0.3613 T12: 0.0297 REMARK 3 T13: 0.0472 T23: -0.0214 REMARK 3 L TENSOR REMARK 3 L11: 2.0297 L22: 2.4023 REMARK 3 L33: 3.0646 L12: 0.4511 REMARK 3 L13: 0.7408 L23: -0.1346 REMARK 3 S TENSOR REMARK 3 S11: -0.0281 S12: 0.0228 S13: -0.0609 REMARK 3 S21: -0.0919 S22: 0.1264 S23: -0.1185 REMARK 3 S31: 0.0379 S32: 0.0869 S33: -0.0983 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS. REMARK 4 REMARK 4 2XIY COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-JUL-10. REMARK 100 THE PDBE ID CODE IS EBI-44465. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-MAY-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91841 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL2000 REMARK 200 DATA SCALING SOFTWARE : HKL2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21175 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.20 REMARK 200 RESOLUTION RANGE LOW (A) : 48.60 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 200 DATA REDUNDANCY : 8.6 REMARK 200 R MERGE (I) : 0.09 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 21.20 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 71.3 REMARK 200 DATA REDUNDANCY IN SHELL : 4.8 REMARK 200 R MERGE FOR SHELL (I) : 0.45 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.25 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: IN-HOUSE PIM-1 STRUCTURE REMARK 200 REMARK 200 REMARK: SOLVED BY RIGID BODY REFINEMENT REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.8 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.9 M (NH4)2HPO4,0.1 M SODIUM REMARK 280 CITRATE PH=5.5 , 0.2M NACL 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 53.91333 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 26.95667 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 40.43500 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 13.47833 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 67.39167 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: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 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 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 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 GLU A 79 -76.35 -95.90 REMARK 500 LEU A 80 127.50 75.68 REMARK 500 ASP A 167 45.84 -143.88 REMARK 500 ASP A 186 73.41 60.39 REMARK 500 ASP A 202 20.93 -152.76 REMARK 500 HIS A 305 -18.06 82.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 GLYCEROL (GOL): ARTIFACT FROM CRYO BUFFER REMARK 600 CHLORIDE ION (CL): ARTIFACT FROM CRYSTALLIZATION BUFFER REMARK 600 DIMETHYLSULFOXIDE (DMS): ARTIFACT FROM SOAKING PROCEDURE REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE XIY A1307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A1308 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A1309 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1310 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2BIK RELATED DB: PDB REMARK 900 HUMAN PIM1 PHOSPHORYLATED ON SER261 REMARK 900 RELATED ID: 2XIX RELATED DB: PDB REMARK 900 PROTEIN KINASE PIM-1 IN COMPLEX WITH FRAGMENT-1 FROM REMARK 900 CRYSTALLOGRAPHIC FRAGMENT SCREEN REMARK 900 RELATED ID: 2C3I RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN PIM1 IN COMPLEX WITH REMARK 900 IMIDAZOPYRIDAZIN I REMARK 900 RELATED ID: 1YWV RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURES OF PROTO-ONCOGENE KINASE PIM1: A REMARK 900 TARGETOF ABERRANT SOMATIC HYPERMUTATIONS IN DIFFUSE LARGE REMARK 900 CELLLYMPHOMA REMARK 900 RELATED ID: 2BZJ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE HUMAN PIM1 IN COMPLEX WITH REMARK 900 A RUTHENIUM ORGANOMETALLIC LIGAND RU3 REMARK 900 RELATED ID: 1YXU RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF KINASE PIM1 IN COMPLEX WITH AMP REMARK 900 RELATED ID: 2J2I RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE HUMAB PIM1 IN COMPLEX WITH REMARK 900 LY333531 REMARK 900 RELATED ID: 1YXT RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF KINASE PIM1 IN COMPLEX WITH REMARK 900 AMPPNP REMARK 900 RELATED ID: 2BZH RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE HUMAN PIM1 IN COMPLEX WITH REMARK 900 A RUTHENIUM ORGANOMETALLIC LIGAND RU1 REMARK 900 RELATED ID: 1YXS RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF KINASE PIM1 WITH P123M MUTATION REMARK 900 RELATED ID: 1XQZ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HPIM-1 KINASE AT 2.1 A REMARK 900 RESOLUTION REMARK 900 RELATED ID: 1YI3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PIM-1 BOUND TO LY294002 REMARK 900 RELATED ID: 2XIZ RELATED DB: PDB REMARK 900 PROTEIN KINASE PIM-1 IN COMPLEX WITH FRAGMENT-3 FROM REMARK 900 CRYSTALLOGRAPHIC FRAGMENT SCREEN REMARK 900 RELATED ID: 1YXV RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF KINASE PIM1 IN COMPLEX WITH 3,4 REMARK 900 -DIHYDROXY-1-METHYLQUINOLIN-2(1H)-ONE REMARK 900 RELATED ID: 1XR1 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HPIM-1 KINASE IN COMPLEX WITH REMARK 900 AMP-PNPAT 2.1 A RESOLUTION REMARK 900 RELATED ID: 2BIL RELATED DB: PDB REMARK 900 THE HUMAN PROTEIN KINASE PIM1 IN COMPLEX WITH ITS REMARK 900 CONSENSUS PEPTIDE PIMTIDE REMARK 900 RELATED ID: 1YHS RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PIM-1 BOUND TO STAUROSPORINE REMARK 900 RELATED ID: 1YXX RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF KINASE PIM1 IN COMPLEX WITH (3E REMARK 900 )-3-[(4-HYDROXYPHENYL)IMINO]-1H-INDOL-2(3H)-ONE REMARK 900 RELATED ID: 1XWS RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE HUMAN PIM1 KINASE DOMAIN REMARK 900 RELATED ID: 2XJ1 RELATED DB: PDB REMARK 900 PROTEIN KINASE PIM-1 IN COMPLEX WITH SMALL MOLECULE REMARK 900 INIBITOR REMARK 900 RELATED ID: 2BZK RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE HUMAN PIM1 IN COMPLEX WITH REMARK 900 AMPPNP AND PIMTIDE REMARK 900 RELATED ID: 2XJ0 RELATED DB: PDB REMARK 900 PROTEIN KINASE PIM-1 IN COMPLEX WITH FRAGMENT-4 FROM REMARK 900 CRYSTALLOGRAPHIC FRAGMENT SCREEN REMARK 900 RELATED ID: 2XJ2 RELATED DB: PDB REMARK 900 PROTEIN KINASE PIM-1 IN COMPLEX WITH SMALL MOLECULE REMARK 900 INHIBITOR REMARK 900 RELATED ID: 1YI4 RELATED DB: PDB REMARK 900 STRUCTURE OF PIM-1 BOUND TO ADENOSINE REMARK 900 RELATED ID: 2BZI RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE HUMAN PIM1 IN COMPLEX WITH REMARK 900 A RUTHENIUM ORGANOMETALLIC LIGAND RU2 REMARK 999 REMARK 999 SEQUENCE REMARK 999 N-TERMINAL GLY FROM TEV CLEAVAGE SITE DBREF 2XIY A 14 313 UNP P11309 PIM1_HUMAN 14 313 SEQADV 2XIY GLY A 13 UNP P11309 EXPRESSION TAG SEQRES 1 A 301 GLY ALA ALA PRO CYS ASN ASP LEU HIS ALA THR LYS LEU SEQRES 2 A 301 ALA PRO GLY LYS GLU LYS GLU PRO LEU GLU SER GLN TYR SEQRES 3 A 301 GLN VAL GLY PRO LEU LEU GLY SER GLY GLY PHE GLY SER SEQRES 4 A 301 VAL TYR SER GLY ILE ARG VAL SER ASP ASN LEU PRO VAL SEQRES 5 A 301 ALA ILE LYS HIS VAL GLU LYS ASP ARG ILE SER ASP TRP SEQRES 6 A 301 GLY GLU LEU PRO ASN GLY THR ARG VAL PRO MET GLU VAL SEQRES 7 A 301 VAL LEU LEU LYS LYS VAL SER SER GLY PHE SER GLY VAL SEQRES 8 A 301 ILE ARG LEU LEU ASP TRP PHE GLU ARG PRO ASP SER PHE SEQRES 9 A 301 VAL LEU ILE LEU GLU ARG PRO GLU PRO VAL GLN ASP LEU SEQRES 10 A 301 PHE ASP PHE ILE THR GLU ARG GLY ALA LEU GLN GLU GLU SEQRES 11 A 301 LEU ALA ARG SER PHE PHE TRP GLN VAL LEU GLU ALA VAL SEQRES 12 A 301 ARG HIS CYS HIS ASN CYS GLY VAL LEU HIS ARG ASP ILE SEQRES 13 A 301 LYS ASP GLU ASN ILE LEU ILE ASP LEU ASN ARG GLY GLU SEQRES 14 A 301 LEU LYS LEU ILE ASP PHE GLY SER GLY ALA LEU LEU LYS SEQRES 15 A 301 ASP THR VAL TYR THR ASP PHE ASP GLY THR ARG VAL TYR SEQRES 16 A 301 SER PRO PRO GLU TRP ILE ARG TYR HIS ARG TYR HIS GLY SEQRES 17 A 301 ARG SER ALA ALA VAL TRP SER LEU GLY ILE LEU LEU TYR SEQRES 18 A 301 ASP MET VAL CYS GLY ASP ILE PRO PHE GLU HIS ASP GLU SEQRES 19 A 301 GLU ILE ILE ARG GLY GLN VAL PHE PHE ARG GLN ARG VAL SEQRES 20 A 301 SER SEP GLU CYS GLN HIS LEU ILE ARG TRP CYS LEU ALA SEQRES 21 A 301 LEU ARG PRO SER ASP ARG PRO THR PHE GLU GLU ILE GLN SEQRES 22 A 301 ASN HIS PRO TRP MET GLN ASP VAL LEU LEU PRO GLN GLU SEQRES 23 A 301 THR ALA GLU ILE HIS LEU HIS SER LEU SER PRO GLY PRO SEQRES 24 A 301 SER LYS MODRES 2XIY SEP A 261 SER PHOSPHOSERINE HET SEP A 261 10 HET XIY A1307 11 HET DMS A1308 4 HET CL A1309 1 HET GOL A1310 6 HETNAM SEP PHOSPHOSERINE HETNAM XIY 2-HYDROXYMETHYL-BENZOIMIDAZOLE HETNAM DMS DIMETHYL SULFOXIDE HETNAM CL CHLORIDE ION HETNAM GOL GLYCEROL HETSYN SEP PHOSPHONOSERINE HETSYN XIY 1H-BENZIMIDAZOL-2-YLMETHANOL FORMUL 2 SEP C3 H8 N O6 P FORMUL 3 XIY C8 H8 N2 O FORMUL 4 DMS C2 H6 O S FORMUL 5 CL CL 1 FORMUL 6 GOL C3 H8 O3 FORMUL 7 HOH *132(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 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 AA 5 TYR A 38 GLY A 47 0 SHEET 2 AA 5 GLY A 50 ARG A 57 -1 O GLY A 50 N GLY A 47 SHEET 3 AA 5 LEU A 62 GLU A 70 -1 O LEU A 62 N ARG A 57 SHEET 4 AA 5 SER A 115 GLU A 121 -1 O PHE A 116 N VAL A 69 SHEET 5 AA 5 LEU A 106 GLU A 111 -1 N LEU A 107 O ILE A 119 SHEET 1 AB 2 TRP A 77 GLY A 78 0 SHEET 2 AB 2 VAL A 86 PRO A 87 -1 O VAL A 86 N GLY A 78 SHEET 1 AC 3 VAL A 126 ASP A 128 0 SHEET 2 AC 3 ILE A 173 ASP A 176 -1 O ILE A 175 N GLN A 127 SHEET 3 AC 3 GLU A 181 LEU A 184 -1 O GLU A 181 N ASP A 176 SHEET 1 AD 2 VAL A 163 LEU A 164 0 SHEET 2 AD 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 1.33 CISPEP 1 GLU A 124 PRO A 125 0 -0.59 SITE 1 AC1 10 PHE A 49 VAL A 52 ALA A 65 LYS A 67 SITE 2 AC1 10 GLU A 121 LEU A 174 ILE A 185 ASP A 186 SITE 3 AC1 10 GOL A1310 HOH A2131 SITE 1 AC2 5 ILE A 133 ASP A 170 ASP A 234 GLY A 238 SITE 2 AC2 5 ASP A 239 SITE 1 AC3 4 LYS A 67 LEU A 120 ILE A 185 ASP A 186 SITE 1 AC4 4 GLN A 127 ASP A 128 ASP A 131 XIY A1307 CRYST1 96.987 96.987 80.870 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 0.010311 0.005953 0.000000 0.00000 SCALE2 0.000000 0.011906 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012366 0.00000