HEADER TRANSPORT PROTEIN 25-JUL-14 4U5L TITLE IMPORTIN-ALPHA MINOR NLS SITE INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: IMPORTIN SUBUNIT ALPHA-1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: IMPORTIN ALPHA P1,KARYOPHERIN SUBUNIT ALPHA-2,PENDULIN,PORE COMPND 5 TARGETING COMPLEX 58 KDA SUBUNIT,PTAC58,RAG COHORT PROTEIN 1,SRP1- COMPND 6 ALPHA; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: KPNA2, RCH1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TPX2, INHIBITOR, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.STEWART,E.VALKOV,R.S.HOLVEY REVDAT 3 08-MAY-24 4U5L 1 REMARK REVDAT 2 08-JUL-15 4U5L 1 JRNL REVDAT 1 13-MAY-15 4U5L 0 JRNL AUTH R.S.HOLVEY,E.VALKOV,D.NEAL,M.STEWART,C.ABELL JRNL TITL SELECTIVE TARGETING OF THE TPX2 SITE OF IMPORTIN-ALPHA USING JRNL TITL 2 FRAGMENT-BASED LIGAND DESIGN. JRNL REF CHEMMEDCHEM V. 10 1232 2015 JRNL REFN ESSN 1860-7187 JRNL PMID 25899172 JRNL DOI 10.1002/CMDC.201500014 REMARK 2 REMARK 2 RESOLUTION. 2.53 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: DEV_1702) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.53 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.83 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 24564 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.110 REMARK 3 FREE R VALUE TEST SET COUNT : 1256 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 19.8338 - 5.2338 1.00 2750 120 0.1510 0.1767 REMARK 3 2 5.2338 - 4.1669 1.00 2625 150 0.1447 0.1757 REMARK 3 3 4.1669 - 3.6439 1.00 2587 144 0.1497 0.1842 REMARK 3 4 3.6439 - 3.3124 1.00 2562 167 0.1830 0.2465 REMARK 3 5 3.3124 - 3.0759 1.00 2565 144 0.2191 0.2657 REMARK 3 6 3.0759 - 2.8951 1.00 2571 132 0.2237 0.2252 REMARK 3 7 2.8951 - 2.7505 1.00 2549 133 0.2328 0.2956 REMARK 3 8 2.7505 - 2.6311 1.00 2557 119 0.2424 0.3346 REMARK 3 9 2.6311 - 2.5300 1.00 2542 147 0.2636 0.3082 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.130 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.37 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 : 0.009 3346 REMARK 3 ANGLE : 1.217 4563 REMARK 3 CHIRALITY : 0.042 549 REMARK 3 PLANARITY : 0.006 585 REMARK 3 DIHEDRAL : 14.761 1223 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 4U5L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-JUL-14. REMARK 100 THE DEPOSITION ID IS D_1000202855. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-SEP-12 REMARK 200 TEMPERATURE (KELVIN) : 100 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 : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9192 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24615 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.530 REMARK 200 RESOLUTION RANGE LOW (A) : 19.833 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 10.40 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.9000 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: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SEE MANUSCRIPT, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 -1.000000 0.000000 0.000000 39.44800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.20450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 45.30200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.20450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 39.44800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 45.30200 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 300 REMARK: BIOLOGICAL UNIT IS THE SAME AS ASYM. 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18750 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 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 A 631 O HOH A 677 1.90 REMARK 500 OE1 GLU A 266 O HOH A 699 1.98 REMARK 500 O HOH A 634 O HOH A 700 2.04 REMARK 500 OD2 ASP A 192 O HOH A 691 2.07 REMARK 500 OD1 ASP A 132 O HOH A 680 2.15 REMARK 500 NZ LYS A 123 O HOH A 654 2.15 REMARK 500 O HOH A 668 O HOH A 689 2.17 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 ASN A 88 41.50 -84.15 REMARK 500 GLN A 109 98.46 -5.37 REMARK 500 HIS A 203 3.06 -67.72 REMARK 500 ASN A 239 160.26 80.62 REMARK 500 LYS A 453 3.83 -69.19 REMARK 500 GLU A 458 -84.38 -40.25 REMARK 500 ARG A 478 38.22 -154.53 REMARK 500 GLU A 480 -56.53 9.64 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 3D6 A 501 DBREF 4U5L A 72 497 UNP P52293 IMA1_MOUSE 72 497 SEQRES 1 A 426 GLY THR VAL ASN TRP SER VAL GLU ASP ILE VAL LYS GLY SEQRES 2 A 426 ILE ASN SER ASN ASN LEU GLU SER GLN LEU GLN ALA THR SEQRES 3 A 426 GLN ALA ALA ARG LYS LEU LEU SER ARG GLU LYS GLN PRO SEQRES 4 A 426 PRO ILE ASP ASN ILE ILE ARG ALA GLY LEU ILE PRO LYS SEQRES 5 A 426 PHE VAL SER PHE LEU GLY LYS THR ASP CYS SER PRO ILE SEQRES 6 A 426 GLN PHE GLU SER ALA TRP ALA LEU THR ASN ILE ALA SER SEQRES 7 A 426 GLY THR SER GLU GLN THR LYS ALA VAL VAL ASP GLY GLY SEQRES 8 A 426 ALA ILE PRO ALA PHE ILE SER LEU LEU ALA SER PRO HIS SEQRES 9 A 426 ALA HIS ILE SER GLU GLN ALA VAL TRP ALA LEU GLY ASN SEQRES 10 A 426 ILE ALA GLY ASP GLY SER ALA PHE ARG ASP LEU VAL ILE SEQRES 11 A 426 LYS HIS GLY ALA ILE ASP PRO LEU LEU ALA LEU LEU ALA SEQRES 12 A 426 VAL PRO ASP LEU SER THR LEU ALA CYS GLY TYR LEU ARG SEQRES 13 A 426 ASN LEU THR TRP THR LEU SER ASN LEU CYS ARG ASN LYS SEQRES 14 A 426 ASN PRO ALA PRO PRO LEU ASP ALA VAL GLU GLN ILE LEU SEQRES 15 A 426 PRO THR LEU VAL ARG LEU LEU HIS HIS ASN ASP PRO GLU SEQRES 16 A 426 VAL LEU ALA ASP SER CYS TRP ALA ILE SER TYR LEU THR SEQRES 17 A 426 ASP GLY PRO ASN GLU ARG ILE GLU MET VAL VAL LYS LYS SEQRES 18 A 426 GLY VAL VAL PRO GLN LEU VAL LYS LEU LEU GLY ALA THR SEQRES 19 A 426 GLU LEU PRO ILE VAL THR PRO ALA LEU ARG ALA ILE GLY SEQRES 20 A 426 ASN ILE VAL THR GLY THR ASP GLU GLN THR GLN LYS VAL SEQRES 21 A 426 ILE ASP ALA GLY ALA LEU ALA VAL PHE PRO SER LEU LEU SEQRES 22 A 426 THR ASN PRO LYS THR ASN ILE GLN LYS GLU ALA THR TRP SEQRES 23 A 426 THR MET SER ASN ILE THR ALA GLY ARG GLN ASP GLN ILE SEQRES 24 A 426 GLN GLN VAL VAL ASN HIS GLY LEU VAL PRO PHE LEU VAL SEQRES 25 A 426 GLY VAL LEU SER LYS ALA ASP PHE LYS THR GLN LYS GLU SEQRES 26 A 426 ALA ALA TRP ALA ILE THR ASN TYR THR SER GLY GLY THR SEQRES 27 A 426 VAL GLU GLN ILE VAL TYR LEU VAL HIS CYS GLY ILE ILE SEQRES 28 A 426 GLU PRO LEU MET ASN LEU LEU SER ALA LYS ASP THR LYS SEQRES 29 A 426 ILE ILE GLN VAL ILE LEU ASP ALA ILE SER ASN ILE PHE SEQRES 30 A 426 GLN ALA ALA GLU LYS LEU GLY GLU THR GLU LYS LEU SER SEQRES 31 A 426 ILE MET ILE GLU GLU CYS GLY GLY LEU ASP LYS ILE GLU SEQRES 32 A 426 ALA LEU GLN ARG HIS GLU ASN GLU SER VAL TYR LYS ALA SEQRES 33 A 426 SER LEU ASN LEU ILE GLU LYS TYR PHE SER HET 3D6 A 501 23 HETNAM 3D6 N~2~-[4-(PYRIDIN-3-YL)BENZYL]-L-LYSINAMIDE FORMUL 2 3D6 C18 H24 N4 O FORMUL 3 HOH *104(H2 O) HELIX 1 AA1 SER A 77 ASN A 86 1 10 HELIX 2 AA2 ASN A 89 ARG A 106 1 18 HELIX 3 AA3 PRO A 111 ALA A 118 1 8 HELIX 4 AA4 LEU A 120 GLY A 129 1 10 HELIX 5 AA5 CYS A 133 SER A 149 1 17 HELIX 6 AA6 THR A 151 GLY A 161 1 11 HELIX 7 AA7 GLY A 162 LEU A 171 1 10 HELIX 8 AA8 HIS A 175 ASP A 192 1 18 HELIX 9 AA9 GLY A 193 HIS A 203 1 11 HELIX 10 AB1 ALA A 205 LEU A 212 1 8 HELIX 11 AB2 ASP A 217 LEU A 221 5 5 HELIX 12 AB3 ALA A 222 CYS A 237 1 16 HELIX 13 AB4 PRO A 245 LEU A 260 1 16 HELIX 14 AB5 ASP A 264 THR A 279 1 16 HELIX 15 AB6 PRO A 282 LYS A 291 1 10 HELIX 16 AB7 VAL A 294 GLY A 303 1 10 HELIX 17 AB8 GLU A 306 VAL A 321 1 16 HELIX 18 AB9 THR A 324 ALA A 334 1 11 HELIX 19 AC1 GLY A 335 ALA A 338 5 4 HELIX 20 AC2 VAL A 339 LEU A 344 1 6 HELIX 21 AC3 LYS A 348 THR A 363 1 16 HELIX 22 AC4 ARG A 366 HIS A 376 1 11 HELIX 23 AC5 LEU A 378 LYS A 388 1 11 HELIX 24 AC6 ASP A 390 GLY A 408 1 19 HELIX 25 AC7 THR A 409 CYS A 419 1 11 HELIX 26 AC8 ILE A 421 LEU A 428 1 8 HELIX 27 AC9 LEU A 429 ALA A 431 5 3 HELIX 28 AD1 ASP A 433 LYS A 453 1 21 HELIX 29 AD2 GLU A 456 CYS A 467 1 12 HELIX 30 AD3 GLY A 468 ALA A 475 1 8 HELIX 31 AD4 LEU A 476 HIS A 479 5 4 HELIX 32 AD5 ASN A 481 PHE A 496 1 16 CISPEP 1 ASN A 241 PRO A 242 0 -2.38 SITE 1 AC1 9 VAL A 321 GLY A 323 THR A 328 SER A 360 SITE 2 AC1 9 ASN A 361 ALA A 364 GLU A 396 TRP A 399 SITE 3 AC1 9 ASN A 403 CRYST1 78.896 90.604 100.409 90.00 90.00 90.00 P 21 21 21 4 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 0.012675 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011037 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009959 0.00000