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