PDB Short entry for 1ZY3 HEADER APOPTOSIS 09-JUN-05 1ZY3 TITLE STRUCTURAL MODEL OF COMPLEX OF BCL-W PROTEIN WITH BID BH3-PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: APOPTOSIS REGULATOR BCL-W; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 2-171; COMPND 5 SYNONYM: BCL-2-LIKE 2 PROTEIN; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: BH3-PEPTIDE FROM BH3 INTERACTING DOMAIN DEATH AGONIST COMPND 10 PROTEIN; COMPND 11 CHAIN: B; COMPND 12 SYNONYM: BID; COMPND 13 ENGINEERED: YES; COMPND 14 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-29B+; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 16 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 17 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 18 EXPRESSION_SYSTEM_PLASMID: PGEX-6P-1 KEYWDS APOPTOSIS, BCL-W, BH3-PEPTIDE EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR A.Y.DENISOV,K.GEHRING REVDAT 4 20-OCT-21 1ZY3 1 REMARK SEQADV REVDAT 3 24-FEB-09 1ZY3 1 VERSN REVDAT 2 28-FEB-06 1ZY3 1 JRNL REVDAT 1 14-FEB-06 1ZY3 0 JRNL AUTH A.Y.DENISOV,G.CHEN,T.SPRULES,T.MOLDOVEANU,P.BEAUPARLANT, JRNL AUTH 2 K.GEHRING JRNL TITL STRUCTURAL MODEL OF THE BCL-W-BID PEPTIDE COMPLEX AND ITS JRNL TITL 2 INTERACTIONS WITH PHOSPHOLIPID MICELLES. JRNL REF BIOCHEMISTRY V. 45 2250 2006 JRNL REFN ISSN 0006-2960 JRNL PMID 16475813 JRNL DOI 10.1021/BI052332S REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : HADDOCK 1.2 REMARK 3 AUTHORS : BONVIN ET AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 200 CONFORMERS WERE OBTAINED IN THE REMARK 3 RIGID BODY DOCKING AND 100 BEST CONFORMERS WERE SELECTED FOR REMARK 3 SEMI-FLEXIBLE SIMULATED ANNEALING FOLLOWING BY REFINEMENT REMARK 4 REMARK 4 1ZY3 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-JUN-05. REMARK 100 THE DEPOSITION ID IS D_1000033254. 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 : 10 MM NACL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.7 MM BCL-W U-15N,13C, 0.7 MM REMARK 210 BID BH3-PEPTIDE, 20 MM PHOSPHATE REMARK 210 BUFFER, 90% H2O, 10% D2O; 0.7 MM REMARK 210 BCL-W U-15N, 0.7 MM BID BH3- REMARK 210 PEPTIDE, 20 MM PHOSPHATE BUFFER, REMARK 210 90% H2O, 10% D2O; 0.7 MM BID BH3- REMARK 210 PEPTIDE U-15N, 0.7 MM BCL-W, 20 REMARK 210 MM PHOSPHATE BUFFER, 90% H2O, 10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : HNCACB; CBCA(CO)HN; 15N-EDITED REMARK 210 NOESY; HNHA; 15N-1H HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : UNITY INOVA; DRX REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 2.0, XEASY 1.3.13, REMARK 210 HADDOCK 1.2 REMARK 210 METHOD USED : RIGID BODY DOCKING, SEMI REMARK 210 -FLEXIBLE SIMULATED ANNEALING, REMARK 210 REFINEMENT USING EXPLICIT WATER REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS, STRUCTURES REMARK 210 WITH THE LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THIS MODEL STRUCTURE WAS OBTAINED USING AMBIGOUS CHEMICAL REMARK 210 SHIFT PERTURBATION CONSTRAINTS, NOE DISTANCES AND HYDROGEN BONDS 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 1-10 REMARK 465 RES C SSSEQI REMARK 465 LEU A 171 REMARK 465 GLU A 172 REMARK 465 HIS A 173 REMARK 465 HIS A 174 REMARK 465 HIS A 175 REMARK 465 HIS A 176 REMARK 465 HIS A 177 REMARK 465 HIS A 178 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 HA LEU A 133 HD1 TRP A 136 1.34 REMARK 500 OE1 GLU A 84 H1 ILE B 201 1.59 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 ASP A 50 -33.49 -151.26 REMARK 500 1 GLU A 51 -72.01 -60.38 REMARK 500 1 PHE A 56 -85.58 -98.13 REMARK 500 1 ARG A 57 -71.12 175.05 REMARK 500 1 ARG A 58 61.29 -160.63 REMARK 500 1 PRO A 71 109.21 -51.84 REMARK 500 1 SER A 73 -159.45 -151.17 REMARK 500 1 ALA A 74 -157.19 -80.60 REMARK 500 1 THR A 131 -70.19 -121.53 REMARK 500 1 TRP A 166 -83.03 -67.46 REMARK 500 1 ARG B 218 31.60 -77.07 REMARK 500 1 SER B 219 92.93 67.59 REMARK 500 2 ASP A 50 -46.41 -146.37 REMARK 500 2 PHE A 56 -85.82 -118.85 REMARK 500 2 ARG A 57 -72.20 175.71 REMARK 500 2 ARG A 58 60.67 -154.55 REMARK 500 2 PRO A 71 106.35 -53.45 REMARK 500 2 SER A 73 -157.22 -146.80 REMARK 500 2 ALA A 74 -167.32 -72.24 REMARK 500 2 MET A 114 61.84 -104.51 REMARK 500 2 THR A 131 -77.10 -124.41 REMARK 500 2 LEU A 155 -20.34 -141.23 REMARK 500 2 GLU A 156 -169.25 -102.86 REMARK 500 2 GLU A 157 -40.14 -136.03 REMARK 500 2 TRP A 166 -58.90 -165.12 REMARK 500 2 SER B 219 178.13 65.93 REMARK 500 3 ASP A 50 -47.67 -132.46 REMARK 500 3 PHE A 56 -96.74 -97.77 REMARK 500 3 ARG A 57 -68.43 170.48 REMARK 500 3 ARG A 58 79.36 -154.21 REMARK 500 3 SER A 61 -54.93 -124.04 REMARK 500 3 PRO A 71 105.70 -54.62 REMARK 500 3 SER A 73 -148.30 -156.78 REMARK 500 3 ALA A 74 -156.62 -93.99 REMARK 500 3 MET A 114 64.07 -106.57 REMARK 500 3 THR A 131 -64.04 -94.96 REMARK 500 3 ALA A 154 20.64 -140.00 REMARK 500 3 ALA A 158 20.02 -77.21 REMARK 500 3 ARG A 159 -34.07 -149.14 REMARK 500 3 GLU A 163 -72.83 -101.46 REMARK 500 3 ASN A 165 -29.20 -173.37 REMARK 500 3 TRP A 166 -73.04 -75.31 REMARK 500 3 ILE B 202 49.82 -150.46 REMARK 500 3 SER B 219 -177.60 67.12 REMARK 500 4 PRO A 32 99.09 -67.40 REMARK 500 4 ASP A 50 -42.59 -162.82 REMARK 500 4 PHE A 56 -92.27 -97.52 REMARK 500 4 ARG A 57 -64.23 179.92 REMARK 500 4 ARG A 58 54.70 -148.26 REMARK 500 4 SER A 73 -132.06 -152.57 REMARK 500 REMARK 500 THIS ENTRY HAS 137 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1MK3 RELATED DB: PDB REMARK 900 BCL-W PROTEIN DBREF 1ZY3 A 1 170 UNP Q92843 BCLW_HUMAN 2 171 DBREF 1ZY3 B 201 220 UNP P55957 BID_HUMAN 82 101 SEQADV 1ZY3 VAL A 116 UNP Q92843 PRO 117 ENGINEERED MUTATION SEQADV 1ZY3 LEU A 171 UNP Q92843 EXPRESSION TAG SEQADV 1ZY3 GLU A 172 UNP Q92843 EXPRESSION TAG SEQADV 1ZY3 HIS A 173 UNP Q92843 EXPRESSION TAG SEQADV 1ZY3 HIS A 174 UNP Q92843 EXPRESSION TAG SEQADV 1ZY3 HIS A 175 UNP Q92843 EXPRESSION TAG SEQADV 1ZY3 HIS A 176 UNP Q92843 EXPRESSION TAG SEQADV 1ZY3 HIS A 177 UNP Q92843 EXPRESSION TAG SEQADV 1ZY3 HIS A 178 UNP Q92843 EXPRESSION TAG SEQADV 1ZY3 LYS B 203 UNP P55957 ARG 84 ENGINEERED MUTATION SEQRES 1 A 178 ALA THR PRO ALA SER ALA PRO ASP THR ARG ALA LEU VAL SEQRES 2 A 178 ALA ASP PHE VAL GLY TYR LYS LEU ARG GLN LYS GLY TYR SEQRES 3 A 178 VAL CYS GLY ALA GLY PRO GLY GLU GLY PRO ALA ALA ASP SEQRES 4 A 178 PRO LEU HIS GLN ALA MET ARG ALA ALA GLY ASP GLU PHE SEQRES 5 A 178 GLU THR ARG PHE ARG ARG THR PHE SER ASP LEU ALA ALA SEQRES 6 A 178 GLN LEU HIS VAL THR PRO GLY SER ALA GLN GLN ARG PHE SEQRES 7 A 178 THR GLN VAL SER ASP GLU LEU PHE GLN GLY GLY PRO ASN SEQRES 8 A 178 TRP GLY ARG LEU VAL ALA PHE PHE VAL PHE GLY ALA ALA SEQRES 9 A 178 LEU CYS ALA GLU SER VAL ASN LYS GLU MET GLU VAL LEU SEQRES 10 A 178 VAL GLY GLN VAL GLN GLU TRP MET VAL ALA TYR LEU GLU SEQRES 11 A 178 THR ARG LEU ALA ASP TRP ILE HIS SER SER GLY GLY TRP SEQRES 12 A 178 ALA GLU PHE THR ALA LEU TYR GLY ASP GLY ALA LEU GLU SEQRES 13 A 178 GLU ALA ARG ARG LEU ARG GLU GLY ASN TRP ALA SER VAL SEQRES 14 A 178 ARG LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 1 B 20 ILE ILE LYS ASN ILE ALA ARG HIS LEU ALA GLN VAL GLY SEQRES 2 B 20 ASP SER MET ASP ARG SER ILE HELIX 1 1 ASP A 8 LYS A 24 1 17 HELIX 2 2 ASP A 39 GLY A 49 1 11 HELIX 3 3 ASP A 50 ARG A 57 1 8 HELIX 4 4 ARG A 58 LEU A 67 1 10 HELIX 5 5 ALA A 74 GLN A 87 1 14 HELIX 6 6 ASN A 91 LYS A 112 1 22 HELIX 7 7 MET A 114 GLU A 130 1 17 HELIX 8 8 LEU A 133 GLY A 141 1 9 HELIX 9 9 TRP A 143 TYR A 150 1 8 HELIX 10 10 ILE B 202 ARG B 218 1 17 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