HEADER TRANSFERASE 28-MAY-21 7OOW TITLE CRYSTAL STRUCTURE OF PIM1 IN COMPLEX WITH ARC-1415 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 MOL_ID: 2; COMPND 7 MOLECULE: INHIBITOR ARC-1415; COMPND 8 CHAIN: B; COMPND 9 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 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630 KEYWDS PIM1, INHIBITOR, KINASE, KINASE SUBSTRATE, STRUCTURAL GENOMICS, KEYWDS 2 STRUCTURAL GENOMICS CONSORTIUM, SGC, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.CHAIKUAD,S.E.DIXON-CLARKE,O.E.NONGA,A.URI,A.BULLOCK,S.KNAPP, AUTHOR 2 STRUCTURAL GENOMICS CONSORTIUM (SGC) REVDAT 4 10-APR-24 7OOW 1 SOURCE REMARK REVDAT 3 31-JAN-24 7OOW 1 REMARK REVDAT 2 15-NOV-23 7OOW 1 LINK ATOM REVDAT 1 04-AUG-21 7OOW 0 JRNL AUTH O.E.NONGA,D.LAVOGINA,E.ENKVIST,K.KESTAV,A.CHAIKUAD, JRNL AUTH 2 S.E.DIXON-CLARKE,A.N.BULLOCK,S.KOPANCHUK,T.IVAN,R.EKAMBARAM, JRNL AUTH 3 K.VIHT,S.KNAPP,A.URI JRNL TITL CRYSTAL STRUCTURE-GUIDED DESIGN OF BISUBSTRATE INHIBITORS JRNL TITL 2 AND PHOTOLUMINESCENT PROBES FOR PROTEIN KINASES OF THE PIM JRNL TITL 3 FAMILY. JRNL REF MOLECULES V. 26 2021 JRNL REFN ESSN 1420-3049 JRNL PMID 34299628 JRNL DOI 10.3390/MOLECULES26144353 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0257 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.70 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 30996 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) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.184 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1547 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) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.00 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2249 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.71 REMARK 3 BIN R VALUE (WORKING SET) : 0.2320 REMARK 3 BIN FREE R VALUE SET COUNT : 120 REMARK 3 BIN FREE R VALUE : 0.2540 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2310 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 17 REMARK 3 SOLVENT ATOMS : 214 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.68 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.47000 REMARK 3 B22 (A**2) : 0.47000 REMARK 3 B33 (A**2) : -1.53000 REMARK 3 B12 (A**2) : 0.24000 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): 0.111 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.104 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.075 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.134 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.958 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2384 ; 0.013 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 2193 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3221 ; 1.412 ; 1.651 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5067 ; 1.312 ; 1.631 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 272 ; 6.735 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 137 ;28.809 ;21.314 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 377 ;13.567 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;15.576 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 283 ; 0.075 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2742 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 538 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 86 REMARK 3 ORIGIN FOR THE GROUP (A): 72.154 55.676 21.724 REMARK 3 T TENSOR REMARK 3 T11: 0.0866 T22: 0.1016 REMARK 3 T33: 0.0626 T12: -0.0837 REMARK 3 T13: -0.0101 T23: -0.0099 REMARK 3 L TENSOR REMARK 3 L11: 2.0815 L22: 2.6688 REMARK 3 L33: 1.4517 L12: 0.6780 REMARK 3 L13: -0.6868 L23: 0.5900 REMARK 3 S TENSOR REMARK 3 S11: 0.1345 S12: -0.0367 S13: 0.1160 REMARK 3 S21: 0.1410 S22: -0.0346 S23: -0.2455 REMARK 3 S31: -0.2773 S32: 0.2853 S33: -0.0999 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 87 A 305 REMARK 3 ORIGIN FOR THE GROUP (A): 54.683 42.459 14.931 REMARK 3 T TENSOR REMARK 3 T11: 0.0156 T22: 0.0409 REMARK 3 T33: 0.0059 T12: -0.0007 REMARK 3 T13: 0.0074 T23: -0.0046 REMARK 3 L TENSOR REMARK 3 L11: 0.4055 L22: 0.5905 REMARK 3 L33: 0.8557 L12: 0.1399 REMARK 3 L13: 0.0540 L23: 0.2377 REMARK 3 S TENSOR REMARK 3 S11: 0.0491 S12: -0.0254 S13: 0.0084 REMARK 3 S21: -0.0313 S22: -0.0178 S23: -0.0183 REMARK 3 S31: -0.0271 S32: -0.0097 S33: -0.0313 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: U VALUES : WITH TLS ADDED HYDROGENS REMARK 3 HAVE BEEN ADDED IN THE RIDING POSITIONS REMARK 4 REMARK 4 7OOW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-JUL-21. REMARK 100 THE DEPOSITION ID IS D_1292116156. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JUL-13 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97625 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32555 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 42.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : 0.09900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : 0.94800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.100 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: 2J2I REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15%(W/V) PEG 10000, 0.2M MAGNESIUM REMARK 280 CHLORIDE, 0.1M TRIS PH 7.9, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277.15K 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 53.81933 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 26.90967 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 40.36450 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 13.45483 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 67.27417 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: DIMERIC 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 400 REMARK 400 COMPOUND REMARK 400 REMARK 400 THE INHIBITOR ARC-1415 IS PEPTIDE-LIKE, A MEMBER OF INHIBITOR CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: INHIBITOR ARC-1415 REMARK 400 CHAIN: B REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: NULL 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 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 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 A 262 CD GLU A 262 OE1 0.085 REMARK 500 DAR B 3 NE DAR B 3 CZ 0.119 REMARK 500 DAR B 3 CZ DAR B 3 NH1 0.091 REMARK 500 DAR B 5 NE DAR B 5 CZ 0.083 REMARK 500 DAR B 5 CZ DAR B 5 NH2 0.082 REMARK 500 DAR B 6 NE DAR B 6 CZ 0.106 REMARK 500 DAR B 6 CZ DAR B 6 NH2 0.080 REMARK 500 DAR B 8 NE DAR B 8 CZ 0.083 REMARK 500 DAR B 8 CZ DAR B 8 NH1 0.084 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 DAR B 3 NE - CZ - NH1 ANGL. DEV. = -5.1 DEGREES REMARK 500 DAR B 4 NE - CZ - NH1 ANGL. DEV. = -8.1 DEGREES REMARK 500 DAR B 4 NE - CZ - NH2 ANGL. DEV. = 7.7 DEGREES REMARK 500 DAR B 5 NH1 - CZ - NH2 ANGL. DEV. = 7.2 DEGREES REMARK 500 DAR B 5 NE - CZ - NH2 ANGL. DEV. = -5.7 DEGREES REMARK 500 DAR B 6 NE - CZ - NH2 ANGL. DEV. = -6.6 DEGREES REMARK 500 DAR B 7 NH1 - CZ - NH2 ANGL. DEV. = 8.2 DEGREES REMARK 500 DAR B 7 NE - CZ - NH2 ANGL. DEV. = -5.4 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 A 81 -34.43 -39.79 REMARK 500 SER A 98 -177.54 174.35 REMARK 500 ASP A 167 47.07 -146.20 REMARK 500 ASP A 186 73.89 62.53 REMARK 500 DAR B 5 -126.38 16.42 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 DAR B 3 DAR B 4 -143.78 REMARK 500 DAR B 4 DAR B 5 -143.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 189 OG REMARK 620 2 HOH A 514 O 106.5 REMARK 620 3 HOH A 521 O 163.6 89.3 REMARK 620 4 HOH A 524 O 88.6 100.1 92.8 REMARK 620 5 HOH A 588 O 79.8 167.3 83.9 91.0 REMARK 620 6 HOH A 640 O 84.0 83.0 94.1 172.5 86.8 REMARK 620 N 1 2 3 4 5 DBREF 7OOW A 1 312 UNP P11309 PIM1_HUMAN 1 312 DBREF 7OOW B 1 9 PDB 7OOW 7OOW 1 9 SEQADV 7OOW SER A 0 UNP P11309 EXPRESSION TAG SEQADV 7OOW GLY A 250 UNP P11309 ARG 250 CONFLICT SEQRES 1 A 313 SER MET LEU LEU SER LYS ILE ASN SER LEU ALA HIS LEU SEQRES 2 A 313 ARG ALA ALA PRO CYS ASN ASP LEU HIS ALA THR LYS LEU SEQRES 3 A 313 ALA PRO GLY LYS GLU LYS GLU PRO LEU GLU SER GLN TYR SEQRES 4 A 313 GLN VAL GLY PRO LEU LEU GLY SER GLY GLY PHE GLY SER SEQRES 5 A 313 VAL TYR SER GLY ILE ARG VAL SER ASP ASN LEU PRO VAL SEQRES 6 A 313 ALA ILE LYS HIS VAL GLU LYS ASP ARG ILE SER ASP TRP SEQRES 7 A 313 GLY GLU LEU PRO ASN GLY THR ARG VAL PRO MET GLU VAL SEQRES 8 A 313 VAL LEU LEU LYS LYS VAL SER SER GLY PHE SER GLY VAL SEQRES 9 A 313 ILE ARG LEU LEU ASP TRP PHE GLU ARG PRO ASP SER PHE SEQRES 10 A 313 VAL LEU ILE LEU GLU ARG PRO GLU PRO VAL GLN ASP LEU SEQRES 11 A 313 PHE ASP PHE ILE THR GLU ARG GLY ALA LEU GLN GLU GLU SEQRES 12 A 313 LEU ALA ARG SER PHE PHE TRP GLN VAL LEU GLU ALA VAL SEQRES 13 A 313 ARG HIS CYS HIS ASN CYS GLY VAL LEU HIS ARG ASP ILE SEQRES 14 A 313 LYS ASP GLU ASN ILE LEU ILE ASP LEU ASN ARG GLY GLU SEQRES 15 A 313 LEU LYS LEU ILE ASP PHE GLY SER GLY ALA LEU LEU LYS SEQRES 16 A 313 ASP THR VAL TYR THR ASP PHE ASP GLY THR ARG VAL TYR SEQRES 17 A 313 SER PRO PRO GLU TRP ILE ARG TYR HIS ARG TYR HIS GLY SEQRES 18 A 313 ARG SER ALA ALA VAL TRP SER LEU GLY ILE LEU LEU TYR SEQRES 19 A 313 ASP MET VAL CYS GLY ASP ILE PRO PHE GLU HIS ASP GLU SEQRES 20 A 313 GLU ILE ILE GLY GLY GLN VAL PHE PHE ARG GLN ARG VAL SEQRES 21 A 313 SER SER GLU CYS GLN HIS LEU ILE ARG TRP CYS LEU ALA SEQRES 22 A 313 LEU ARG PRO SER ASP ARG PRO THR PHE GLU GLU ILE GLN SEQRES 23 A 313 ASN HIS PRO TRP MET GLN ASP VAL LEU LEU PRO GLN GLU SEQRES 24 A 313 THR ALA GLU ILE HIS LEU HIS SER LEU SER PRO GLY PRO SEQRES 25 A 313 SER SEQRES 1 B 9 6J9 AZ1 DAR DAR DAR DAR DAR DAR NH2 HET 6J9 B 1 15 HET AZ1 B 2 11 HET DAR B 3 11 HET DAR B 4 11 HET DAR B 5 11 HET DAR B 6 11 HET DAR B 7 11 HET DAR B 8 11 HET NH2 B 9 1 HET MG A 401 1 HET EDO A 402 4 HET EDO A 403 4 HET EDO A 404 4 HET EDO A 405 4 HETNAM 6J9 4-(PIPERAZIN-1-YL)-7H-PYRROLO[2,3-D]PYRIMIDINE HETNAM AZ1 AZELAIC ACID HETNAM DAR D-ARGININE HETNAM NH2 AMINO GROUP HETNAM MG MAGNESIUM ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 6J9 C10 H13 N5 FORMUL 2 AZ1 C9 H16 O4 FORMUL 2 DAR 6(C6 H15 N4 O2 1+) FORMUL 2 NH2 H2 N FORMUL 3 MG MG 2+ FORMUL 4 EDO 4(C2 H6 O2) FORMUL 8 HOH *214(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 CYS 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 ASP A 108 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 N1 6J9 B 1 C AZ1 B 2 1555 1555 1.34 LINK C9 AZ1 B 2 N DAR B 3 1555 1555 1.34 LINK C DAR B 3 N DAR B 4 1555 1555 1.34 LINK C DAR B 4 N DAR B 5 1555 1555 1.34 LINK C DAR B 5 N DAR B 6 1555 1555 1.33 LINK C DAR B 6 N DAR B 7 1555 1555 1.33 LINK C DAR B 7 N DAR B 8 1555 1555 1.33 LINK C DAR B 8 N NH2 B 9 1555 1555 1.32 LINK OG SER A 189 MG MG A 401 1555 1555 2.22 LINK MG MG A 401 O HOH A 514 1555 1555 2.01 LINK MG MG A 401 O HOH A 521 1555 1555 2.05 LINK MG MG A 401 O HOH A 524 1555 1555 2.12 LINK MG MG A 401 O HOH A 588 1555 1555 2.16 LINK MG MG A 401 O HOH A 640 1555 1555 2.24 CISPEP 1 GLU A 124 PRO A 125 0 -4.93 CRYST1 98.614 98.614 80.729 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 0.010141 0.005855 0.000000 0.00000 SCALE2 0.000000 0.011709 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012387 0.00000