PDB Short entry for 2K7Z HEADER HYDROLASE 28-AUG-08 2K7Z TITLE SOLUTION STRUCTURE OF THE CATALYTIC DOMAIN OF PROCASPASE-8 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CASPASE-8; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 213-479; COMPND 5 SYNONYM: CASP-8, ICE-LIKE APOPTOTIC PROTEASE 5, MORT1-ASSOCIATED CED- COMPND 6 3 HOMOLOG, MACH, FADD-HOMOLOGOUS ICE/CED-3-LIKE PROTEASE, FADD-LIKE COMPND 7 ICE, FLICE, APOPTOTIC CYSTEINE PROTEASE, APOPTOTIC PROTEASE MCH-5, COMPND 8 CAP4; COMPND 9 EC: 3.4.22.61; COMPND 10 ENGINEERED: YES; COMPND 11 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CASP8, MCH5; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PQE-50 KEYWDS CASPASE, APOPTOSIS, INITIATOR CASPASE, PROCASPASE, CYTOPLASM, KEYWDS 2 HYDROLASE, PROTEASE, THIOL PROTEASE, ZYMOGEN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR N.KELLER,O.ZERBE,J.MARES,M.G.GRUETTER REVDAT 4 14-JUN-23 2K7Z 1 REMARK REVDAT 3 20-OCT-21 2K7Z 1 SEQADV REVDAT 2 19-FEB-20 2K7Z 1 REMARK SEQADV REVDAT 1 24-MAR-09 2K7Z 0 JRNL AUTH N.KELLER,J.MARES,O.ZERBE,M.G.GRUTTER JRNL TITL STRUCTURAL AND BIOCHEMICAL STUDIES ON PROCASPASE-8: NEW JRNL TITL 2 INSIGHTS ON INITIATOR CASPASE ACTIVATION. JRNL REF STRUCTURE V. 17 438 2009 JRNL REFN ISSN 0969-2126 JRNL PMID 19278658 JRNL DOI 10.1016/J.STR.2008.12.019 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 6.0, CYANA 2.2 REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO AND KOLLM (AMBER), GUNTERT, MUMENTHALER REMARK 3 AND WUTHRICH (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: RESTRAINT MD IN EXPLICIT WATER USING REMARK 3 AMBER 6.0 REMARK 4 REMARK 4 2K7Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-AUG-08. REMARK 100 THE DEPOSITION ID IS D_1000100790. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 305 REMARK 210 PH : 8.0 REMARK 210 IONIC STRENGTH : 0.1 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.8 MM [U-99% 13C; U-99% 15N] REMARK 210 PROCASPASE8, 10 MM DTT, 100 MM REMARK 210 SODIUM CHLORIDE, 20 MM [U-2H] REMARK 210 TRIS, 90% H2O/10% D2O; 0.8 MM [U- REMARK 210 100% 13C; U-100% 15N; 80% 2H] REMARK 210 PROCASPASE8, 10 MM DTT, 100 MM REMARK 210 SODIUM CHLORIDE, 20 MM [U-2H] REMARK 210 TRIS, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCACB; 3D HN(COCA)CB; 3D REMARK 210 HNCO; 3D HN(CA)CO; 3D HN(CO)CG; REMARK 210 3D HNCG; 3D HCCH-COSY; 3D 1H-15N REMARK 210 NOESY; 3D 1H-13C NOESY; HN(CACO) REMARK 210 NH; 3D HCCH-TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 2.2, XEASY 1.55, CARA REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 MET A 214 REMARK 465 ARG A 215 REMARK 465 GLY A 216 REMARK 465 SER A 217 REMARK 465 GLU A 218 REMARK 465 SER A 219 REMARK 465 GLN A 220 REMARK 465 THR A 221 REMARK 465 LEU A 222 REMARK 465 ASP A 223 REMARK 465 THR A 405 REMARK 465 VAL A 406 REMARK 465 ASN A 407 REMARK 465 ASN A 408 REMARK 465 CYS A 409 REMARK 465 VAL A 410 REMARK 465 SER A 411 REMARK 465 TYR A 412 REMARK 465 ARG A 413 REMARK 465 ASN A 414 REMARK 465 ASN A 447 REMARK 465 TYR A 448 REMARK 465 GLU A 449 REMARK 465 VAL A 450 REMARK 465 SER A 451 REMARK 465 ASN A 452 REMARK 465 LYS A 453 REMARK 465 ASP A 454 REMARK 465 ASP A 455 REMARK 465 LYS A 456 REMARK 465 LYS A 457 REMARK 465 ASN A 458 REMARK 465 MET A 459 REMARK 465 GLY A 460 REMARK 465 LYS A 461 REMARK 465 GLN A 462 REMARK 465 MET A 463 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 HG1 THR A 373 OE2 GLU A 376 1.36 REMARK 500 O TYR A 334 HG SER A 338 1.57 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 5 ARG A 432 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 5 ARG A 432 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 18 TYR A 380 CB - CG - CD2 ANGL. DEV. = -3.7 DEGREES REMARK 500 18 ARG A 430 NE - CZ - NH1 ANGL. DEV. = 3.2 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 1 LYS A 229 93.38 -56.78 REMARK 500 1 ASN A 240 43.94 -81.34 REMARK 500 1 THR A 263 -65.54 -91.71 REMARK 500 1 ASP A 285 -167.79 -72.54 REMARK 500 1 ASP A 286 93.60 -57.53 REMARK 500 1 LYS A 320 99.30 61.68 REMARK 500 1 CYS A 345 77.76 -154.11 REMARK 500 1 PRO A 346 79.78 -69.52 REMARK 500 1 ASP A 374 -64.18 -125.80 REMARK 500 1 GLN A 378 -58.47 -121.85 REMARK 500 1 TYR A 380 -176.93 -64.93 REMARK 500 1 SER A 387 163.52 71.32 REMARK 500 1 ASP A 395 21.17 48.45 REMARK 500 1 GLN A 423 101.25 -54.27 REMARK 500 1 SER A 424 7.86 57.70 REMARK 500 1 GLN A 465 63.99 -114.50 REMARK 500 1 PHE A 476 77.78 -113.10 REMARK 500 2 TYR A 226 12.93 48.05 REMARK 500 2 MET A 228 93.11 -65.41 REMARK 500 2 VAL A 251 78.16 -118.91 REMARK 500 2 ARG A 260 -74.14 -110.56 REMARK 500 2 THR A 263 -75.83 -77.88 REMARK 500 2 LYS A 282 78.63 -115.36 REMARK 500 2 SER A 305 7.93 59.26 REMARK 500 2 ALA A 331 160.39 60.16 REMARK 500 2 CYS A 345 73.69 -154.37 REMARK 500 2 GLU A 372 -63.91 -94.91 REMARK 500 2 SER A 375 88.13 -48.36 REMARK 500 2 GLU A 377 -72.48 -59.22 REMARK 500 2 GLN A 378 -65.40 -126.22 REMARK 500 2 TYR A 380 -178.36 -65.09 REMARK 500 2 SER A 387 161.65 62.56 REMARK 500 2 ILE A 393 84.45 -158.41 REMARK 500 2 GLN A 465 -62.69 174.43 REMARK 500 3 TYR A 226 10.71 51.06 REMARK 500 3 LYS A 229 59.12 -105.20 REMARK 500 3 SER A 230 13.52 58.32 REMARK 500 3 PHE A 244 3.61 -150.28 REMARK 500 3 ASP A 259 79.00 -63.23 REMARK 500 3 ASN A 261 94.36 -64.02 REMARK 500 3 HIS A 278 34.41 72.36 REMARK 500 3 LYS A 282 80.08 57.37 REMARK 500 3 PRO A 283 88.81 -68.59 REMARK 500 3 ASP A 286 109.53 -54.13 REMARK 500 3 CYS A 312 76.84 -117.90 REMARK 500 3 TYR A 324 37.40 -70.86 REMARK 500 3 LEU A 336 -81.68 -82.60 REMARK 500 3 CYS A 345 80.09 -154.33 REMARK 500 3 PRO A 346 78.24 -69.11 REMARK 500 3 SER A 347 -36.35 -131.61 REMARK 500 REMARK 500 THIS ENTRY HAS 373 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 5 TYR A 421 0.07 SIDE CHAIN REMARK 500 8 TYR A 380 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 15932 RELATED DB: BMRB DBREF 2K7Z A 217 479 UNP Q14790 CASP8_HUMAN 217 479 SEQADV 2K7Z MET A 214 UNP Q14790 EXPRESSION TAG SEQADV 2K7Z ARG A 215 UNP Q14790 EXPRESSION TAG SEQADV 2K7Z GLY A 216 UNP Q14790 EXPRESSION TAG SEQADV 2K7Z ALA A 360 UNP Q14790 CYS 360 ENGINEERED MUTATION SEQRES 1 A 266 MET ARG GLY SER GLU SER GLN THR LEU ASP LYS VAL TYR SEQRES 2 A 266 GLN MET LYS SER LYS PRO ARG GLY TYR CYS LEU ILE ILE SEQRES 3 A 266 ASN ASN HIS ASN PHE ALA LYS ALA ARG GLU LYS VAL PRO SEQRES 4 A 266 LYS LEU HIS SER ILE ARG ASP ARG ASN GLY THR HIS LEU SEQRES 5 A 266 ASP ALA GLY ALA LEU THR THR THR PHE GLU GLU LEU HIS SEQRES 6 A 266 PHE GLU ILE LYS PRO HIS ASP ASP CYS THR VAL GLU GLN SEQRES 7 A 266 ILE TYR GLU ILE LEU LYS ILE TYR GLN LEU MET ASP HIS SEQRES 8 A 266 SER ASN MET ASP CYS PHE ILE CYS CYS ILE LEU SER HIS SEQRES 9 A 266 GLY ASP LYS GLY ILE ILE TYR GLY THR ASP GLY GLN GLU SEQRES 10 A 266 ALA PRO ILE TYR GLU LEU THR SER GLN PHE THR GLY LEU SEQRES 11 A 266 LYS CYS PRO SER LEU ALA GLY LYS PRO LYS VAL PHE PHE SEQRES 12 A 266 ILE GLN ALA ALA GLN GLY ASP ASN TYR GLN LYS GLY ILE SEQRES 13 A 266 PRO VAL GLU THR ASP SER GLU GLU GLN PRO TYR LEU GLU SEQRES 14 A 266 MET ASP LEU SER SER PRO GLN THR ARG TYR ILE PRO ASP SEQRES 15 A 266 GLU ALA ASP PHE LEU LEU GLY MET ALA THR VAL ASN ASN SEQRES 16 A 266 CYS VAL SER TYR ARG ASN PRO ALA GLU GLY THR TRP TYR SEQRES 17 A 266 ILE GLN SER LEU CYS GLN SER LEU ARG GLU ARG CYS PRO SEQRES 18 A 266 ARG GLY ASP ASP ILE LEU THR ILE LEU THR GLU VAL ASN SEQRES 19 A 266 TYR GLU VAL SER ASN LYS ASP ASP LYS LYS ASN MET GLY SEQRES 20 A 266 LYS GLN MET PRO GLN PRO THR PHE THR LEU ARG LYS LYS SEQRES 21 A 266 LEU VAL PHE PRO SER ASP HELIX 1 1 VAL A 251 HIS A 255 5 5 HELIX 2 2 HIS A 264 GLU A 276 1 13 HELIX 3 3 THR A 288 LYS A 297 1 10 HELIX 4 4 LYS A 297 ASP A 303 1 7 HELIX 5 5 PRO A 332 THR A 337 1 6 HELIX 6 6 SER A 338 THR A 341 5 4 HELIX 7 7 SER A 347 LYS A 351 5 5 HELIX 8 8 SER A 424 CYS A 433 1 10 SHEET 1 A 5 GLU A 280 HIS A 284 0 SHEET 2 A 5 TYR A 235 ILE A 239 1 N CYS A 236 O LYS A 282 SHEET 3 A 5 ILE A 311 CYS A 313 1 O ILE A 311 N LEU A 237 SHEET 4 A 5 VAL A 354 PHE A 356 1 O VAL A 354 N CYS A 312 SHEET 5 A 5 LEU A 400 LEU A 401 1 O LEU A 400 N PHE A 355 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000