HEADER TRANSFERASE 17-MAY-17 5O13 TITLE CRYSTAL STRUCTURE OF PIM1 KINASE IN COMPLEX WITH SMALL-MOLECULE TITLE 2 INHIBITOR 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 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 KEYWDS KINASE, PIM1, CX-6258, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR G.DUBIN,J.BOGUSZ REVDAT 3 17-JAN-24 5O13 1 REMARK REVDAT 2 16-OCT-19 5O13 1 REMARK REVDAT 1 01-NOV-17 5O13 0 JRNL AUTH J.BOGUSZ,K.ZRUBEK,K.P.REMBACZ,P.GRUDNIK,P.GOLIK, JRNL AUTH 2 M.ROMANOWSKA,B.WLADYKA,G.DUBIN JRNL TITL STRUCTURAL ANALYSIS OF PIM1 KINASE COMPLEXES WITH JRNL TITL 2 ATP-COMPETITIVE INHIBITORS. JRNL REF SCI REP V. 7 13399 2017 JRNL REFN ESSN 2045-2322 JRNL PMID 29042609 JRNL DOI 10.1038/S41598-017-13557-Z REMARK 2 REMARK 2 RESOLUTION. 2.44 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.44 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.26 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 15317 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) : 0.162 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 834 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) : 2.44 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.51 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1095 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.48 REMARK 3 BIN R VALUE (WORKING SET) : 0.2380 REMARK 3 BIN FREE R VALUE SET COUNT : 64 REMARK 3 BIN FREE R VALUE : 0.3040 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2160 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 39 REMARK 3 SOLVENT ATOMS : 90 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.56 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.88000 REMARK 3 B22 (A**2) : 0.88000 REMARK 3 B33 (A**2) : -2.85000 REMARK 3 B12 (A**2) : 0.44000 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): 0.242 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.206 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.134 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.709 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.928 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2261 ; 0.018 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2083 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3076 ; 2.027 ; 1.973 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4764 ; 0.874 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 271 ; 6.901 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 106 ;34.186 ;22.925 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 349 ;14.920 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;16.303 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 327 ; 0.107 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2556 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 558 ; 0.006 ; 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): 1088 ; 2.789 ; 3.229 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1089 ; 2.789 ; 3.233 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1357 ; 4.140 ; 4.835 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1358 ; 4.142 ; 4.841 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1173 ; 3.825 ; 3.591 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1174 ; 3.824 ; 3.593 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1720 ; 5.830 ; 5.258 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2661 ; 7.789 ;27.309 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2662 ; 7.787 ;27.318 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 : 1 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 34 A 305 REMARK 3 ORIGIN FOR THE GROUP (A): -79.1718 56.4990 -1.1694 REMARK 3 T TENSOR REMARK 3 T11: 0.0667 T22: 0.0500 REMARK 3 T33: 0.0565 T12: 0.0281 REMARK 3 T13: 0.0250 T23: -0.0226 REMARK 3 L TENSOR REMARK 3 L11: 1.6289 L22: 1.1036 REMARK 3 L33: 1.4621 L12: 0.0313 REMARK 3 L13: 0.4111 L23: -0.1969 REMARK 3 S TENSOR REMARK 3 S11: -0.0233 S12: -0.0081 S13: -0.1316 REMARK 3 S21: -0.0673 S22: 0.0535 S23: -0.0906 REMARK 3 S31: 0.0364 S32: 0.1278 S33: -0.0302 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5O13 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-MAY-17. REMARK 100 THE DEPOSITION ID IS D_1200003961. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-JUN-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.1 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 : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16181 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.440 REMARK 200 RESOLUTION RANGE LOW (A) : 29.260 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 38.5000 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 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: 4ALW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TRIS, POTASSIUM SODIUM TARTRATE REMARK 280 TETRAHYDRATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 54.51000 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 27.25500 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 40.88250 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 13.62750 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 68.13750 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 TOTAL BURIED SURFACE AREA: 270 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12680 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL 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 HIS A 16 REMARK 465 HIS A 17 REMARK 465 HIS A 18 REMARK 465 HIS A 19 REMARK 465 HIS A 20 REMARK 465 HIS A 21 REMARK 465 SER A 22 REMARK 465 GLN A 23 REMARK 465 ASP A 24 REMARK 465 PRO A 25 REMARK 465 ASN A 26 REMARK 465 SER A 27 REMARK 465 MET A 28 REMARK 465 LYS A 29 REMARK 465 GLU A 30 REMARK 465 LYS A 31 REMARK 465 GLU A 32 REMARK 465 PRO A 33 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 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 GLN A 39 CG CD OE1 NE2 REMARK 470 ILE A 56 CG1 CG2 CD1 REMARK 470 VAL A 58 CG1 CG2 REMARK 470 SER A 59 OG REMARK 470 ASN A 61 CG OD1 ND2 REMARK 470 ASP A 72 CG OD1 OD2 REMARK 470 ARG A 73 CD NE CZ NH1 NH2 REMARK 470 SER A 75 OG REMARK 470 ASP A 76 CG OD1 OD2 REMARK 470 LEU A 80 CG CD1 CD2 REMARK 470 PRO A 81 CG CD REMARK 470 ASN A 82 CG OD1 ND2 REMARK 470 THR A 84 OG1 CG2 REMARK 470 ARG A 105 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 114 CG OD1 OD2 REMARK 470 GLU A 135 CG CD OE1 OE2 REMARK 470 GLU A 243 CG CD OE1 OE2 REMARK 470 ARG A 274 CG CD NE CZ NH1 NH2 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 OD2 ASP A 170 O HOH A 501 1.77 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. = 3.7 DEGREES REMARK 500 ARG A 145 NE - CZ - NH2 ANGL. DEV. = -4.6 DEGREES REMARK 500 ARG A 166 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG A 221 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 221 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG A 268 NE - CZ - NH2 ANGL. DEV. = 3.2 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 SER A 36 -2.18 -40.50 REMARK 500 SER A 59 -65.59 -23.04 REMARK 500 SER A 75 -81.21 -65.91 REMARK 500 ASN A 82 -30.07 -30.60 REMARK 500 SER A 98 -171.54 -66.21 REMARK 500 ASP A 167 45.95 -142.22 REMARK 500 ASP A 186 82.34 61.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 78 GLU A 79 -149.30 REMARK 500 SER A 97 SER A 98 143.33 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 9G5 A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IMD A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 403 DBREF 5O13 A 29 313 UNP P11309 PIM1_HUMAN 29 313 SEQADV 5O13 HIS A 16 UNP P11309 EXPRESSION TAG SEQADV 5O13 HIS A 17 UNP P11309 EXPRESSION TAG SEQADV 5O13 HIS A 18 UNP P11309 EXPRESSION TAG SEQADV 5O13 HIS A 19 UNP P11309 EXPRESSION TAG SEQADV 5O13 HIS A 20 UNP P11309 EXPRESSION TAG SEQADV 5O13 HIS A 21 UNP P11309 EXPRESSION TAG SEQADV 5O13 SER A 22 UNP P11309 EXPRESSION TAG SEQADV 5O13 GLN A 23 UNP P11309 EXPRESSION TAG SEQADV 5O13 ASP A 24 UNP P11309 EXPRESSION TAG SEQADV 5O13 PRO A 25 UNP P11309 EXPRESSION TAG SEQADV 5O13 ASN A 26 UNP P11309 EXPRESSION TAG SEQADV 5O13 SER A 27 UNP P11309 EXPRESSION TAG SEQADV 5O13 MET A 28 UNP P11309 EXPRESSION TAG SEQRES 1 A 298 HIS HIS HIS HIS HIS HIS SER GLN ASP PRO ASN SER MET SEQRES 2 A 298 LYS GLU LYS GLU PRO LEU GLU SER GLN TYR GLN VAL GLY SEQRES 3 A 298 PRO LEU LEU GLY SER GLY GLY PHE GLY SER VAL TYR SER SEQRES 4 A 298 GLY ILE ARG VAL SER ASP ASN LEU PRO VAL ALA ILE LYS SEQRES 5 A 298 HIS VAL GLU LYS ASP ARG ILE SER ASP TRP GLY GLU LEU SEQRES 6 A 298 PRO ASN GLY THR ARG VAL PRO MET GLU VAL VAL LEU LEU SEQRES 7 A 298 LYS LYS VAL SER SER GLY PHE SER GLY VAL ILE ARG LEU SEQRES 8 A 298 LEU ASP TRP PHE GLU ARG PRO ASP SER PHE VAL LEU ILE SEQRES 9 A 298 LEU GLU ARG PRO GLU PRO VAL GLN ASP LEU PHE ASP PHE SEQRES 10 A 298 ILE THR GLU ARG GLY ALA LEU GLN GLU GLU LEU ALA ARG SEQRES 11 A 298 SER PHE PHE TRP GLN VAL LEU GLU ALA VAL ARG HIS CYS SEQRES 12 A 298 HIS ASN CSX GLY VAL LEU HIS ARG ASP ILE LYS ASP GLU SEQRES 13 A 298 ASN ILE LEU ILE ASP LEU ASN ARG GLY GLU LEU LYS LEU SEQRES 14 A 298 ILE ASP PHE GLY SER GLY ALA LEU LEU LYS ASP THR VAL SEQRES 15 A 298 TYR THR ASP PHE ASP GLY THR ARG VAL TYR SER PRO PRO SEQRES 16 A 298 GLU TRP ILE ARG TYR HIS ARG TYR HIS GLY ARG SER ALA SEQRES 17 A 298 ALA VAL TRP SER LEU GLY ILE LEU LEU TYR ASP MET VAL SEQRES 18 A 298 CYS GLY ASP ILE PRO PHE GLU HIS ASP GLU GLU ILE ILE SEQRES 19 A 298 ARG GLY GLN VAL PHE PHE ARG GLN ARG VAL SER SEP GLU SEQRES 20 A 298 CYS GLN HIS LEU ILE ARG TRP CYS LEU ALA LEU ARG PRO SEQRES 21 A 298 SER ASP ARG PRO THR PHE GLU GLU ILE GLN ASN HIS PRO SEQRES 22 A 298 TRP MET GLN ASP VAL LEU LEU PRO GLN GLU THR ALA GLU SEQRES 23 A 298 ILE HIS LEU HIS SER LEU SER PRO GLY PRO SER LYS MODRES 5O13 CSX A 161 CYS MODIFIED RESIDUE MODRES 5O13 SEP A 261 SER MODIFIED RESIDUE HET CSX A 161 7 HET SEP A 261 10 HET 9G5 A 401 33 HET IMD A 402 5 HET CL A 403 1 HETNAM CSX S-OXY CYSTEINE HETNAM SEP PHOSPHOSERINE HETNAM 9G5 (3~{E})-5-CHLORANYL-3-[[5-[3-[(4-METHYL-1,4-DIAZEPAN-1- HETNAM 2 9G5 YL)CARBONYL]PHENYL]FURAN-2-YL]METHYLIDENE]-1~{H}- HETNAM 3 9G5 INDOL-2-ONE HETNAM IMD IMIDAZOLE HETNAM CL CHLORIDE ION HETSYN SEP PHOSPHONOSERINE FORMUL 1 CSX C3 H7 N O3 S FORMUL 1 SEP C3 H8 N O6 P FORMUL 2 9G5 C26 H24 CL N3 O3 FORMUL 3 IMD C3 H5 N2 1+ FORMUL 4 CL CL 1- FORMUL 5 HOH *90(H2 O) HELIX 1 AA1 ASP A 72 ILE A 74 5 3 HELIX 2 AA2 MET A 88 SER A 97 1 10 HELIX 3 AA3 LEU A 129 GLY A 137 1 9 HELIX 4 AA4 GLN A 140 CSX A 161 1 22 HELIX 5 AA5 LYS A 169 GLU A 171 5 3 HELIX 6 AA6 THR A 204 SER A 208 5 5 HELIX 7 AA7 PRO A 209 HIS A 216 1 8 HELIX 8 AA8 HIS A 219 GLY A 238 1 20 HELIX 9 AA9 HIS A 244 GLY A 251 1 8 HELIX 10 AB1 SER A 260 LEU A 271 1 12 HELIX 11 AB2 ARG A 274 ARG A 278 5 5 HELIX 12 AB3 THR A 280 ASN A 286 1 7 HELIX 13 AB4 HIS A 287 GLN A 291 5 5 HELIX 14 AB5 LEU A 295 LEU A 304 1 10 SHEET 1 AA1 5 TYR A 38 GLY A 47 0 SHEET 2 AA1 5 GLY A 50 ARG A 57 -1 O SER A 54 N GLY A 41 SHEET 3 AA1 5 LEU A 62 GLU A 70 -1 O HIS A 68 N SER A 51 SHEET 4 AA1 5 SER A 115 GLU A 121 -1 O LEU A 120 N ALA A 65 SHEET 5 AA1 5 LEU A 106 GLU A 111 -1 N LEU A 107 O ILE A 119 SHEET 1 AA2 2 TRP A 77 GLU A 79 0 SHEET 2 AA2 2 ARG A 85 PRO A 87 -1 O VAL A 86 N GLY A 78 SHEET 1 AA3 3 VAL A 126 ASP A 128 0 SHEET 2 AA3 3 ILE A 173 ASP A 176 -1 O ILE A 175 N GLN A 127 SHEET 3 AA3 3 GLU A 181 LEU A 184 -1 O GLU A 181 N ASP A 176 SHEET 1 AA4 2 VAL A 163 LEU A 164 0 SHEET 2 AA4 2 ALA A 191 LEU A 192 -1 O ALA A 191 N LEU A 164 LINK C ASN A 160 N CSX A 161 1555 1555 1.32 LINK C CSX A 161 N GLY A 162 1555 1555 1.32 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 -4.80 SITE 1 AC1 9 LEU A 44 PHE A 49 ALA A 65 LYS A 67 SITE 2 AC1 9 VAL A 126 ASP A 128 ASP A 131 LEU A 174 SITE 3 AC1 9 ILE A 185 SITE 1 AC2 5 GLU A 153 ASN A 160 SEP A 261 GLN A 264 SITE 2 AC2 5 HOH A 554 SITE 1 AC3 2 ARG A 205 TRP A 212 CRYST1 96.735 96.735 81.765 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 0.010337 0.005968 0.000000 0.00000 SCALE2 0.000000 0.011937 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012230 0.00000