HEADER APOPTOSIS 09-FEB-05 1YSW TITLE SOLUTION STRUCTURE OF THE ANTI-APOPTOTIC PROTEIN BCL-2 COMPLEXED WITH TITLE 2 AN ACYL-SULFONAMIDE-BASED LIGAND COMPND MOL_ID: 1; COMPND 2 MOLECULE: APOPTOSIS REGULATOR BCL-2; COMPND 3 CHAIN: A; COMPND 4 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: BCL2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); 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: PET28B KEYWDS COMPLEX, APOPTOSIS EXPDTA SOLUTION NMR AUTHOR T.OLTERSDORF,S.W.ELMORE,A.R.SHOEMAKER,R.C.ARMSTRONG,D.J.AUGERI, AUTHOR 2 B.A.BELLI,M.BRUNCKO,T.L.DECKWERTH,J.DINGES,P.J.HAJDUK,M.K.JOSEPH, AUTHOR 3 S.KITADA,S.J.KORSMEYER,A.R.KUNZER,A.LETAI,C.LI,M.J.MITTEN, AUTHOR 4 D.G.NETTESHEIM,S.NG,P.M.NIMMER,J.M.O'CONNOR,A.OLEKSIJEW,A.M.PETROS, AUTHOR 5 J.C.REED,W.SHEN,S.K.TAHIR,C.B.THOMPSON,K.J.TOMASELLI,B.WANG, AUTHOR 6 M.D.WENDT,H.ZHANG,S.W.FESIK,S.H.ROSENBERG REVDAT 5 22-MAY-24 1YSW 1 REMARK REVDAT 4 02-MAR-22 1YSW 1 REMARK SEQADV REVDAT 3 17-NOV-09 1YSW 1 REMARK TITLE REVDAT 2 24-FEB-09 1YSW 1 VERSN REVDAT 1 07-JUN-05 1YSW 0 JRNL AUTH T.OLTERSDORF,S.W.ELMORE,A.R.SHOEMAKER,R.C.ARMSTRONG, JRNL AUTH 2 D.J.AUGERI,B.A.BELLI,M.BRUNCKO,T.L.DECKWERTH,J.DINGES, JRNL AUTH 3 P.J.HAJDUK,M.K.JOSEPH,S.KITADA,S.J.KORSMEYER,A.R.KUNZER, JRNL AUTH 4 A.LETAI,C.LI,M.J.MITTEN,D.G.NETTESHEIM,S.NG,P.M.NIMMER, JRNL AUTH 5 J.M.O'CONNOR,A.OLEKSIJEW,A.M.PETROS,J.C.REED,W.SHEN, JRNL AUTH 6 S.K.TAHIR,C.B.THOMPSON,K.J.TOMASELLI,B.WANG,M.D.WENDT, JRNL AUTH 7 H.ZHANG,S.W.FESIK,S.H.ROSENBERG JRNL TITL AN INHIBITOR OF BCL-2 FAMILY PROTEINS INDUCES REGRESSION OF JRNL TITL 2 SOLID TUMOURS JRNL REF NATURE V. 435 677 2005 JRNL REFN ISSN 0028-0836 JRNL PMID 15902208 JRNL DOI 10.1038/NATURE03579 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1YSW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-MAR-05. REMARK 100 THE DEPOSITION ID IS D_1000031892. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 8.0 REMARK 210 IONIC STRENGTH : 25 MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM BCL-2 U-15N,13C, 25 MM REMARK 210 DEUTERATED TRIS, 1 MM DEUTERATED REMARK 210 DITHIOTHREITOL, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_13C REMARK 210 -EDITED_12C-FILTERED_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 : NULL 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: 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 O HIS A 181 OG1 THR A 184 1.81 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 TYR A 7 CE2 TYR A 7 CD2 -0.341 REMARK 500 TYR A 16 CZ TYR A 16 CE2 -0.158 REMARK 500 THR A 184 CB THR A 184 OG1 0.524 REMARK 500 GLY A 200 C GLY A 200 O 0.851 REMARK 500 GLY A 200 C PRO A 201 N -0.247 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 TYR A 7 CG - CD2 - CE2 ANGL. DEV. = -40.1 DEGREES REMARK 500 TYR A 7 OH - CZ - CE2 ANGL. DEV. = 36.7 DEGREES REMARK 500 TYR A 7 CE1 - CZ - CE2 ANGL. DEV. = -37.1 DEGREES REMARK 500 TYR A 7 CZ - CE2 - CD2 ANGL. DEV. = 38.4 DEGREES REMARK 500 TYR A 16 CG - CD2 - CE2 ANGL. DEV. = -34.3 DEGREES REMARK 500 TYR A 16 OH - CZ - CE2 ANGL. DEV. = 27.5 DEGREES REMARK 500 TYR A 16 CE1 - CZ - CE2 ANGL. DEV. = -34.0 DEGREES REMARK 500 TYR A 16 CZ - CE2 - CD2 ANGL. DEV. = 19.2 DEGREES REMARK 500 THR A 184 CA - CB - OG1 ANGL. DEV. = -23.4 DEGREES REMARK 500 GLY A 200 N - CA - C ANGL. DEV. = 31.7 DEGREES REMARK 500 GLY A 200 CA - C - O ANGL. DEV. = -38.3 DEGREES REMARK 500 GLY A 200 CA - C - N ANGL. DEV. = 29.3 DEGREES REMARK 500 GLY A 200 O - C - N ANGL. DEV. = -37.1 DEGREES REMARK 500 PRO A 201 C - N - CA ANGL. DEV. = 33.8 DEGREES REMARK 500 PRO A 201 C - N - CD ANGL. DEV. = -40.5 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 ALA A 2 76.36 -166.09 REMARK 500 ALA A 30 -77.71 -73.52 REMARK 500 GLU A 36 87.68 59.74 REMARK 500 THR A 39 -66.84 69.84 REMARK 500 GLU A 40 32.90 -149.64 REMARK 500 ALA A 41 152.57 67.44 REMARK 500 ARG A 107 35.06 -164.97 REMARK 500 ASP A 108 -70.35 -127.29 REMARK 500 HIS A 117 -168.28 73.36 REMARK 500 THR A 119 144.66 177.49 REMARK 500 ARG A 161 -79.43 -91.14 REMARK 500 GLU A 162 39.61 179.50 REMARK 500 HIS A 181 -67.27 -134.30 REMARK 500 TYR A 199 60.46 -111.27 REMARK 500 PRO A 201 173.47 -11.26 REMARK 500 MET A 203 -80.93 64.26 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 200 PRO A 201 -116.18 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 TYR A 16 0.14 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 GLY A 200 104.76 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 43B A 1000 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1G5M RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF SAME PROTEIN, ISOFORM 1, UNCOMPLEXED REMARK 900 RELATED ID: 1GJH RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF SAME PROTEIN, ISOFORM 2, UNCOMPLEXED REMARK 900 RELATED ID: 1YSG RELATED DB: PDB REMARK 900 RELATED ID: 1YSI RELATED DB: PDB REMARK 900 RELATED ID: 1YSX RELATED DB: PDB REMARK 900 RELATED ID: 1YSN RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 RESIDUES 49-88 (SEQUENCE DATABASE RESIDUES 45-84) REMARK 999 ARE NOT PRESENT DUE TO A LOOP DELETION. DBREF 1YSW A 1 32 UNP P10415 BCL2_HUMAN 3 34 DBREF 1YSW A 89 203 UNP P10415 BCL2_HUMAN 91 205 SEQADV 1YSW ASP A 32 UNP P10415 INSERTION SEQADV 1YSW ASP A 33 UNP P10415 INSERTION SEQADV 1YSW VAL A 34 UNP P10415 INSERTION SEQADV 1YSW GLU A 35 UNP P10415 INSERTION SEQADV 1YSW GLU A 36 UNP P10415 INSERTION SEQADV 1YSW ASN A 37 UNP P10415 INSERTION SEQADV 1YSW ARG A 38 UNP P10415 INSERTION SEQADV 1YSW THR A 39 UNP P10415 INSERTION SEQADV 1YSW GLU A 40 UNP P10415 INSERTION SEQADV 1YSW ALA A 41 UNP P10415 INSERTION SEQADV 1YSW PRO A 42 UNP P10415 INSERTION SEQADV 1YSW GLU A 43 UNP P10415 INSERTION SEQADV 1YSW GLY A 44 UNP P10415 INSERTION SEQADV 1YSW THR A 45 UNP P10415 INSERTION SEQADV 1YSW GLU A 46 UNP P10415 INSERTION SEQADV 1YSW SER A 47 UNP P10415 INSERTION SEQADV 1YSW GLU A 48 UNP P10415 INSERTION SEQRES 1 A 164 HIS ALA GLY ARG THR GLY TYR ASP ASN ARG GLU ILE VAL SEQRES 2 A 164 MET LYS TYR ILE HIS TYR LYS LEU SER GLN ARG GLY TYR SEQRES 3 A 164 GLU TRP ASP ALA GLY ASP ASP VAL GLU GLU ASN ARG THR SEQRES 4 A 164 GLU ALA PRO GLU GLY THR GLU SER GLU VAL VAL HIS LEU SEQRES 5 A 164 THR LEU ARG GLN ALA GLY ASP ASP PHE SER ARG ARG TYR SEQRES 6 A 164 ARG ARG ASP PHE ALA GLU MET SER SER GLN LEU HIS LEU SEQRES 7 A 164 THR PRO PHE THR ALA ARG GLY ARG PHE ALA THR VAL VAL SEQRES 8 A 164 GLU GLU LEU PHE ARG ASP GLY VAL ASN TRP GLY ARG ILE SEQRES 9 A 164 VAL ALA PHE PHE GLU PHE GLY GLY VAL MET CYS VAL GLU SEQRES 10 A 164 SER VAL ASN ARG GLU MET SER PRO LEU VAL ASP ASN ILE SEQRES 11 A 164 ALA LEU TRP MET THR GLU TYR LEU ASN ARG HIS LEU HIS SEQRES 12 A 164 THR TRP ILE GLN ASP ASN GLY GLY TRP ASP ALA PHE VAL SEQRES 13 A 164 GLU LEU TYR GLY PRO SER MET ARG HET 43B A1000 78 HETNAM 43B 3-NITRO-N-{4-[2-(2-PHENYLETHYL)-1,3-BENZOTHIAZOL-5- HETNAM 2 43B YL]BENZOYL}-4-{[2-(PHENYLSULFANYL) HETNAM 3 43B ETHYL]AMINO}BENZENESULFONAMIDE FORMUL 2 43B C36 H30 N4 O5 S3 HELIX 1 1 ASP A 8 GLN A 23 1 16 HELIX 2 2 GLY A 44 TYR A 105 1 22 HELIX 3 3 ASP A 108 HIS A 117 1 10 HELIX 4 4 THR A 119 PHE A 135 1 17 HELIX 5 5 ASN A 140 GLU A 162 1 23 HELIX 6 6 PRO A 165 HIS A 181 1 17 HELIX 7 7 HIS A 181 ASN A 189 1 9 HELIX 8 8 GLY A 191 TYR A 199 1 9 SITE 1 AC1 15 ALA A 97 ASP A 100 PHE A 101 TYR A 105 SITE 2 AC1 15 PHE A 109 MET A 112 GLU A 133 LEU A 134 SITE 3 AC1 15 TRP A 141 GLY A 142 VAL A 145 ALA A 146 SITE 4 AC1 15 PHE A 150 PHE A 195 TYR A 199 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