HEADER TRANSFERASE 16-AUG-06 2J2I TITLE CRYSTAL STRUCTURE OF THE HUMAB PIM1 IN COMPLEX WITH LY333531 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTO-ONCOGENE SERINE/THREONINE-PROTEIN KINASE PIM-1; COMPND 3 CHAIN: B; COMPND 4 FRAGMENT: RESIDUES 92-403; COMPND 5 SYNONYM: HUMAN PIM1; COMPND 6 EC: 2.7.11.1; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: 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 BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_VECTOR: P11-TORONTO KEYWDS TRANSFERASE, NUCLEOTIDE-BINDING, ALTERNATIVE INITIATION, KEYWDS 2 SERINE/THREONINE-PROTEIN KINASE, ATP-BINDING, METAL-BINDING, PROTO- KEYWDS 3 ONCOGENE, KINASE, CANCER, LEUKEMIA, MANGANESE, NUCLEAR PROTEIN, KEYWDS 4 PROTO- ONCOGENE, PHOSPHORYLATION EXPDTA X-RAY DIFFRACTION AUTHOR J.E.DEBRECZENI,A.N.BULLOCK,F.VON DELFT,M.SUNDSTROM,C.ARROWSMITH, AUTHOR 2 A.EDWARDS,J.WEIGELT,S.KNAPP REVDAT 10 13-DEC-23 2J2I 1 COMPND REMARK HETNAM REVDAT 9 08-MAY-19 2J2I 1 REMARK REVDAT 8 06-MAR-19 2J2I 1 REMARK REVDAT 7 04-APR-18 2J2I 1 REMARK REVDAT 6 28-FEB-18 2J2I 1 SOURCE JRNL REVDAT 5 24-JAN-18 2J2I 1 AUTHOR REVDAT 4 13-JUL-11 2J2I 1 VERSN REVDAT 3 03-NOV-09 2J2I 1 AUTHOR JRNL REVDAT 2 24-FEB-09 2J2I 1 VERSN REVDAT 1 13-FEB-07 2J2I 0 JRNL AUTH O.FEDOROV,B.MARSDEN,V.POGACIC,P.RELLOS,S.MULLER,A.N.BULLOCK, JRNL AUTH 2 J.SCHWALLER,M.SUNDSTROM,S.KNAPP JRNL TITL A SYSTEMATIC INTERACTION MAP OF VALIDATED KINASE INHIBITORS JRNL TITL 2 WITH SER/THR KINASES. JRNL REF PROC. NATL. ACAD. SCI. V. 104 20523 2007 JRNL REF 2 U.S.A. JRNL REFN ESSN 1091-6490 JRNL PMID 18077363 JRNL DOI 10.1073/PNAS.0708800104 REMARK 2 REMARK 2 RESOLUTION. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 85.13 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 32879 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) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1765 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2335 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3190 REMARK 3 BIN FREE R VALUE SET COUNT : 146 REMARK 3 BIN FREE R VALUE : 0.3240 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2183 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 40 REMARK 3 SOLVENT ATOMS : 168 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) : 26.59 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.34000 REMARK 3 B22 (A**2) : 0.34000 REMARK 3 B33 (A**2) : -0.52000 REMARK 3 B12 (A**2) : 0.17000 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): 0.112 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.106 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.075 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.924 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.953 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2349 ; 0.011 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 1607 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3203 ; 1.305 ; 1.991 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3821 ; 0.882 ; 3.004 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 276 ; 5.467 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 112 ;33.508 ;23.036 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 368 ;11.661 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;15.932 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 334 ; 0.080 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2598 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 498 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 425 ; 0.202 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1633 ; 0.185 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1102 ; 0.177 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1154 ; 0.080 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 135 ; 0.148 ; 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): 9 ; 0.137 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 38 ; 0.327 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 10 ; 0.198 ; 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 ; 0.761 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2207 ; 1.207 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1120 ; 1.631 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 994 ; 2.626 ; 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 : 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 : B 33 B 124 REMARK 3 ORIGIN FOR THE GROUP (A): 37.8342 2.5384 9.9362 REMARK 3 T TENSOR REMARK 3 T11: 0.0558 T22: -0.1010 REMARK 3 T33: -0.0776 T12: 0.0071 REMARK 3 T13: 0.0250 T23: 0.0039 REMARK 3 L TENSOR REMARK 3 L11: 2.1662 L22: 4.3935 REMARK 3 L33: 3.4262 L12: -0.7921 REMARK 3 L13: -0.3595 L23: -1.0352 REMARK 3 S TENSOR REMARK 3 S11: -0.0569 S12: -0.1575 S13: 0.2026 REMARK 3 S21: 0.4423 S22: 0.1399 S23: -0.0918 REMARK 3 S31: -0.5074 S32: -0.0460 S33: -0.0830 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 : B 125 B 305 REMARK 3 ORIGIN FOR THE GROUP (A): 40.0831 -20.3782 -0.8686 REMARK 3 T TENSOR REMARK 3 T11: -0.0516 T22: -0.0358 REMARK 3 T33: -0.0657 T12: -0.0204 REMARK 3 T13: -0.0005 T23: 0.0247 REMARK 3 L TENSOR REMARK 3 L11: 1.0884 L22: 1.1698 REMARK 3 L33: 1.3957 L12: 0.0023 REMARK 3 L13: -0.3692 L23: 0.2473 REMARK 3 S TENSOR REMARK 3 S11: 0.0272 S12: 0.1540 S13: 0.0223 REMARK 3 S21: 0.0484 S22: 0.0573 S23: -0.0430 REMARK 3 S31: -0.0185 S32: -0.0732 S33: -0.0845 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 2J2I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-AUG-06. REMARK 100 THE DEPOSITION ID IS D_1290029725. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-APR-06 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : NULL 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 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : VARIMAX MIRRORS REMARK 200 OPTICS : VARIMAX MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU IMAGE PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34673 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 25.090 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 5.270 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.91 REMARK 200 R MERGE FOR SHELL (I) : 0.50000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.500 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 2BIK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M NA2SO4, 0.1 M BIS-TRIS-PROPANE REMARK 280 PH 7.5, 20% PEG3350, 10% ETHYLENE-GLYCOL, 0.5% DMSO, SITTING REMARK 280 DROP, VAPOR DIFFUSION, 277 K, VAPOR DIFFUSION, SITTING DROP 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 53.57733 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 26.78867 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 40.18300 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 13.39433 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 66.97167 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: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN B, ARG 341 TO GLY 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 B 1 REMARK 465 LEU B 2 REMARK 465 LEU B 3 REMARK 465 SER B 4 REMARK 465 LYS B 5 REMARK 465 ILE B 6 REMARK 465 ASN B 7 REMARK 465 SER B 8 REMARK 465 LEU B 9 REMARK 465 ALA B 10 REMARK 465 HIS B 11 REMARK 465 LEU B 12 REMARK 465 ARG B 13 REMARK 465 ALA B 14 REMARK 465 ALA B 15 REMARK 465 PRO B 16 REMARK 465 CYS B 17 REMARK 465 ASN B 18 REMARK 465 ASP B 19 REMARK 465 LEU B 20 REMARK 465 HIS B 21 REMARK 465 ALA B 22 REMARK 465 THR B 23 REMARK 465 LYS B 24 REMARK 465 LEU B 25 REMARK 465 ALA B 26 REMARK 465 PRO B 27 REMARK 465 GLY B 28 REMARK 465 LYS B 29 REMARK 465 GLU B 30 REMARK 465 LYS B 31 REMARK 465 GLU B 32 REMARK 465 SER B 306 REMARK 465 LEU B 307 REMARK 465 SER B 308 REMARK 465 PRO B 309 REMARK 465 GLY B 310 REMARK 465 PRO B 311 REMARK 465 SER B 312 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 LEU B 34 CG CD1 CD2 REMARK 470 GLN B 39 CD OE1 NE2 REMARK 470 ILE B 56 CD1 REMARK 470 ASP B 72 CG OD1 OD2 REMARK 470 GLU B 79 CD OE1 OE2 REMARK 470 LEU B 80 CG CD1 CD2 REMARK 470 THR B 84 OG1 CG2 REMARK 470 ASP B 202 CG OD1 OD2 REMARK 470 GLU B 243 CG CD OE1 OE2 REMARK 470 ARG B 274 CD NE CZ NH1 NH2 REMARK 470 GLN B 297 CG CD OE1 NE2 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 B 2053 O HOH B 2056 2.11 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 B 167 44.98 -144.72 REMARK 500 ASP B 186 81.11 69.56 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 SO4 B 1306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LY4 B 1307 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1XQZ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HPIM-1 KINASE AT 2. 1 A RESOLUTION REMARK 900 RELATED ID: 1XR1 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HPIM-1 KINASE IN COMPLEX WITH AMP-PNPAT 2.1 A REMARK 900 RESOLUTION REMARK 900 RELATED ID: 1XWS RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE HUMAN PIM1 KINASE DOMAIN REMARK 900 RELATED ID: 1YHS RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PIM-1 BOUND TO STAUROSPORINE REMARK 900 RELATED ID: 1YI3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PIM-1 BOUND TO LY294002 REMARK 900 RELATED ID: 1YI4 RELATED DB: PDB REMARK 900 STRUCTURE OF PIM-1 BOUND TO ADENOSINE REMARK 900 RELATED ID: 1YWV RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURES OF PROTO-ONCOGENE KINASE PIM1: A TARGETOF REMARK 900 ABERRANT SOMATIC HYPERMUTATIONS IN DIFFUSE LARGE CELLLYMPHOMA REMARK 900 RELATED ID: 1YXS RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF KINASE PIM1 WITH P123M MUTATION REMARK 900 RELATED ID: 1YXT RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF KINASE PIM1 IN COMPLEX WITH AMPPNP REMARK 900 RELATED ID: 1YXU RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF KINASE PIM1 IN COMPLEX WITH AMP REMARK 900 RELATED ID: 1YXV RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF KINASE PIM1 IN COMPLEX WITH 3,4-DIHYDROXY-1- REMARK 900 METHYLQUINOLIN-2(1H )-ONE REMARK 900 RELATED ID: 1YXX RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF KINASE PIM1 IN COMPLEX WITH (3E)-3-[(4- REMARK 900 HYDROXYPHENYL)IMINO]-1H- INDOL-2(3H)-ONE REMARK 900 RELATED ID: 2BIK RELATED DB: PDB REMARK 900 HUMAN PIM1 PHOSPHORYLATED ON SER261 REMARK 900 RELATED ID: 2BIL RELATED DB: PDB REMARK 900 THE HUMAN PROTEIN KINASE PIM1 IN COMPLEX WITH ITS CONSENSUS PEPTIDE REMARK 900 PIMTIDE 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: 2BZK RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE HUMAN PIM1 IN COMPLEX WITH AMPPNP AND REMARK 900 PIMTIDE REMARK 900 RELATED ID: 2C3I RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN PIM1 IN COMPLEX WITH IMIDAZOPYRIDAZIN I REMARK 999 REMARK 999 SEQUENCE REMARK 999 SEQADV 2BIK GLY B 250 UNP P11309 ARG 250 VARIANT DBREF 2J2I B 1 312 UNP P11309 PIM1_HUMAN 92 403 SEQADV 2J2I GLY B 250 UNP P11309 ARG 341 ENGINEERED MUTATION SEQRES 1 B 312 MET LEU LEU SER LYS ILE ASN SER LEU ALA HIS LEU ARG SEQRES 2 B 312 ALA ALA PRO CYS ASN ASP LEU HIS ALA THR LYS LEU ALA SEQRES 3 B 312 PRO GLY LYS GLU LYS GLU PRO LEU GLU SER GLN TYR GLN SEQRES 4 B 312 VAL GLY PRO LEU LEU GLY SER GLY GLY PHE GLY SER VAL SEQRES 5 B 312 TYR SER GLY ILE ARG VAL SER ASP ASN LEU PRO VAL ALA SEQRES 6 B 312 ILE LYS HIS VAL GLU LYS ASP ARG ILE SER ASP TRP GLY SEQRES 7 B 312 GLU LEU PRO ASN GLY THR ARG VAL PRO MET GLU VAL VAL SEQRES 8 B 312 LEU LEU LYS LYS VAL SER SER GLY PHE SER GLY VAL ILE SEQRES 9 B 312 ARG LEU LEU ASP TRP PHE GLU ARG PRO ASP SER PHE VAL SEQRES 10 B 312 LEU ILE LEU GLU ARG PRO GLU PRO VAL GLN ASP LEU PHE SEQRES 11 B 312 ASP PHE ILE THR GLU ARG GLY ALA LEU GLN GLU GLU LEU SEQRES 12 B 312 ALA ARG SER PHE PHE TRP GLN VAL LEU GLU ALA VAL ARG SEQRES 13 B 312 HIS CYS HIS ASN CYS GLY VAL LEU HIS ARG ASP ILE LYS SEQRES 14 B 312 ASP GLU ASN ILE LEU ILE ASP LEU ASN ARG GLY GLU LEU SEQRES 15 B 312 LYS LEU ILE ASP PHE GLY SER GLY ALA LEU LEU LYS ASP SEQRES 16 B 312 THR VAL TYR THR ASP PHE ASP GLY THR ARG VAL TYR SER SEQRES 17 B 312 PRO PRO GLU TRP ILE ARG TYR HIS ARG TYR HIS GLY ARG SEQRES 18 B 312 SER ALA ALA VAL TRP SER LEU GLY ILE LEU LEU TYR ASP SEQRES 19 B 312 MET VAL CYS GLY ASP ILE PRO PHE GLU HIS ASP GLU GLU SEQRES 20 B 312 ILE ILE GLY GLY GLN VAL PHE PHE ARG GLN ARG VAL SER SEQRES 21 B 312 SER GLU CYS GLN HIS LEU ILE ARG TRP CYS LEU ALA LEU SEQRES 22 B 312 ARG PRO SER ASP ARG PRO THR PHE GLU GLU ILE GLN ASN SEQRES 23 B 312 HIS PRO TRP MET GLN ASP VAL LEU LEU PRO GLN GLU THR SEQRES 24 B 312 ALA GLU ILE HIS LEU HIS SER LEU SER PRO GLY PRO SER HET SO4 B1306 5 HET LY4 B1307 70 HETNAM SO4 SULFATE ION HETNAM LY4 (9R)-9-[(DIMETHYLAMINO)METHYL]-6,7,10,11-TETRAHYDRO-9H, HETNAM 2 LY4 18H-5,21:12,17-DIMETHENODIBENZO[E,K]PYRROLO[3,4-H][1, HETNAM 3 LY4 4,13]OXADIA ZACYCLOHEXADECINE-18,20-DIONE HETSYN LY4 LY333531 FORMUL 2 SO4 O4 S 2- FORMUL 3 LY4 C28 H28 N4 O3 FORMUL 4 HOH *168(H2 O) HELIX 1 1 PRO B 33 GLN B 37 1 5 HELIX 2 2 ASP B 72 ILE B 74 5 3 HELIX 3 3 MET B 88 SER B 97 1 10 HELIX 4 4 LEU B 129 GLY B 137 1 9 HELIX 5 5 GLN B 140 CYS B 161 1 22 HELIX 6 6 LYS B 169 GLU B 171 5 3 HELIX 7 7 THR B 204 SER B 208 5 5 HELIX 8 8 PRO B 209 HIS B 216 1 8 HELIX 9 9 HIS B 219 GLY B 238 1 20 HELIX 10 10 HIS B 244 GLY B 251 1 8 HELIX 11 11 SER B 260 LEU B 271 1 12 HELIX 12 12 ARG B 274 ARG B 278 5 5 HELIX 13 13 THR B 280 ASN B 286 1 7 HELIX 14 14 HIS B 287 GLN B 291 5 5 HELIX 15 15 LEU B 295 LEU B 304 1 10 SHEET 1 BA 5 TYR B 38 GLY B 47 0 SHEET 2 BA 5 GLY B 50 ARG B 57 -1 O GLY B 50 N GLY B 47 SHEET 3 BA 5 LEU B 62 GLU B 70 -1 O LEU B 62 N ARG B 57 SHEET 4 BA 5 SER B 115 GLU B 121 -1 O PHE B 116 N VAL B 69 SHEET 5 BA 5 LEU B 106 GLU B 111 -1 N LEU B 107 O ILE B 119 SHEET 1 BB 2 TRP B 77 GLU B 79 0 SHEET 2 BB 2 ARG B 85 PRO B 87 -1 O VAL B 86 N GLY B 78 SHEET 1 BC 3 VAL B 126 ASP B 128 0 SHEET 2 BC 3 ILE B 173 ASP B 176 -1 O ILE B 175 N GLN B 127 SHEET 3 BC 3 GLU B 181 LEU B 184 -1 O GLU B 181 N ASP B 176 SHEET 1 BD 2 VAL B 163 LEU B 164 0 SHEET 2 BD 2 ALA B 191 LEU B 192 -1 O ALA B 191 N LEU B 164 CISPEP 1 GLU B 124 PRO B 125 0 -7.68 CISPEP 2 GLU B 124 PRO B 125 0 -9.40 SITE 1 AC1 7 ARG B 156 ARG B 258 SER B 261 PHE B 281 SITE 2 AC1 7 HOH B2166 HOH B2167 HOH B2168 SITE 1 AC2 19 LEU B 44 GLY B 45 PHE B 49 VAL B 52 SITE 2 AC2 19 ALA B 65 LYS B 67 GLU B 89 ILE B 104 SITE 3 AC2 19 LEU B 120 GLU B 121 ARG B 122 PRO B 123 SITE 4 AC2 19 VAL B 126 ASP B 128 GLU B 171 ASN B 172 SITE 5 AC2 19 LEU B 174 ILE B 185 ASP B 186 CRYST1 98.157 98.157 80.366 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 0.010188 0.005882 0.000000 0.00000 SCALE2 0.000000 0.011764 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012443 0.00000