HEADER TRANSFERASE 09-MAR-17 5NDT TITLE CRYSTAL STRUCTURE OF HUMAN PIM-1 KINASE IN COMPLEX WITH A CONSENSUS TITLE 2 PEPTIDE AND FRAGMENT LIKE MOLECULE (E)-3-(2-(THIOPHEN-2-YL)VINYL)-3, TITLE 3 4-DIHYDROQUINOXALIN-2(1H)-ONE 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 MUTATION: YES; COMPND 7 OTHER_DETAILS: ISOFROM 2 OF PIM-1 KINASE; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: PIMTIDE; COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES; COMPND 12 OTHER_DETAILS: PIM-1 CONSENSUS PEPTIDE 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(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PLIC-SGC; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 14 ORGANISM_COMMON: HUMAN; SOURCE 15 ORGANISM_TAXID: 9606 KEYWDS SERINE THREONINE KINASE, TRANSFERASE, PROTO-ONCOGENE, FRAGMENT, PIM- KEYWDS 2 1, CONSENSUS PEPTIDE EXPDTA X-RAY DIFFRACTION AUTHOR C.SIEFKER,A.HEINE,G.KLEBE REVDAT 3 17-JAN-24 5NDT 1 REMARK REVDAT 2 14-AUG-19 5NDT 1 REMARK REVDAT 1 16-MAY-18 5NDT 0 JRNL AUTH C.SIEFKER,A.HEINE,K.HARDES,A.STEINMETZER,G.KLEBE JRNL TITL A CRYSTALLOGRAPHIC FRAGMENT STUDY WITH HUMAN PIM-1 KINASE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.99 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.66 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 30585 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.162 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1529 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 42.6737 - 4.4137 1.00 2716 142 0.1565 0.1865 REMARK 3 2 4.4137 - 3.5038 1.00 2643 140 0.1412 0.1646 REMARK 3 3 3.5038 - 3.0610 1.00 2674 140 0.1586 0.1957 REMARK 3 4 3.0610 - 2.7812 1.00 2652 140 0.1613 0.1943 REMARK 3 5 2.7812 - 2.5819 1.00 2633 139 0.1704 0.2198 REMARK 3 6 2.5819 - 2.4297 1.00 2670 140 0.1690 0.2082 REMARK 3 7 2.4297 - 2.3080 1.00 2619 138 0.1603 0.2182 REMARK 3 8 2.3080 - 2.2076 0.98 2589 137 0.2167 0.2735 REMARK 3 9 2.2076 - 2.1226 1.00 2638 138 0.1693 0.1842 REMARK 3 10 2.1226 - 2.0493 1.00 2619 138 0.2033 0.2426 REMARK 3 11 2.0493 - 1.9853 0.99 2603 137 0.1783 0.1999 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.770 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 2332 REMARK 3 ANGLE : 0.756 3166 REMARK 3 CHIRALITY : 0.052 338 REMARK 3 PLANARITY : 0.005 424 REMARK 3 DIHEDRAL : 20.816 1375 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 33 THROUGH 96 ) REMARK 3 ORIGIN FOR THE GROUP (A): 135.4462 2.9832 8.1886 REMARK 3 T TENSOR REMARK 3 T11: 0.4877 T22: 0.3640 REMARK 3 T33: 0.4170 T12: -0.0344 REMARK 3 T13: 0.0420 T23: -0.0012 REMARK 3 L TENSOR REMARK 3 L11: 1.4619 L22: 1.8419 REMARK 3 L33: 1.6030 L12: -0.8528 REMARK 3 L13: 0.5044 L23: -0.1738 REMARK 3 S TENSOR REMARK 3 S11: -0.2391 S12: 0.2401 S13: 0.2212 REMARK 3 S21: 0.1708 S22: 0.1663 S23: 0.1225 REMARK 3 S31: -0.3557 S32: -0.1680 S33: -0.0000 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 97 THROUGH 161 ) REMARK 3 ORIGIN FOR THE GROUP (A): 142.9740 -9.0719 3.5832 REMARK 3 T TENSOR REMARK 3 T11: 0.3031 T22: 0.2876 REMARK 3 T33: 0.3210 T12: -0.0581 REMARK 3 T13: 0.0168 T23: 0.0149 REMARK 3 L TENSOR REMARK 3 L11: 0.6277 L22: 1.8258 REMARK 3 L33: 2.1438 L12: -0.3958 REMARK 3 L13: 0.3543 L23: 0.0678 REMARK 3 S TENSOR REMARK 3 S11: 0.0414 S12: 0.0401 S13: 0.0992 REMARK 3 S21: 0.0470 S22: 0.0681 S23: -0.1724 REMARK 3 S31: -0.2366 S32: 0.1258 S33: 0.0001 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 162 THROUGH 250 ) REMARK 3 ORIGIN FOR THE GROUP (A): 132.3096 -17.6785 -0.8896 REMARK 3 T TENSOR REMARK 3 T11: 0.2807 T22: 0.3099 REMARK 3 T33: 0.3041 T12: -0.0069 REMARK 3 T13: -0.0071 T23: 0.0278 REMARK 3 L TENSOR REMARK 3 L11: 1.4229 L22: 1.7041 REMARK 3 L33: 2.0462 L12: 0.3880 REMARK 3 L13: 0.0189 L23: 0.0813 REMARK 3 S TENSOR REMARK 3 S11: 0.1205 S12: 0.0832 S13: 0.0533 REMARK 3 S21: -0.0282 S22: -0.0145 S23: 0.1209 REMARK 3 S31: -0.1264 S32: -0.2567 S33: -0.0000 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 251 THROUGH 305 ) REMARK 3 ORIGIN FOR THE GROUP (A): 144.2410 -27.3412 -2.8083 REMARK 3 T TENSOR REMARK 3 T11: 0.3053 T22: 0.3218 REMARK 3 T33: 0.3001 T12: -0.0153 REMARK 3 T13: -0.0169 T23: 0.0052 REMARK 3 L TENSOR REMARK 3 L11: 1.1140 L22: 1.3711 REMARK 3 L33: 2.1495 L12: -0.3944 REMARK 3 L13: 0.0616 L23: 0.1027 REMARK 3 S TENSOR REMARK 3 S11: 0.0860 S12: 0.0467 S13: -0.2990 REMARK 3 S21: -0.0043 S22: -0.0501 S23: -0.1130 REMARK 3 S31: 0.3722 S32: 0.1735 S33: -0.0001 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 2 THROUGH 10 ) REMARK 3 ORIGIN FOR THE GROUP (A): 134.0019 -11.2241 -12.8062 REMARK 3 T TENSOR REMARK 3 T11: 0.5938 T22: 0.5031 REMARK 3 T33: 0.4703 T12: 0.0495 REMARK 3 T13: 0.0221 T23: 0.1269 REMARK 3 L TENSOR REMARK 3 L11: 1.2108 L22: 0.1870 REMARK 3 L33: 0.2271 L12: -0.2350 REMARK 3 L13: -0.3418 L23: 0.0627 REMARK 3 S TENSOR REMARK 3 S11: -0.2739 S12: 1.2534 S13: -0.2799 REMARK 3 S21: -0.2042 S22: 0.1641 S23: 0.6519 REMARK 3 S31: 0.3593 S32: -0.9925 S33: -0.0144 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5NDT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-MAR-17. REMARK 100 THE DEPOSITION ID IS D_1200003342. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-JUL-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : SI-111 CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : SILICON REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30602 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.985 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 8.390 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.5600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.99 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 8.34 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.480 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: 3WE8 REMARK 200 REMARK 200 REMARK: HEXAGONAL ROD REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HEPES NACL GLYCEROL DTT BIS-TRIS REMARK 280 -PROPANE PEG3350 ETHYLENE-GLYCOL DMSO, PH 7.0, VAPOR DIFFUSION, REMARK 280 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 53.58533 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 26.79267 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 40.18900 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 13.39633 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 66.98167 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 3.0 KCAL/MOL 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 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 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 465 LYS A 313 REMARK 465 ALA B 1 REMARK 465 PRO B 11 REMARK 465 PRO B 12 REMARK 465 THR B 13 REMARK 465 ALA B 14 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 PRO A 33 CG CD REMARK 470 LEU A 34 CD1 CD2 REMARK 470 GLU A 35 CD OE1 OE2 REMARK 470 SER A 36 OG REMARK 470 GLN A 39 CD OE1 NE2 REMARK 470 ILE A 56 CD1 REMARK 470 VAL A 58 CG1 CG2 REMARK 470 SER A 59 OG REMARK 470 GLU A 70 CG CD OE1 OE2 REMARK 470 ARG A 73 CG CD NE CZ NH1 NH2 REMARK 470 SER A 75 OG REMARK 470 ASP A 76 OD1 OD2 REMARK 470 GLU A 79 CG CD OE1 OE2 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 LYS A 94 CE NZ REMARK 470 SER A 98 OG REMARK 470 GLU A 124 CG CD OE1 OE2 REMARK 470 ASP A 200 OD1 REMARK 470 ASP A 202 OD1 OD2 REMARK 470 ARG A 214 NH1 NH2 REMARK 470 GLN A 252 OE1 NE2 REMARK 470 ARG A 274 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 297 CG CD OE1 NE2 REMARK 470 LYS B 3 CG CD CE NZ REMARK 470 ARG B 5 NH1 NH2 REMARK 470 HIS B 7 O 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 A 60 16.37 -157.94 REMARK 500 PRO A 81 62.43 -61.02 REMARK 500 ASN A 82 -0.38 -177.05 REMARK 500 ASP A 167 44.13 -151.37 REMARK 500 ASP A 186 78.28 63.42 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 8UB A 402 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 8UB A 402 DBREF 5NDT A 1 313 UNP P11309 PIM1_HUMAN 1 313 DBREF 5NDT B 1 14 PDB 5NDT 5NDT 1 14 SEQADV 5NDT GLY A 250 UNP P11309 ARG 250 ENGINEERED MUTATION SEQRES 1 A 313 MET LEU LEU SER LYS ILE ASN SER LEU ALA HIS LEU ARG SEQRES 2 A 313 ALA ALA PRO CYS ASN ASP LEU HIS ALA THR LYS LEU ALA SEQRES 3 A 313 PRO GLY LYS GLU LYS GLU PRO LEU GLU SER GLN TYR GLN SEQRES 4 A 313 VAL GLY PRO LEU LEU GLY SER GLY GLY PHE GLY SER VAL SEQRES 5 A 313 TYR SER GLY ILE ARG VAL SER ASP ASN LEU PRO VAL ALA SEQRES 6 A 313 ILE LYS HIS VAL GLU LYS ASP ARG ILE SER ASP TRP GLY SEQRES 7 A 313 GLU LEU PRO ASN GLY THR ARG VAL PRO MET GLU VAL VAL SEQRES 8 A 313 LEU LEU LYS LYS VAL SER SER GLY PHE SER GLY VAL ILE SEQRES 9 A 313 ARG LEU LEU ASP TRP PHE GLU ARG PRO ASP SER PHE VAL SEQRES 10 A 313 LEU ILE LEU GLU ARG PRO GLU PRO VAL GLN ASP LEU PHE SEQRES 11 A 313 ASP PHE ILE THR GLU ARG GLY ALA LEU GLN GLU GLU LEU SEQRES 12 A 313 ALA ARG SER PHE PHE TRP GLN VAL LEU GLU ALA VAL ARG SEQRES 13 A 313 HIS CYS HIS ASN CYS GLY VAL LEU HIS ARG ASP ILE LYS SEQRES 14 A 313 ASP GLU ASN ILE LEU ILE ASP LEU ASN ARG GLY GLU LEU SEQRES 15 A 313 LYS LEU ILE ASP PHE GLY SER GLY ALA LEU LEU LYS ASP SEQRES 16 A 313 THR VAL TYR THR ASP PHE ASP GLY THR ARG VAL TYR SER SEQRES 17 A 313 PRO PRO GLU TRP ILE ARG TYR HIS ARG TYR HIS GLY ARG SEQRES 18 A 313 SER ALA ALA VAL TRP SER LEU GLY ILE LEU LEU TYR ASP SEQRES 19 A 313 MET VAL CYS GLY ASP ILE PRO PHE GLU HIS ASP GLU GLU SEQRES 20 A 313 ILE ILE GLY GLY GLN VAL PHE PHE ARG GLN ARG VAL SER SEQRES 21 A 313 SER GLU CYS GLN HIS LEU ILE ARG TRP CYS LEU ALA LEU SEQRES 22 A 313 ARG PRO SER ASP ARG PRO THR PHE GLU GLU ILE GLN ASN SEQRES 23 A 313 HIS PRO TRP MET GLN ASP VAL LEU LEU PRO GLN GLU THR SEQRES 24 A 313 ALA GLU ILE HIS LEU HIS SER LEU SER PRO GLY PRO SER SEQRES 25 A 313 LYS SEQRES 1 B 14 ALA ARG LYS ARG ARG ARG HIS PRO SER GLY PRO PRO THR SEQRES 2 B 14 ALA HET GOL A 401 6 HET 8UB A 402 12 HETNAM GOL GLYCEROL HETNAM 8UB 3-(2-THIOPHEN-2-YLETHENYL)-1~{H}-QUINOXALIN-2-ONE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 GOL C3 H8 O3 FORMUL 4 8UB C14 H10 N2 O S FORMUL 5 HOH *122(H2 O) HELIX 1 AA1 PRO A 33 GLN A 37 1 5 HELIX 2 AA2 ASP A 72 ILE A 74 5 3 HELIX 3 AA3 MET A 88 SER A 97 1 10 HELIX 4 AA4 LEU A 129 GLY A 137 1 9 HELIX 5 AA5 GLN A 140 CYS A 161 1 22 HELIX 6 AA6 LYS A 169 GLU A 171 5 3 HELIX 7 AA7 THR A 204 SER A 208 5 5 HELIX 8 AA8 PRO A 209 HIS A 216 1 8 HELIX 9 AA9 HIS A 219 GLY A 238 1 20 HELIX 10 AB1 HIS A 244 GLY A 251 1 8 HELIX 11 AB2 SER A 260 LEU A 271 1 12 HELIX 12 AB3 ARG A 274 ARG A 278 5 5 HELIX 13 AB4 THR A 280 ASN A 286 1 7 HELIX 14 AB5 HIS A 287 GLN A 291 5 5 HELIX 15 AB6 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 PRO A 42 SHEET 3 AA1 5 PRO A 63 GLU A 70 -1 O ILE A 66 N TYR A 53 SHEET 4 AA1 5 SER A 115 GLU A 121 -1 O LEU A 118 N LYS A 67 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 CISPEP 1 GLU A 124 PRO A 125 0 -3.32 SITE 1 AC1 6 TYR A 233 PRO A 241 GLU A 247 GLN A 252 SITE 2 AC1 6 PHE A 254 ARG A 256 SITE 1 AC2 8 PHE A 49 VAL A 52 ALA A 65 LYS A 67 SITE 2 AC2 8 GLU A 121 LEU A 174 HOH A 528 HOH A 587 CRYST1 98.528 98.528 80.378 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 0.010149 0.005860 0.000000 0.00000 SCALE2 0.000000 0.011720 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012441 0.00000