HEADER TRANSFERASE 10-JAN-07 2OI4 TITLE CRYSTAL STRUCTURE OF HUMAN PIM1 IN COMPLEX WITH FLUORINATED RUTHENIUM TITLE 2 PYRIDOCARBAZOLE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTO-ONCOGENE SERINE/THREONINE-PROTEIN KINASE PIM-1; COMPND 3 CHAIN: X; COMPND 4 EC: 2.7.11.1; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: 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 BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PLIC-SGC1 KEYWDS TRANSFERASE, PIM1, KINASE, ATP-BINDING, PHOSPHORYLATION EXPDTA X-RAY DIFFRACTION AUTHOR J.MAKSIMOSKA,E.MEGGERS REVDAT 6 27-DEC-23 2OI4 1 REMARK REVDAT 5 20-OCT-21 2OI4 1 REMARK SEQADV REVDAT 4 25-APR-18 2OI4 1 COMPND REMARK HETNAM REVDAT 3 24-FEB-09 2OI4 1 VERSN REVDAT 2 20-NOV-07 2OI4 1 JRNL REVDAT 1 10-APR-07 2OI4 0 JRNL AUTH N.PAGANO,J.MAKSIMOSKA,H.BREGMAN,D.S.WILLIAMS,R.D.WEBSTER, JRNL AUTH 2 F.XUE,E.MEGGERS JRNL TITL RUTHENIUM HALF-SANDWICH COMPLEXES AS PROTEIN KINASE JRNL TITL 2 INHIBITORS: DERIVATIZATION OF THE PYRIDOCARBAZOLE JRNL TITL 3 PHARMACOPHORE LIGAND. JRNL REF ORG.BIOMOL.CHEM. V. 5 1218 2007 JRNL REFN ISSN 1477-0520 JRNL PMID 17406720 JRNL DOI 10.1039/B700433H REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.54 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.1 REMARK 3 NUMBER OF REFLECTIONS : 19812 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) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1087 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1492 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.01 REMARK 3 BIN R VALUE (WORKING SET) : 0.2570 REMARK 3 BIN FREE R VALUE SET COUNT : 73 REMARK 3 BIN FREE R VALUE : 0.4310 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2232 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 59 REMARK 3 SOLVENT ATOMS : 165 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.62 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.01000 REMARK 3 B22 (A**2) : -0.01000 REMARK 3 B33 (A**2) : 0.01000 REMARK 3 B12 (A**2) : 0.00000 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): 0.214 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.197 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.135 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.384 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.915 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2342 ; 0.019 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3168 ; 1.893 ; 1.976 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 273 ; 7.924 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 114 ;36.523 ;22.982 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 376 ;16.434 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;17.690 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 326 ; 0.132 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1798 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1064 ; 0.221 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1511 ; 0.312 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 159 ; 0.191 ; 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): 38 ; 0.295 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 10 ; 0.156 ; 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): 1403 ; 1.430 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2202 ; 2.164 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1221 ; 3.204 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 966 ; 4.619 ; 4.500 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 : NULL 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 RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2OI4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-JAN-07. REMARK 100 THE DEPOSITION ID IS D_1000041163. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-FEB-06 REMARK 200 TEMPERATURE (KELVIN) : 128 REMARK 200 PH : 6.5 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 RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTALCLEAR (MSC/RIGAKU) REMARK 200 DATA SCALING SOFTWARE : CRYSTALCLEAR (MSC/RIGAKU) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20939 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 26.720 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.700 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.1 REMARK 200 DATA REDUNDANCY : 2.730 REMARK 200 R MERGE (I) : 0.10400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.2000 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 (%) : 96.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.59 REMARK 200 R MERGE FOR SHELL (I) : 0.45000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM BIS-TRIS PROPANE, 0.2M MGCL2, REMARK 280 20% PEG 3350, 10% ETHILENE GLYCOL, 0.3% DMSO, SITTING DROP, PH REMARK 280 6.5, VAPOR 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 53.78133 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 26.89067 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 40.33600 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 13.44533 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 67.22667 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 APPLY THE FOLLOWING TO CHAINS: X 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 MET X 1 REMARK 465 LEU X 2 REMARK 465 LEU X 3 REMARK 465 SER X 4 REMARK 465 LYS X 5 REMARK 465 ILE X 6 REMARK 465 ASN X 7 REMARK 465 SER X 8 REMARK 465 LEU X 9 REMARK 465 ALA X 10 REMARK 465 HIS X 11 REMARK 465 LEU X 12 REMARK 465 ARG X 13 REMARK 465 ALA X 14 REMARK 465 ALA X 15 REMARK 465 PRO X 16 REMARK 465 CYS X 17 REMARK 465 ASN X 18 REMARK 465 ASP X 19 REMARK 465 LEU X 20 REMARK 465 HIS X 21 REMARK 465 ALA X 22 REMARK 465 THR X 23 REMARK 465 LYS X 24 REMARK 465 LEU X 25 REMARK 465 ALA X 26 REMARK 465 PRO X 27 REMARK 465 GLY X 28 REMARK 465 LYS X 29 REMARK 465 GLU X 30 REMARK 465 LYS X 31 REMARK 465 LEU X 307 REMARK 465 SER X 308 REMARK 465 PRO X 309 REMARK 465 GLY X 310 REMARK 465 PRO X 311 REMARK 465 SER X 312 REMARK 465 LYS X 313 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLU X 32 N CA CB CG CD OE1 OE2 REMARK 480 GLN X 39 OE1 NE2 REMARK 480 ASN X 61 CB CG OD1 ND2 REMARK 480 ASP X 72 CG OD1 OD2 REMARK 480 SER X 75 CB OG REMARK 480 GLU X 79 CB CG CD OE1 OE2 REMARK 480 LEU X 80 CB CG CD1 CD2 REMARK 480 ARG X 179 CZ NH1 NH2 REMARK 480 ASP X 239 OD1 OD2 REMARK 480 GLU X 243 CG CD OE1 OE2 REMARK 480 SER X 306 CB OG REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU X 32 CA GLU X 32 C 0.207 REMARK 500 GLN X 39 CD GLN X 39 OE1 -0.309 REMARK 500 GLN X 39 CD GLN X 39 NE2 0.451 REMARK 500 ASN X 61 CA ASN X 61 CB -0.164 REMARK 500 ASP X 72 CB ASP X 72 CG -0.265 REMARK 500 LEU X 80 CA LEU X 80 CB 2.348 REMARK 500 ARG X 179 NE ARG X 179 CZ -0.394 REMARK 500 ASP X 239 CG ASP X 239 OD1 0.196 REMARK 500 ASP X 239 CG ASP X 239 OD2 -0.176 REMARK 500 ARG X 258 CZ ARG X 258 NH1 0.083 REMARK 500 SER X 306 CA SER X 306 CB -0.145 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 GLU X 32 CB - CA - C ANGL. DEV. = -31.0 DEGREES REMARK 500 GLU X 32 N - CA - C ANGL. DEV. = 16.6 DEGREES REMARK 500 GLU X 32 CA - C - O ANGL. DEV. = 115.1 DEGREES REMARK 500 GLN X 39 CG - CD - NE2 ANGL. DEV. = -21.4 DEGREES REMARK 500 ASN X 61 N - CA - CB ANGL. DEV. = 13.7 DEGREES REMARK 500 SER X 75 CB - CA - C ANGL. DEV. = 15.2 DEGREES REMARK 500 GLU X 79 CA - CB - CG ANGL. DEV. = -13.9 DEGREES REMARK 500 LEU X 80 CB - CA - C ANGL. DEV. = -30.5 DEGREES REMARK 500 LEU X 80 N - CA - CB ANGL. DEV. = -49.6 DEGREES REMARK 500 LEU X 80 CA - CB - CG ANGL. DEV. = -24.8 DEGREES REMARK 500 ARG X 179 CD - NE - CZ ANGL. DEV. = 25.2 DEGREES REMARK 500 ARG X 179 NE - CZ - NH1 ANGL. DEV. = -19.7 DEGREES REMARK 500 ARG X 179 NE - CZ - NH2 ANGL. DEV. = 15.6 DEGREES REMARK 500 LEU X 184 CB - CG - CD1 ANGL. DEV. = -11.6 DEGREES REMARK 500 ASP X 239 CB - CG - OD1 ANGL. DEV. = -5.4 DEGREES REMARK 500 ARG X 256 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG X 258 NE - CZ - NH2 ANGL. DEV. = -5.2 DEGREES REMARK 500 SER X 306 N - CA - CB ANGL. DEV. = 15.2 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 PRO X 81 -41.30 -12.23 REMARK 500 ASN X 82 -73.62 -53.37 REMARK 500 ASP X 167 46.12 -149.51 REMARK 500 ASP X 186 71.74 73.35 REMARK 500 ASP X 202 42.39 -153.16 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 GLU X 32 PRO X 33 111.19 REMARK 500 HIS X 305 SER X 306 -140.75 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 GLN X 39 0.13 SIDE CHAIN REMARK 500 ARG X 179 0.12 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 GLU X 32 12.12 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 X 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE JM1 X 1000 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO X 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO X 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO X 1004 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EPE X 2691 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2BZH RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE HUMAN PIM1 IN COMPLEX WITH A RUTHENIUM REMARK 900 ORGANOMETALLIC LIGAND RU1 REMARK 900 RELATED ID: 2BZI RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE HUMAN PIM1 IN COMPLEX WITH A RUTHENIUM REMARK 900 ORGANOMETALLIC LIGAND RU2 REMARK 900 RELATED ID: 2BZJ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE HUMAN PIM1 IN COMPLEX WITH A RUTHENIUM REMARK 900 ORGANOMETALLIC LIGAND RU3 REMARK 900 RELATED ID: 1YHS RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PIM-1 BOUND TO STAUROSPORINE DBREF 2OI4 X 1 313 UNP P11309 PIM1_HUMAN 92 404 SEQADV 2OI4 GLY X 250 UNP P11309 ARG 341 ENGINEERED MUTATION SEQRES 1 X 313 MET LEU LEU SER LYS ILE ASN SER LEU ALA HIS LEU ARG SEQRES 2 X 313 ALA ALA PRO CYS ASN ASP LEU HIS ALA THR LYS LEU ALA SEQRES 3 X 313 PRO GLY LYS GLU LYS GLU PRO LEU GLU SER GLN TYR GLN SEQRES 4 X 313 VAL GLY PRO LEU LEU GLY SER GLY GLY PHE GLY SER VAL SEQRES 5 X 313 TYR SER GLY ILE ARG VAL SER ASP ASN LEU PRO VAL ALA SEQRES 6 X 313 ILE LYS HIS VAL GLU LYS ASP ARG ILE SER ASP TRP GLY SEQRES 7 X 313 GLU LEU PRO ASN GLY THR ARG VAL PRO MET GLU VAL VAL SEQRES 8 X 313 LEU LEU LYS LYS VAL SER SER GLY PHE SER GLY VAL ILE SEQRES 9 X 313 ARG LEU LEU ASP TRP PHE GLU ARG PRO ASP SER PHE VAL SEQRES 10 X 313 LEU ILE LEU GLU ARG PRO GLU PRO VAL GLN ASP LEU PHE SEQRES 11 X 313 ASP PHE ILE THR GLU ARG GLY ALA LEU GLN GLU GLU LEU SEQRES 12 X 313 ALA ARG SER PHE PHE TRP GLN VAL LEU GLU ALA VAL ARG SEQRES 13 X 313 HIS CYS HIS ASN CYS GLY VAL LEU HIS ARG ASP ILE LYS SEQRES 14 X 313 ASP GLU ASN ILE LEU ILE ASP LEU ASN ARG GLY GLU LEU SEQRES 15 X 313 LYS LEU ILE ASP PHE GLY SER GLY ALA LEU LEU LYS ASP SEQRES 16 X 313 THR VAL TYR THR ASP PHE ASP GLY THR ARG VAL TYR SER SEQRES 17 X 313 PRO PRO GLU TRP ILE ARG TYR HIS ARG TYR HIS GLY ARG SEQRES 18 X 313 SER ALA ALA VAL TRP SER LEU GLY ILE LEU LEU TYR ASP SEQRES 19 X 313 MET VAL CYS GLY ASP ILE PRO PHE GLU HIS ASP GLU GLU SEQRES 20 X 313 ILE ILE GLY GLY GLN VAL PHE PHE ARG GLN ARG VAL SER SEQRES 21 X 313 SER GLU CYS GLN HIS LEU ILE ARG TRP CYS LEU ALA LEU SEQRES 22 X 313 ARG PRO SER ASP ARG PRO THR PHE GLU GLU ILE GLN ASN SEQRES 23 X 313 HIS PRO TRP MET GLN ASP VAL LEU LEU PRO GLN GLU THR SEQRES 24 X 313 ALA GLU ILE HIS LEU HIS SER LEU SER PRO GLY PRO SER SEQRES 25 X 313 LYS HET CL X1001 1 HET JM1 X1000 31 HET EDO X1002 4 HET EDO X1003 4 HET EDO X1004 4 HET EPE X2691 15 HETNAM CL CHLORIDE ION HETNAM JM1 FLUORINATED PYRIDOCARBAZOLE CYCLOPENTADIENYL RU(CO) HETNAM 2 JM1 COMPLEX HETNAM EDO 1,2-ETHANEDIOL HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETSYN EDO ETHYLENE GLYCOL HETSYN EPE HEPES FORMUL 2 CL CL 1- FORMUL 3 JM1 C23 H12 F N3 O3 RU 1+ FORMUL 4 EDO 3(C2 H6 O2) FORMUL 7 EPE C8 H18 N2 O4 S FORMUL 8 HOH *165(H2 O) HELIX 1 1 ASP X 72 ILE X 74 5 3 HELIX 2 2 MET X 88 SER X 97 1 10 HELIX 3 3 LEU X 129 GLY X 137 1 9 HELIX 4 4 GLN X 140 CYS X 161 1 22 HELIX 5 5 LYS X 169 GLU X 171 5 3 HELIX 6 6 THR X 204 SER X 208 5 5 HELIX 7 7 PRO X 209 HIS X 216 1 8 HELIX 8 8 HIS X 219 GLY X 238 1 20 HELIX 9 9 HIS X 244 GLY X 251 1 8 HELIX 10 10 SER X 260 LEU X 271 1 12 HELIX 11 11 ARG X 274 ARG X 278 5 5 HELIX 12 12 THR X 280 ASN X 286 1 7 HELIX 13 13 HIS X 287 GLN X 291 5 5 HELIX 14 14 LEU X 295 LEU X 304 1 10 SHEET 1 A 5 TYR X 38 GLY X 47 0 SHEET 2 A 5 GLY X 50 ARG X 57 -1 O SER X 54 N GLY X 41 SHEET 3 A 5 PRO X 63 GLU X 70 -1 O ILE X 66 N TYR X 53 SHEET 4 A 5 SER X 115 GLU X 121 -1 O LEU X 120 N ALA X 65 SHEET 5 A 5 LEU X 106 GLU X 111 -1 N ASP X 108 O ILE X 119 SHEET 1 B 2 TRP X 77 GLY X 78 0 SHEET 2 B 2 VAL X 86 PRO X 87 -1 O VAL X 86 N GLY X 78 SHEET 1 C 3 VAL X 126 ASP X 128 0 SHEET 2 C 3 ILE X 173 ASP X 176 -1 O ILE X 175 N GLN X 127 SHEET 3 C 3 GLU X 181 LEU X 184 -1 O GLU X 181 N ASP X 176 SHEET 1 D 2 VAL X 163 LEU X 164 0 SHEET 2 D 2 ALA X 191 LEU X 192 -1 O ALA X 191 N LEU X 164 CISPEP 1 GLU X 124 PRO X 125 0 -6.30 SITE 1 AC1 6 VAL X 69 GLU X 70 ARG X 73 THR X 196 SITE 2 AC1 6 EDO X1002 HOH X2794 SITE 1 AC2 15 LEU X 44 GLY X 45 PHE X 49 VAL X 52 SITE 2 AC2 15 ALA X 65 LYS X 67 ILE X 104 LEU X 120 SITE 3 AC2 15 GLU X 121 ARG X 122 PRO X 123 GLU X 171 SITE 4 AC2 15 LEU X 174 ILE X 185 ASP X 186 SITE 1 AC3 5 GLY X 47 GLY X 48 VAL X 69 ARG X 73 SITE 2 AC3 5 CL X1001 SITE 1 AC4 5 LEU X 34 GLU X 35 VAL X 40 ILE X 66 SITE 2 AC4 5 HIS X 68 SITE 1 AC5 4 GLN X 257 ARG X 258 ASN X 286 HOH X2850 SITE 1 AC6 13 GLY X 48 PHE X 49 LYS X 67 VAL X 69 SITE 2 AC6 13 PRO X 87 GLU X 89 ASP X 167 ASP X 186 SITE 3 AC6 13 GLY X 188 SER X 189 ASP X 202 HOH X2709 SITE 4 AC6 13 HOH X2807 CRYST1 98.104 98.104 80.672 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 0.010193 0.005885 0.000000 0.00000 SCALE2 0.000000 0.011770 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012396 0.00000