HEADER APOPTOSIS 08-FEB-05 1YSN
TITLE SOLUTION STRUCTURE OF THE ANTI-APOPTOTIC PROTEIN BCL-XL COMPLEXED WITH
TITLE 2 AN ACYL-SULFONAMIDE-BASED LIGAND
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: APOPTOSIS REGULATOR BCL-X;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: BCL-2-LIKE 1 PROTEIN;
COMPND 5 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: BCL2L1, BCL2L, BCLX;
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: PET30B
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 29-NOV-23 1YSN 1 REMARK
REVDAT 4 02-MAR-22 1YSN 1 REMARK SEQADV
REVDAT 3 24-FEB-09 1YSN 1 VERSN
REVDAT 2 18-DEC-07 1YSN 1 REMARK
REVDAT 1 07-JUN-05 1YSN 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 1YSN 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_1000031885.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 303
REMARK 210 PH : 7.0
REMARK 210 IONIC STRENGTH : 50 MM
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : 1 MM BCL-XL U-15N,13C, 50 MM
REMARK 210 SODIUM PHOSPHATE, 5 MM
REMARK 210 DEUTERATED DITHIOTHREITOL, 100%
REMARK 210 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 GLY A 200 H ALA A 204 1.55
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 PHE A 101 CG PHE A 101 CD1 -0.776
REMARK 500 PHE A 101 CD1 PHE A 101 CE1 0.620
REMARK 500 GLU A 162 CD GLU A 162 OE2 0.110
REMARK 500 GLU A 183 CD GLU A 183 OE2 0.110
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 PHE A 101 CB - CG - CD1 ANGL. DEV. = -8.3 DEGREES
REMARK 500 PHE A 101 CD1 - CE1 - CZ ANGL. DEV. = -21.2 DEGREES
REMARK 500 GLU A 183 N - CA - CB ANGL. DEV. = 20.8 DEGREES
REMARK 500 ASP A 193 CB - CG - OD2 ANGL. DEV. = -5.5 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 MET A 3 156.89 171.16
REMARK 500 ALA A 4 -152.48 -139.66
REMARK 500 TYR A 26 -172.97 -67.98
REMARK 500 SER A 27 -89.61 176.05
REMARK 500 TRP A 28 140.04 62.67
REMARK 500 SER A 29 -158.78 -179.92
REMARK 500 SER A 32 -175.74 -171.04
REMARK 500 VAL A 34 -97.04 -143.62
REMARK 500 GLU A 35 118.63 170.53
REMARK 500 ARG A 38 154.23 176.22
REMARK 500 THR A 39 80.71 -176.50
REMARK 500 GLU A 40 -73.85 -159.13
REMARK 500 ALA A 41 99.07 179.89
REMARK 500 THR A 45 130.25 58.39
REMARK 500 SER A 47 -151.79 -91.47
REMARK 500 GLU A 48 50.23 -170.47
REMARK 500 ALA A 89 -149.52 -135.67
REMARK 500 LYS A 91 -72.23 -38.14
REMARK 500 ARG A 169 -73.57 -66.32
REMARK 500 HIS A 181 10.62 -143.40
REMARK 500 LEU A 182 -45.08 -148.68
REMARK 500 ASP A 193 -31.22 -35.82
REMARK 500 LEU A 198 -71.55 -118.88
REMARK 500 TYR A 199 53.20 -102.39
REMARK 500 ASN A 201 -85.21 -43.52
REMARK 500 ASN A 202 -33.90 -35.97
REMARK 500 HIS A 217 -72.50 -65.80
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 PHE A 101 0.09 SIDE CHAIN
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: 1LXL RELATED DB: PDB
REMARK 900 SOLUTION STRUCTURE OF THE SAME PROTEIN, UNCOMPLEXED
REMARK 900 RELATED ID: 1MAZ RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF THE SAME PROTEIN, UNCOMPLEXED
REMARK 900 RELATED ID: 1BXL RELATED DB: PDB
REMARK 900 SOLUTION STRUCTURE OF THE SAME PROTEIN COMPLEXED WITH THE BAK
REMARK 900 PEPTIDE
REMARK 900 RELATED ID: 1G5J RELATED DB: PDB
REMARK 900 SOLUTION STRUCTURE OF THE SAME PROTEIN COMPLEXED WITH THE BAD
REMARK 900 PEPTIDE
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: 1YSW 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 1YSN A 5 48 UNP Q07817 BCLX_HUMAN 1 44
DBREF 1YSN A 89 213 UNP Q07817 BCLX_HUMAN 85 209
SEQADV 1YSN MET A 1 UNP Q07817 CLONING ARTIFACT
SEQADV 1YSN SER A 2 UNP Q07817 CLONING ARTIFACT
SEQADV 1YSN MET A 3 UNP Q07817 CLONING ARTIFACT
SEQADV 1YSN ALA A 4 UNP Q07817 CLONING ARTIFACT
SEQADV 1YSN LEU A 214 UNP Q07817 CLONING ARTIFACT
SEQADV 1YSN GLU A 215 UNP Q07817 CLONING ARTIFACT
SEQADV 1YSN HIS A 216 UNP Q07817 CLONING ARTIFACT
SEQADV 1YSN HIS A 217 UNP Q07817 CLONING ARTIFACT
SEQADV 1YSN HIS A 218 UNP Q07817 CLONING ARTIFACT
SEQADV 1YSN HIS A 219 UNP Q07817 CLONING ARTIFACT
SEQADV 1YSN HIS A 220 UNP Q07817 CLONING ARTIFACT
SEQADV 1YSN HIS A 181 UNP Q07817 CLONING ARTIFACT
SEQRES 1 A 181 MET SER MET ALA MET SER GLN SER ASN ARG GLU LEU VAL
SEQRES 2 A 181 VAL ASP PHE LEU SER TYR LYS LEU SER GLN LYS GLY TYR
SEQRES 3 A 181 SER TRP SER GLN PHE SER ASP VAL GLU GLU ASN ARG THR
SEQRES 4 A 181 GLU ALA PRO GLU GLY THR GLU SER GLU ALA VAL LYS GLN
SEQRES 5 A 181 ALA LEU ARG GLU ALA GLY ASP GLU PHE GLU LEU ARG TYR
SEQRES 6 A 181 ARG ARG ALA PHE SER ASP LEU THR SER GLN LEU HIS ILE
SEQRES 7 A 181 THR PRO GLY THR ALA TYR GLN SER PHE GLU GLN VAL VAL
SEQRES 8 A 181 ASN GLU LEU PHE ARG ASP GLY VAL ASN TRP GLY ARG ILE
SEQRES 9 A 181 VAL ALA PHE PHE SER PHE GLY GLY ALA LEU CYS VAL GLU
SEQRES 10 A 181 SER VAL ASP LYS GLU MET GLN VAL LEU VAL SER ARG ILE
SEQRES 11 A 181 ALA ALA TRP MET ALA THR TYR LEU ASN ASP HIS LEU GLU
SEQRES 12 A 181 PRO TRP ILE GLN GLU ASN GLY GLY TRP ASP THR PHE VAL
SEQRES 13 A 181 GLU LEU TYR GLY ASN ASN ALA ALA ALA GLU SER ARG LYS
SEQRES 14 A 181 GLY GLN GLU ARG LEU GLU HIS HIS HIS HIS HIS HIS
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 GLN A 7 GLN A 23 1 17
HELIX 2 2 ALA A 89 TYR A 105 1 17
HELIX 3 3 TYR A 105 SER A 114 1 10
HELIX 4 4 ALA A 123 LEU A 134 1 12
HELIX 5 5 ASN A 140 LYS A 161 1 22
HELIX 6 6 GLN A 164 LEU A 178 1 15
HELIX 7 7 LEU A 182 GLN A 187 1 6
HELIX 8 8 GLY A 190 VAL A 196 1 7
HELIX 9 9 GLY A 200 HIS A 221 1 22
SITE 1 AC1 18 ALA A 97 GLU A 100 ARG A 104 TYR A 105
SITE 2 AC1 18 ALA A 108 LEU A 112 GLN A 115 VAL A 130
SITE 3 AC1 18 GLU A 133 LEU A 134 ASN A 140 TRP A 141
SITE 4 AC1 18 GLY A 142 ARG A 143 VAL A 145 ALA A 146
SITE 5 AC1 18 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