PDB Short entry for 4D9U HEADER TRANSFERASE/TRANSFERASE INHIBITOR 12-JAN-12 4D9U TITLE RSK2 C-TERMINAL KINASE DOMAIN, (E)-TERT-BUTYL 3-(4-AMINO-7-(3- TITLE 2 HYDROXYPROPYL)-5-P-TOLYL-7H-PYRROLO[2,3-D]PYRIMIDIN-6-YL)-2- TITLE 3 CYANOACRYLATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBOSOMAL PROTEIN S6 KINASE ALPHA-3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 399-740; COMPND 5 SYNONYM: S6K-ALPHA-3, 90 KDA RIBOSOMAL PROTEIN S6 KINASE 3, P90-RSK COMPND 6 3, P90RSK3, INSULIN-STIMULATED PROTEIN KINASE 1, ISPK-1, MAP KINASE- COMPND 7 ACTIVATED PROTEIN KINASE 1B, MAPK-ACTIVATED PROTEIN KINASE 1B, MAPKAP COMPND 8 KINASE 1B, MAPKAPK-1B, RIBOSOMAL S6 KINASE 2, RSK-2, PP90RSK2; COMPND 9 EC: 2.7.11.1; COMPND 10 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: ISPK1, MAPKAPK1B, RPS6KA3, RSK2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET46 KEYWDS KINASE, REVERSIBLE INHIBITOR, PHOSPHORYLATION, TRANSFERASE- KEYWDS 2 TRANSFERASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR I.M.SERAFIMOVA,M.A.PUFALL,S.KRISHNAN,K.DUDA,M.S.COHEN,R.L.MAGLATHLIN, AUTHOR 2 J.M.MCFARLAND,R.M.MILLER,M.FRODIN,J.TAUNTON REVDAT 4 13-SEP-23 4D9U 1 REMARK SEQADV LINK REVDAT 3 16-MAY-12 4D9U 1 JRNL REVDAT 2 25-APR-12 4D9U 1 JRNL REVDAT 1 11-APR-12 4D9U 0 JRNL AUTH I.M.SERAFIMOVA,M.A.PUFALL,S.KRISHNAN,K.DUDA,M.S.COHEN, JRNL AUTH 2 R.L.MAGLATHLIN,J.M.MCFARLAND,R.M.MILLER,M.FRODIN,J.TAUNTON JRNL TITL REVERSIBLE TARGETING OF NONCATALYTIC CYSTEINES WITH JRNL TITL 2 CHEMICALLY TUNED ELECTROPHILES. JRNL REF NAT.CHEM.BIOL. V. 8 471 2012 JRNL REFN ISSN 1552-4450 JRNL PMID 22466421 JRNL DOI 10.1038/NCHEMBIO.925 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_613 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.10 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.040 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 13693 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.276 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1370 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 46.1264 - 5.1685 1.00 1387 155 0.2001 0.2548 REMARK 3 2 5.1685 - 4.1032 1.00 1276 141 0.1693 0.2402 REMARK 3 3 4.1032 - 3.5847 1.00 1234 138 0.1827 0.2338 REMARK 3 4 3.5847 - 3.2571 1.00 1244 138 0.2096 0.3012 REMARK 3 5 3.2571 - 3.0237 1.00 1208 134 0.2286 0.3482 REMARK 3 6 3.0237 - 2.8454 1.00 1214 135 0.2292 0.3230 REMARK 3 7 2.8454 - 2.7029 1.00 1202 134 0.2342 0.3187 REMARK 3 8 2.7029 - 2.5853 1.00 1178 131 0.2437 0.3186 REMARK 3 9 2.5853 - 2.4858 1.00 1192 131 0.2609 0.3429 REMARK 3 10 2.4858 - 2.4000 0.99 1188 133 0.2889 0.3301 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.83 REMARK 3 K_SOL : 0.32 REMARK 3 B_SOL : 46.01 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.370 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.920 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 59.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 63.49 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 6.79370 REMARK 3 B22 (A**2) : 6.79370 REMARK 3 B33 (A**2) : -13.58740 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 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 : 0.008 2496 REMARK 3 ANGLE : 1.100 3384 REMARK 3 CHIRALITY : 0.074 372 REMARK 3 PLANARITY : 0.005 433 REMARK 3 DIHEDRAL : 14.911 919 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 408:587) REMARK 3 ORIGIN FOR THE GROUP (A): -28.8095 16.6500 -15.3407 REMARK 3 T TENSOR REMARK 3 T11: 0.4643 T22: 0.4572 REMARK 3 T33: 0.3229 T12: 0.1728 REMARK 3 T13: -0.0177 T23: -0.0016 REMARK 3 L TENSOR REMARK 3 L11: 1.0402 L22: 1.0067 REMARK 3 L33: 1.0311 L12: 0.4101 REMARK 3 L13: -0.5643 L23: 0.5392 REMARK 3 S TENSOR REMARK 3 S11: -0.0360 S12: -0.3291 S13: 0.0996 REMARK 3 S21: 0.3329 S22: 0.0198 S23: 0.1401 REMARK 3 S31: 0.4592 S32: 0.2779 S33: 0.0308 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 588:647) REMARK 3 ORIGIN FOR THE GROUP (A): -9.5770 22.0996 -27.6203 REMARK 3 T TENSOR REMARK 3 T11: 0.3663 T22: 0.7818 REMARK 3 T33: 0.3433 T12: 0.2300 REMARK 3 T13: 0.0248 T23: -0.0830 REMARK 3 L TENSOR REMARK 3 L11: 0.3769 L22: 1.0302 REMARK 3 L33: 0.5288 L12: 0.6025 REMARK 3 L13: 0.2598 L23: 0.4228 REMARK 3 S TENSOR REMARK 3 S11: -0.3586 S12: -0.3137 S13: 0.0424 REMARK 3 S21: -0.0029 S22: 0.4248 S23: -0.4185 REMARK 3 S31: 0.1578 S32: 0.5626 S33: -0.0139 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 648:667) REMARK 3 ORIGIN FOR THE GROUP (A): -7.2230 31.4935 -23.7775 REMARK 3 T TENSOR REMARK 3 T11: 0.2474 T22: 0.8187 REMARK 3 T33: 0.3900 T12: -0.1357 REMARK 3 T13: -0.0761 T23: -0.2397 REMARK 3 L TENSOR REMARK 3 L11: 0.1977 L22: 0.2391 REMARK 3 L33: 0.3605 L12: -0.0896 REMARK 3 L13: -0.2616 L23: 0.1587 REMARK 3 S TENSOR REMARK 3 S11: 0.0429 S12: -0.2334 S13: -0.0534 REMARK 3 S21: 0.1281 S22: 0.1697 S23: -0.2583 REMARK 3 S31: -0.0083 S32: 0.5943 S33: 0.1524 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 668:714) REMARK 3 ORIGIN FOR THE GROUP (A): -16.8444 27.9977 -27.9160 REMARK 3 T TENSOR REMARK 3 T11: 0.4273 T22: 0.6970 REMARK 3 T33: 0.3716 T12: -0.0854 REMARK 3 T13: -0.0347 T23: -0.0727 REMARK 3 L TENSOR REMARK 3 L11: 0.4351 L22: 1.0166 REMARK 3 L33: 0.7958 L12: 0.0915 REMARK 3 L13: -0.2717 L23: 0.7392 REMARK 3 S TENSOR REMARK 3 S11: -0.0773 S12: -0.0846 S13: 0.0108 REMARK 3 S21: -0.3011 S22: 0.3161 S23: -0.0473 REMARK 3 S31: -0.3036 S32: 0.2489 S33: -0.1100 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 4D9U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-JAN-12. REMARK 100 THE DEPOSITION ID IS D_1000070063. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUL-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : DOUBLE FLAT CRYSTAL, SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13695 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 46.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 8.000 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : 0.09300 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 2QR8 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM TRIS, PH 8.5, 25% PEG 3350, REMARK 280 HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 146.50000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 23.35000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 23.35000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 73.25000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 23.35000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 23.35000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 219.75000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 23.35000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 23.35000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 73.25000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 23.35000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 23.35000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 219.75000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 146.50000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2540 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27510 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -40.0 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 350 BIOMT1 2 0.000000 1.000000 0.000000 -46.70000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 46.70000 REMARK 350 BIOMT3 2 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 399 REMARK 465 GLN A 400 REMARK 465 THR A 401 REMARK 465 VAL A 402 REMARK 465 GLY A 403 REMARK 465 VAL A 404 REMARK 465 HIS A 405 REMARK 465 SER A 406 REMARK 465 ILE A 407 REMARK 465 SER A 715 REMARK 465 PRO A 716 REMARK 465 VAL A 717 REMARK 465 LEU A 718 REMARK 465 GLU A 719 REMARK 465 PRO A 720 REMARK 465 VAL A 721 REMARK 465 GLY A 722 REMARK 465 ARG A 723 REMARK 465 SER A 724 REMARK 465 THR A 725 REMARK 465 LEU A 726 REMARK 465 ALA A 727 REMARK 465 GLN A 728 REMARK 465 ARG A 729 REMARK 465 ARG A 730 REMARK 465 GLY A 731 REMARK 465 ILE A 732 REMARK 465 LYS A 733 REMARK 465 LYS A 734 REMARK 465 ILE A 735 REMARK 465 THR A 736 REMARK 465 SER A 737 REMARK 465 THR A 738 REMARK 465 ALA A 739 REMARK 465 LEU A 740 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 VAL A 408 CG1 CG2 REMARK 470 GLN A 409 CG CD OE1 NE2 REMARK 470 GLN A 410 CG CD OE1 NE2 REMARK 470 LEU A 411 CG CD1 CD2 REMARK 470 HIS A 412 CG ND1 CD2 CE1 NE2 REMARK 470 ARG A 413 CG CD NE CZ NH1 NH2 REMARK 470 ASN A 414 CG OD1 ND2 REMARK 470 SER A 415 OG REMARK 470 PHE A 584 CB CG CD1 CD2 CE1 CE2 CZ REMARK 470 VAL A 585 CB CG1 CG2 REMARK 470 GLU A 588 CG CD OE1 OE2 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 NH1 ARG A 675 O HOH A 1029 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 CB CYS A 579 SG CYS A 579 7465 1.68 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 LEU A 501 CA - CB - CG ANGL. DEV. = 18.0 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 GLN A 410 16.39 -67.07 REMARK 500 SER A 415 -129.53 -71.36 REMARK 500 ILE A 416 -158.71 -132.06 REMARK 500 LYS A 425 -135.32 -110.15 REMARK 500 ASP A 539 36.53 -165.33 REMARK 500 LEU A 540 54.70 -69.61 REMARK 500 ASN A 583 167.35 -48.20 REMARK 500 PHE A 584 -58.05 136.43 REMARK 500 VAL A 585 53.29 -112.59 REMARK 500 GLU A 588 -22.26 63.15 REMARK 500 HIS A 681 45.45 -98.87 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 THE UNBOUND FORM OF THE INHIBITOR IS (E)-TERT-BUTYL 3-(4-AMINO-7-(3- REMARK 600 HYDROXYPROPYL)-5-P-TOLYL-7H-PYRROLO[2,3-D]PYRIMIDIN-6-YL)-2- REMARK 600 CYANOACRYLATE. UPON REACTION WITH PROTEIN, THE DOUBLE BOND BETWEEN REMARK 600 C11 AND C12 OPENS UP AND THE LIGAND COVALENTLY BINDS TO CYS436. 0JH REMARK 600 REPRESENTS THE BOUND FORM OF THIS INHIBITOR. 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 NA A 901 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 471 O REMARK 620 2 HIS A 473 O 106.7 REMARK 620 3 ILE A 476 O 109.9 91.4 REMARK 620 4 THR A 478 OG1 84.0 165.5 94.1 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 0JH A 900 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 901 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4D9T RELATED DB: PDB DBREF 4D9U A 399 740 UNP P51812 KS6A3_HUMAN 399 740 SEQADV 4D9U GLU A 591 UNP P51812 LYS 591 ENGINEERED MUTATION SEQRES 1 A 342 MET GLN THR VAL GLY VAL HIS SER ILE VAL GLN GLN LEU SEQRES 2 A 342 HIS ARG ASN SER ILE GLN PHE THR ASP GLY TYR GLU VAL SEQRES 3 A 342 LYS GLU ASP ILE GLY VAL GLY SER TYR SER VAL CYS LYS SEQRES 4 A 342 ARG CYS ILE HIS LYS ALA THR ASN MET GLU PHE ALA VAL SEQRES 5 A 342 LYS ILE ILE ASP LYS SER LYS ARG ASP PRO THR GLU GLU SEQRES 6 A 342 ILE GLU ILE LEU LEU ARG TYR GLY GLN HIS PRO ASN ILE SEQRES 7 A 342 ILE THR LEU LYS ASP VAL TYR ASP ASP GLY LYS TYR VAL SEQRES 8 A 342 TYR VAL VAL THR GLU LEU MET LYS GLY GLY GLU LEU LEU SEQRES 9 A 342 ASP LYS ILE LEU ARG GLN LYS PHE PHE SER GLU ARG GLU SEQRES 10 A 342 ALA SER ALA VAL LEU PHE THR ILE THR LYS THR VAL GLU SEQRES 11 A 342 TYR LEU HIS ALA GLN GLY VAL VAL HIS ARG ASP LEU LYS SEQRES 12 A 342 PRO SER ASN ILE LEU TYR VAL ASP GLU SER GLY ASN PRO SEQRES 13 A 342 GLU SER ILE ARG ILE CYS ASP PHE GLY PHE ALA LYS GLN SEQRES 14 A 342 LEU ARG ALA GLU ASN GLY LEU LEU MET THR PRO CYS TYR SEQRES 15 A 342 THR ALA ASN PHE VAL ALA PRO GLU VAL LEU GLU ARG GLN SEQRES 16 A 342 GLY TYR ASP ALA ALA CYS ASP ILE TRP SER LEU GLY VAL SEQRES 17 A 342 LEU LEU TYR THR MET LEU THR GLY TYR THR PRO PHE ALA SEQRES 18 A 342 ASN GLY PRO ASP ASP THR PRO GLU GLU ILE LEU ALA ARG SEQRES 19 A 342 ILE GLY SER GLY LYS PHE SER LEU SER GLY GLY TYR TRP SEQRES 20 A 342 ASN SER VAL SER ASP THR ALA LYS ASP LEU VAL SER LYS SEQRES 21 A 342 MET LEU HIS VAL ASP PRO HIS GLN ARG LEU THR ALA ALA SEQRES 22 A 342 LEU VAL LEU ARG HIS PRO TRP ILE VAL HIS TRP ASP GLN SEQRES 23 A 342 LEU PRO GLN TYR GLN LEU ASN ARG GLN ASP ALA PRO HIS SEQRES 24 A 342 LEU VAL LYS GLY ALA MET ALA ALA THR TYR SER ALA LEU SEQRES 25 A 342 ASN ARG ASN GLN SER PRO VAL LEU GLU PRO VAL GLY ARG SEQRES 26 A 342 SER THR LEU ALA GLN ARG ARG GLY ILE LYS LYS ILE THR SEQRES 27 A 342 SER THR ALA LEU HET 0JH A 900 32 HET NA A 901 1 HETNAM 0JH TERT-BUTYL (2S)-3-[4-AMINO-7-(3-HYDROXYPROPYL)-5-(4- HETNAM 2 0JH METHYLPHENYL)-7H-PYRROLO[2,3-D]PYRIMIDIN-6-YL]-2- HETNAM 3 0JH CYANOPROPANOATE HETNAM NA SODIUM ION HETSYN 0JH (E)-TERT-BUTYL 3-(4-AMINO-7-(3-HYDROXYPROPYL)-5-P- HETSYN 2 0JH TOLYL-7H-PYRROLO[2,3-D]PYRIMIDIN-6-YL)-2- HETSYN 3 0JH CYANOACRYLATE, BOUND FORM FORMUL 2 0JH C24 H29 N5 O3 FORMUL 3 NA NA 1+ FORMUL 4 HOH *31(H2 O) HELIX 1 1 LEU A 411 SER A 415 5 5 HELIX 2 2 GLN A 417 GLY A 421 1 5 HELIX 3 3 PRO A 460 GLY A 471 1 12 HELIX 4 4 GLU A 500 ARG A 507 1 8 HELIX 5 5 SER A 512 GLN A 533 1 22 HELIX 6 6 LYS A 541 SER A 543 5 3 HELIX 7 7 ASN A 553 GLU A 555 5 3 HELIX 8 8 GLU A 588 GLY A 614 1 27 HELIX 9 9 THR A 625 GLY A 636 1 12 HELIX 10 10 GLY A 642 ASN A 646 5 5 HELIX 11 11 SER A 649 HIS A 661 1 13 HELIX 12 12 THR A 669 LEU A 674 1 6 HELIX 13 13 HIS A 676 HIS A 681 1 6 HELIX 14 14 TRP A 682 LEU A 685 5 4 HELIX 15 15 ALA A 695 ASN A 711 1 17 SHEET 1 A 5 TYR A 422 VAL A 430 0 SHEET 2 A 5 SER A 434 HIS A 441 -1 O CYS A 436 N ILE A 428 SHEET 3 A 5 GLU A 447 ASP A 454 -1 O ILE A 452 N VAL A 435 SHEET 4 A 5 TYR A 488 GLU A 494 -1 O VAL A 491 N LYS A 451 SHEET 5 A 5 LEU A 479 ASP A 484 -1 N LYS A 480 O VAL A 492 SHEET 1 B 2 VAL A 535 VAL A 536 0 SHEET 2 B 2 LYS A 566 GLN A 567 -1 O LYS A 566 N VAL A 536 SHEET 1 C 2 ILE A 545 TYR A 547 0 SHEET 2 C 2 ILE A 557 ILE A 559 -1 O ARG A 558 N LEU A 546 SSBOND 1 CYS A 579 CYS A 579 1555 7465 2.03 LINK SG CYS A 436 C11 0JH A 900 1555 1555 1.95 LINK O GLY A 471 NA NA A 901 1555 1555 2.40 LINK O HIS A 473 NA NA A 901 1555 1555 2.28 LINK O ILE A 476 NA NA A 901 1555 1555 2.31 LINK OG1 THR A 478 NA NA A 901 1555 1555 2.43 CISPEP 1 ASN A 583 PHE A 584 0 8.31 SITE 1 AC1 17 ILE A 428 GLY A 429 VAL A 430 GLY A 431 SITE 2 AC1 17 SER A 434 VAL A 435 CYS A 436 ALA A 449 SITE 3 AC1 17 LYS A 451 LEU A 467 ILE A 477 VAL A 491 SITE 4 AC1 17 THR A 493 GLU A 494 MET A 496 CYS A 560 SITE 5 AC1 17 ASP A 561 SITE 1 AC2 4 GLY A 471 HIS A 473 ILE A 476 THR A 478 CRYST1 46.700 46.700 293.000 90.00 90.00 90.00 P 41 21 2 8 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 0.021413 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021413 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003413 0.00000