PDB Short entry for 2LP8 HEADER APOPTOSIS/APOPTOSIS ACTIVATOR 03-FEB-12 2LP8 TITLE SOLUTION STRUCTURE OF AN APOPTOSIS ACTIVATING PHOTOSWITCHABLE BAK TITLE 2 PEPTIDE BOUND TO BCL-XL COMPND MOL_ID: 1; COMPND 2 MOLECULE: BCL-2-LIKE PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BCL2-L-1, APOPTOSIS REGULATOR BCL-X; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: BCL-2 HOMOLOGOUS ANTAGONIST/KILLER; COMPND 8 CHAIN: B; COMPND 9 FRAGMENT: BH3 DOMAIN RESIDUES 72-87; COMPND 10 SYNONYM: APOPTOSIS REGULATOR BAK, BCL-2-LIKE PROTEIN 7, BCL2-L-7; COMPND 11 ENGINEERED: YES; COMPND 12 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: BCL2L, BCL2L1, BCLX; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET19B; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606 KEYWDS APOPTOSIS, AZOBENZENE, PHOTOSWITCH, PHOTOCONTROL, APOPTOSIS KEYWDS 2 INHIBITOR, APOPTOSIS-APOPTOSIS ACTIVATOR COMPLEX EXPDTA SOLUTION NMR NUMMDL 21 AUTHOR P.WYSOCZANSKI,R.J.MART,J.E.LOVERIDGE,C.WILLIAMS,S.B.-M.WHITTAKER, AUTHOR 2 M.P.CRUMP,R.K.ALLEMANN REVDAT 4 18-AUG-21 2LP8 1 REMARK SEQADV LINK ATOM REVDAT 3 23-MAY-12 2LP8 1 JRNL REVDAT 2 09-MAY-12 2LP8 1 JRNL REVDAT 1 18-APR-12 2LP8 0 JRNL AUTH P.WYSOCZANSKI,R.J.MART,E.J.LOVERIDGE,C.WILLIAMS, JRNL AUTH 2 S.B.WHITTAKER,M.P.CRUMP,R.K.ALLEMANN JRNL TITL NMR SOLUTION STRUCTURE OF A PHOTOSWITCHABLE APOPTOSIS JRNL TITL 2 ACTIVATING BAK PEPTIDE BOUND TO BCL-X(L). JRNL REF J.AM.CHEM.SOC. V. 134 7644 2012 JRNL REFN ISSN 0002-7863 JRNL PMID 22515821 JRNL DOI 10.1021/JA302390A REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS, ARIA 2.3 REMARK 3 AUTHORS : BRUNGER A. T. ET.AL. (CNS), LINGE, O'DONOGHUE AND REMARK 3 NILGES (ARIA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2LP8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-FEB-12. REMARK 100 THE DEPOSITION ID IS D_1000102661. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.3 REMARK 210 IONIC STRENGTH : 50 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM [U-98% 13C U-98% 15N] BCL- REMARK 210 XL, 1.1 MM PHOTOSWITCHABLE BAK, REMARK 210 5 MM SODIUM PHOSPHATE, 5 MM 2- REMARK 210 MERCAPTOETHANOL, 90% H2O/10% D2O; REMARK 210 1 MM [U-98% 13C U-98% 15N] BCL- REMARK 210 XL, 1.1 MM PHOTOSWITCHABLE BAK, REMARK 210 5 MM SODIUM PHOSPHATE, 90% H2O/ REMARK 210 10% D2O; 1 MM [U-98% 13C U-98% REMARK 210 15N] BCL-XL, 1.1 MM REMARK 210 PHOTOSWITCHABLE BAK, 5 MM SODIUM REMARK 210 PHOSPHATE, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HCCH-TOCSY; 3D CBCA(CO)NH; 3D REMARK 210 C(CO)NH; 3D HNCO; 3D HNCA; 3D REMARK 210 HNCACB; 3D H(CCO)NH; 3D 1H-15N REMARK 210 NOESY; 3D 1H-13C NOESY; 13C, 15N REMARK 210 F1, F2 FILTERED 2D 1H-1H NOESY; REMARK 210 13C, 15N F1, F2 FILTERED 2D 1H- REMARK 210 1H TOCSY; 13C, 15N F2F 2D 1H-1H REMARK 210 NOESY; 3D 1H-15N TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : ARIA 2.3, NMRPIPE REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 500 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 21 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY 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: 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 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 VAL A 86 HA2 GLY B 1005 1.33 REMARK 500 HA LEU A 134 HB2 LEU A 138 1.34 REMARK 500 O SER A 43 H LYS A 47 1.57 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 18 ARG A 99 NE - CZ - NH1 ANGL. DEV. = 3.1 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 1 SER A 2 -59.81 -132.67 REMARK 500 1 ASP A 29 -23.81 -171.97 REMARK 500 1 VAL A 30 -70.83 -47.17 REMARK 500 1 GLU A 36 -80.51 -89.70 REMARK 500 1 PRO A 38 -175.82 -58.01 REMARK 500 1 THR A 41 -75.50 -67.78 REMARK 500 1 PRO A 76 165.92 -29.03 REMARK 500 1 THR A 78 3.37 -69.10 REMARK 500 1 GLN A 120 -7.36 -52.28 REMARK 500 1 GLU A 171 104.81 65.87 REMARK 500 1 HIS A 173 -157.84 48.19 REMARK 500 1 HIS A 181 -174.92 65.76 REMARK 500 1 CYS B1003 -140.32 65.10 REMARK 500 1 VAL B1004 -79.30 40.86 REMARK 500 1 ASN B1016 -51.62 -178.26 REMARK 500 2 ASP A 29 -26.06 -164.86 REMARK 500 2 VAL A 30 -75.11 -59.81 REMARK 500 2 GLU A 36 -69.27 -137.15 REMARK 500 2 PRO A 38 -171.54 -68.30 REMARK 500 2 THR A 41 -76.97 -69.09 REMARK 500 2 ARG A 62 -39.44 -35.81 REMARK 500 2 HIS A 73 63.95 60.74 REMARK 500 2 PRO A 76 167.36 -31.05 REMARK 500 2 GLU A 171 144.88 73.12 REMARK 500 2 HIS A 177 -31.49 -138.28 REMARK 500 2 GLU A 179 -88.86 59.85 REMARK 500 2 HIS A 182 21.46 -150.42 REMARK 500 2 CYS B1003 -155.90 -119.36 REMARK 500 2 VAL B1004 -84.68 46.90 REMARK 500 2 ALA B1007 -153.50 -99.67 REMARK 500 2 LEU B1008 -74.96 64.43 REMARK 500 3 SER A 2 -48.19 -137.19 REMARK 500 3 ASP A 29 -23.90 -161.52 REMARK 500 3 VAL A 30 -72.43 -53.91 REMARK 500 3 GLU A 36 -88.37 -101.06 REMARK 500 3 PRO A 38 -173.27 -55.53 REMARK 500 3 THR A 41 -75.02 -68.80 REMARK 500 3 PRO A 76 167.37 -29.33 REMARK 500 3 THR A 78 1.93 -65.67 REMARK 500 3 GLN A 120 -8.05 -54.51 REMARK 500 3 LEU A 170 -63.51 -99.87 REMARK 500 3 GLU A 171 -158.70 -113.66 REMARK 500 3 LEU A 178 106.83 65.19 REMARK 500 3 CYS B1003 -150.46 -122.90 REMARK 500 3 VAL B1004 -92.42 42.27 REMARK 500 3 ASN B1016 29.87 -155.30 REMARK 500 4 VAL A 30 -73.27 -53.57 REMARK 500 4 GLU A 36 -84.25 -103.77 REMARK 500 4 THR A 41 -75.36 -80.50 REMARK 500 4 HIS A 73 66.22 64.18 REMARK 500 REMARK 500 THIS ENTRY HAS 285 RAMACHANDRAN OUTLIERS. 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 14 TYR A 61 0.06 SIDE CHAIN REMARK 500 15 TYR A 155 0.06 SIDE CHAIN REMARK 500 18 ARG A 99 0.09 SIDE CHAIN REMARK 500 20 TYR A 155 0.05 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 33B B 1100 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 18238 RELATED DB: BMRB REMARK 900 RELATED ID: 2LPC RELATED DB: PDB REMARK 900 RELATED ID: 18250 RELATED DB: BMRB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE AUTHOR STATES THAT THERE IS A DELETION OF RESIDUES 45-84 AND REMARK 999 RESIDUES 210-233. RESIDUES ARE CONTINUOUSLY NUMBERED IGNORING THE REMARK 999 DELETION. DBREF 2LP8 A 1 44 UNP Q07817 B2CL1_HUMAN 1 44 DBREF 2LP8 A 45 169 UNP Q07817 B2CL1_HUMAN 85 209 DBREF 2LP8 B 1002 1017 UNP Q16611 BAK_HUMAN 72 87 SEQADV 2LP8 LEU A 170 UNP Q07817 EXPRESSION TAG SEQADV 2LP8 GLU A 171 UNP Q07817 EXPRESSION TAG SEQADV 2LP8 HIS A 172 UNP Q07817 EXPRESSION TAG SEQADV 2LP8 HIS A 173 UNP Q07817 EXPRESSION TAG SEQADV 2LP8 HIS A 174 UNP Q07817 EXPRESSION TAG SEQADV 2LP8 HIS A 175 UNP Q07817 EXPRESSION TAG SEQADV 2LP8 HIS A 176 UNP Q07817 EXPRESSION TAG SEQADV 2LP8 HIS A 177 UNP Q07817 EXPRESSION TAG SEQADV 2LP8 LEU A 178 UNP Q07817 EXPRESSION TAG SEQADV 2LP8 GLU A 179 UNP Q07817 EXPRESSION TAG SEQADV 2LP8 HIS A 180 UNP Q07817 EXPRESSION TAG SEQADV 2LP8 HIS A 181 UNP Q07817 EXPRESSION TAG SEQADV 2LP8 HIS A 182 UNP Q07817 EXPRESSION TAG SEQADV 2LP8 HIS A 183 UNP Q07817 EXPRESSION TAG SEQADV 2LP8 HIS A 184 UNP Q07817 EXPRESSION TAG SEQADV 2LP8 HIS A 185 UNP Q07817 EXPRESSION TAG SEQADV 2LP8 ACE B 1001 UNP Q16611 ACETYLATION SEQADV 2LP8 CYS B 1003 UNP Q16611 GLN 73 ENGINEERED MUTATION SEQADV 2LP8 ALA B 1007 UNP Q16611 GLN 77 ENGINEERED MUTATION SEQADV 2LP8 ALA B 1010 UNP Q16611 ILE 80 ENGINEERED MUTATION SEQADV 2LP8 PHE B 1011 UNP Q16611 ILE 81 ENGINEERED MUTATION SEQADV 2LP8 CYS B 1014 UNP Q16611 ASP 84 ENGINEERED MUTATION SEQADV 2LP8 NH2 B 1018 UNP Q16611 AMIDATION SEQRES 1 A 185 MET SER GLN SER ASN ARG GLU LEU VAL VAL ASP PHE LEU SEQRES 2 A 185 SER TYR LYS LEU SER GLN LYS GLY TYR SER TRP SER GLN SEQRES 3 A 185 PHE SER ASP VAL GLU GLU ASN ARG THR GLU ALA PRO GLU SEQRES 4 A 185 GLY THR GLU SER GLU ALA VAL LYS GLN ALA LEU ARG GLU SEQRES 5 A 185 ALA GLY ASP GLU PHE GLU LEU ARG TYR ARG ARG ALA PHE SEQRES 6 A 185 SER ASP LEU THR SER GLN LEU HIS ILE THR PRO GLY THR SEQRES 7 A 185 ALA TYR GLN SER PHE GLU GLN VAL VAL ASN GLU LEU PHE SEQRES 8 A 185 ARG ASP GLY VAL ASN TRP GLY ARG ILE VAL ALA PHE PHE SEQRES 9 A 185 SER PHE GLY GLY ALA LEU CYS VAL GLU SER VAL ASP LYS SEQRES 10 A 185 GLU MET GLN VAL LEU VAL SER ARG ILE ALA ALA TRP MET SEQRES 11 A 185 ALA THR TYR LEU ASN ASP HIS LEU GLU PRO TRP ILE GLN SEQRES 12 A 185 GLU ASN GLY GLY TRP ASP THR PHE VAL GLU LEU TYR GLY SEQRES 13 A 185 ASN ASN ALA ALA ALA GLU SER ARG LYS GLY GLN GLU ARG SEQRES 14 A 185 LEU GLU HIS HIS HIS HIS HIS HIS LEU GLU HIS HIS HIS SEQRES 15 A 185 HIS HIS HIS SEQRES 1 B 18 ACE GLY CYS VAL GLY ARG ALA LEU ALA ALA PHE GLY ASP SEQRES 2 B 18 CYS ILE ASN ARG NH2 HET ACE B1001 6 HET NH2 B1018 3 HET 33B B1100 42 HETNAM ACE ACETYL GROUP HETNAM NH2 AMINO GROUP HETNAM 33B 3,3'-(E)-DIAZENE-1,2-DIYLBIS{6-[(CHLOROACETYL) HETNAM 2 33B AMINO]BENZENESULFONIC ACID} FORMUL 2 ACE C2 H4 O FORMUL 2 NH2 H2 N FORMUL 3 33B C16 H14 CL2 N4 O8 S2 HELIX 1 1 SER A 4 GLN A 19 1 16 HELIX 2 2 TRP A 24 SER A 28 5 5 HELIX 3 3 GLU A 42 HIS A 73 1 32 HELIX 4 4 THR A 78 ASP A 93 1 16 HELIX 5 5 ASN A 96 LYS A 117 1 22 HELIX 6 6 VAL A 121 HIS A 137 1 17 HELIX 7 7 HIS A 137 ASN A 145 1 9 HELIX 8 8 GLY A 147 GLY A 156 1 10 HELIX 9 9 ASN A 157 ARG A 169 1 13 HELIX 10 10 VAL B 1004 GLY B 1012 1 9 HELIX 11 11 ASP B 1013 ILE B 1015 5 3 LINK C ACE B1001 N GLY B1002 1555 1555 1.33 LINK SG CYS B1003 C1 33B B1100 1555 1555 1.81 LINK SG CYS B1014 C20 33B B1100 1555 1555 1.81 LINK C ARG B1017 N NH2 B1018 1555 1555 1.32 SITE 1 AC1 5 CYS B1003 ALA B1007 ALA B1010 PHE B1011 SITE 2 AC1 5 CYS B1014 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