PDB Short entry for 1TFT HEADER APOPTOSIS 27-MAY-04 1TFT TITLE NMR STRUCTURE OF AN ANTAGONISTS OF THE XIAP-CASPASE-9 INTERACTION TITLE 2 COMPLEXED TO THE BIR3 DOMAIN OF XIAP COMPND MOL_ID: 1; COMPND 2 MOLECULE: BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: BIR3 OF XIAP: RESIDUES 241-356; COMPND 5 SYNONYM: INHIBITOR OF APOPTOSIS PROTEIN 3, X-LINKED INHIBITOR OF COMPND 6 APOPTOSIS PROTEIN, X-LINKED IAP, IAP-LIKE PROTEIN, HILP; COMPND 7 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: BIRC4, API3, IAP3, XIAP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28B KEYWDS COMPLEX, LIGAND-PROTEIN, APOPTOSIS, BIR, XIAP EXPDTA SOLUTION NMR MDLTYP MINIMIZED AVERAGE AUTHOR T.K.OOST,C.SUN,R.C.ARMSTRONG,A.S.AL-ASSAAD,S.F.BETZ,T.L.DECKWERTH, AUTHOR 2 S.W.ELMORE,R.P.MEADOWS,E.T.OLEJNICZAK,A.K.OLEKSIJEW,T.OLTERSDORF, AUTHOR 3 S.H.ROSENBERG,A.R.SHOEMAKER,H.ZOU,S.W.FESIK REVDAT 3 02-MAR-22 1TFT 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 1TFT 1 VERSN REVDAT 1 03-MAY-05 1TFT 0 JRNL AUTH T.K.OOST,C.SUN,R.C.ARMSTRONG,A.S.AL-ASSAAD,S.F.BETZ, JRNL AUTH 2 T.L.DECKWERTH,H.DING,S.W.ELMORE,R.P.MEADOWS,E.T.OLEJNICZAK, JRNL AUTH 3 A.K.OLEKSIJEW,T.OLTERSDORF,S.H.ROSENBERG,A.R.SHOEMAKER, JRNL AUTH 4 K.J.TOMASELLI,H.ZOU,S.W.FESIK JRNL TITL DISCOVERY OF POTENT ANTAGONISTS OF THE ANTIAPOPTOTIC PROTEIN JRNL TITL 2 XIAP FOR THE TREATMENT OF CANCER. JRNL REF J.MED.CHEM. V. 47 4417 2004 JRNL REFN ISSN 0022-2623 JRNL PMID 15317454 JRNL DOI 10.1021/JM040037K REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 2000 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1TFT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-JUN-04. REMARK 100 THE DEPOSITION ID IS D_1000022610. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 7.2 REMARK 210 IONIC STRENGTH : 20MM TRIS REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : U-15N, 0.8MM BIR3,20MM TRIS, REMARK 210 2MMDTT; U-15N,13C 0.8MM BIR3, REMARK 210 20MM TRIS, 2MMDTT REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY; 2D_13C,15N REMARK 210 FILTERED NOESY; 2D_13C,15N REMARK 210 FILTERED TOCSY; 3D_13C,15N REMARK 210 FILTERED ,13C SEPARATED NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL 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 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 ALA A 243 84.17 62.11 REMARK 500 VAL A 244 46.56 -102.47 REMARK 500 SER A 245 -64.61 -171.59 REMARK 500 ASP A 247 -57.18 -164.21 REMARK 500 PHE A 250 72.29 56.83 REMARK 500 ASN A 252 -66.87 -157.98 REMARK 500 SER A 253 -62.70 -177.83 REMARK 500 ASN A 255 99.24 -58.74 REMARK 500 ARG A 258 -62.21 -170.45 REMARK 500 ASN A 259 75.30 58.52 REMARK 500 MET A 262 -50.50 -167.43 REMARK 500 ASP A 264 -62.25 -137.76 REMARK 500 TYR A 277 -50.81 -152.62 REMARK 500 SER A 278 -78.36 -132.92 REMARK 500 ASP A 296 -49.43 83.14 REMARK 500 LYS A 297 101.16 -57.47 REMARK 500 HIS A 302 -66.75 70.74 REMARK 500 TYR A 324 84.72 -157.15 REMARK 500 LEU A 344 -49.29 -167.45 REMARK 500 LEU A 348 176.62 59.67 REMARK 500 GLU A 349 75.62 60.56 REMARK 500 CYS A 351 81.67 59.60 REMARK 500 VAL A 353 -67.41 71.78 REMARK 500 ARG A 354 48.19 -169.93 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 ZN A 999 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 300 SG REMARK 620 2 CYS A 303 SG 108.7 REMARK 620 3 HIS A 320 ND1 110.1 109.9 REMARK 620 4 CYS A 327 SG 109.2 110.0 109.0 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 ZN A 999 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 997 A 998 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1TFQ RELATED DB: PDB REMARK 900 ANOTHER ANTAGONIST/BIR3 COMPLEX STRUCTURE REMARK 900 RELATED ID: 1G3F RELATED DB: PDB REMARK 900 SMAC PEPTIDE/BIR3 COMPLEX STRUCTURE DBREF 1TFT A 241 356 UNP P98170 BIRC4_HUMAN 241 356 SEQADV 1TFT MET A 240 UNP P98170 INITIATING METHIONINE SEQRES 1 A 117 MET SER ASP ALA VAL SER SER ASP ARG ASN PHE PRO ASN SEQRES 2 A 117 SER THR ASN LEU PRO ARG ASN PRO SER MET ALA ASP TYR SEQRES 3 A 117 GLU ALA ARG ILE PHE THR PHE GLY THR TRP ILE TYR SER SEQRES 4 A 117 VAL ASN LYS GLU GLN LEU ALA ARG ALA GLY PHE TYR ALA SEQRES 5 A 117 LEU GLY GLU GLY ASP LYS VAL LYS CYS PHE HIS CYS GLY SEQRES 6 A 117 GLY GLY LEU THR ASP TRP LYS PRO SER GLU ASP PRO TRP SEQRES 7 A 117 GLU GLN HIS ALA LYS TRP TYR PRO GLY CYS LYS TYR LEU SEQRES 8 A 117 LEU GLU GLN LYS GLY GLN GLU TYR ILE ASN ASN ILE HIS SEQRES 9 A 117 LEU THR HIS SER LEU GLU GLU CYS LEU VAL ARG THR THR HET ZN A 999 1 HET 997 A 998 81 HETNAM ZN ZINC ION HETNAM 997 1-[3,3-DIMETHYL-2-(2-METHYLAMINO-PROPIONYLAMINO)- HETNAM 2 997 BUTYRYL]-4-PHENOXY-PYRROLIDINE-2-CARBOXYLIC ACID(1,2, HETNAM 3 997 3,4-TETRAHYDRO-NAPHTHALEN-1-YL)-AMIDE HETSYN 997 N-METHYLALANYL-3-METHYLVALYL-4-PHENOXY-N-(1,2,3,4- HETSYN 2 997 TETRAHYDRONAPHTHALEN-1-YL)PROLINAMIDE FORMUL 2 ZN ZN 2+ FORMUL 3 997 C31 H42 N4 O4 HELIX 1 1 ASP A 264 GLY A 273 1 10 HELIX 2 2 ASN A 280 GLY A 288 1 9 HELIX 3 3 ASP A 315 TYR A 324 1 10 HELIX 4 4 CYS A 327 LYS A 334 1 8 HELIX 5 5 LYS A 334 HIS A 343 1 10 SHEET 1 A 3 PHE A 289 ALA A 291 0 SHEET 2 A 3 VAL A 298 CYS A 300 -1 O LYS A 299 N TYR A 290 SHEET 3 A 3 GLY A 306 LEU A 307 -1 O LEU A 307 N VAL A 298 LINK SG CYS A 300 ZN ZN A 999 1555 1555 2.10 LINK SG CYS A 303 ZN ZN A 999 1555 1555 2.10 LINK ND1 HIS A 320 ZN ZN A 999 1555 1555 2.21 LINK SG CYS A 327 ZN ZN A 999 1555 1555 2.10 SITE 1 AC1 4 CYS A 300 CYS A 303 HIS A 320 CYS A 327 SITE 1 AC2 11 LYS A 297 LYS A 299 GLY A 306 LEU A 307 SITE 2 AC2 11 THR A 308 ASP A 309 LYS A 311 GLU A 314 SITE 3 AC2 11 GLN A 319 TRP A 323 TYR A 324 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