PDB Short entry for 2OTK HEADER DE NOVO PROTEIN, PEPTIDE BINDING PROTEIN08-FEB-07 2OTK TITLE STRUCTURE OF ALZHEIMER AB PEPTIDE IN COMPLEX WITH AN ENGINEERED TITLE 2 BINDING PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMYLOID BETA A4 PROTEIN; COMPND 3 CHAIN: C; COMPND 4 FRAGMENT: RESIDUES 672-711; COMPND 5 SYNONYM: IGG-BINDING PROTEIN A, STAPHYLOCOCCAL PROTEIN A; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: ZAB3 AFFIBODY DIMER; COMPND 8 CHAIN: E, F; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: ENGINEERED BINDING PROTEIN; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROTEIN-PEPTIDE COMPLEX, BETA-HAIRPIN, INTERMOLECULAR BETA-SHEET, DE KEYWDS 2 NOVO PROTEIN, PEPTIDE BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 24 AUTHOR W.HOYER,T.HARD REVDAT 4 04-DEC-19 2OTK 1 REMARK REVDAT 3 24-FEB-09 2OTK 1 VERSN REVDAT 2 22-APR-08 2OTK 1 JRNL REVDAT 1 12-FEB-08 2OTK 0 JRNL AUTH W.HOYER,C.GRONWALL,A.JONSSON,S.STAHL,T.HARD JRNL TITL STABILIZATION OF A BETA-HAIRPIN IN MONOMERIC ALZHEIMER'S JRNL TITL 2 AMYLOID-BETA PEPTIDE INHIBITS AMYLOID FORMATION. JRNL REF PROC.NATL.ACAD.SCI.USA V. 105 5099 2008 JRNL REFN ISSN 0027-8424 JRNL PMID 18375754 JRNL DOI 10.1073/PNAS.0711731105 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.GRONWALL,A.JONSSON,S.LINDSTROM,E.GUNNERIUSSON,S.STAHL, REMARK 1 AUTH 2 N.HERNE REMARK 1 TITL SELECTION AND CHARACTERIZATION OF AFFIBODY LIGANDS BINDING REMARK 1 TITL 2 TO ALZHEIMER AMYLOID BETA PEPTIDES REMARK 1 REF J.BIOTECHNOL. V. 128 162 2007 REMARK 1 REFN ISSN 0168-1656 REMARK 1 PMID 17088007 REMARK 1 DOI 10.1016/J.JBIOTEC.2006.09.013 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XPLOR-NIH 2.15.0 REMARK 3 AUTHORS : KUSZEWSKI ET AL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2OTK COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-FEB-07. REMARK 100 THE DEPOSITION ID IS D_1000041567. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 298 REMARK 210 PH : 7.2; 7.2 REMARK 210 IONIC STRENGTH : 20 MM SODIUM PHOPHATE; 20 MM REMARK 210 SODIUM PHOSPHATE REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 400 UM [U-100% 13C; U-100% 15N] REMARK 210 ABETA PEPTIDE, 400 UM ZAB3 REMARK 210 DIMERS, 20 MM NA-PHOSPHATE REMARK 210 BUFFER, 90% H2O/10% D2O; 400 UM REMARK 210 ABETA PEPTIDE, 400 UM [U-100% REMARK 210 13C; U-100% 15N] ZAB3 DIMERS, 20 REMARK 210 MM NA-PHOSPHATE BUFFER, 90% H2O/ REMARK 210 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XPLOR-NIH 2.15.0, CCPNMR REMARK 210 ANALYSIS 1.10, NMRPIPE 2.3 REMARK 210 METHOD USED : AB INITIO SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 24 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY,STRUCTURES REMARK 210 WITH THE LEAST RESTRAINT REMARK 210 VIOLATIONS,STRUCTURES WITH THE REMARK 210 LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: INTERMOLECULAR NOES ASSIGNED BASED ON 3D F1 (13C,15N) REMARK 210 -FILTERED, F2 (13C OR 15N)-EDITED NOESY EXPERIMENTS 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, E, F 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 1-24 REMARK 465 RES C SSSEQI REMARK 465 ASP C 1 REMARK 465 ALA C 2 REMARK 465 GLU C 3 REMARK 465 PHE C 4 REMARK 465 ARG C 5 REMARK 465 HIS C 6 REMARK 465 ASP C 7 REMARK 465 SER C 8 REMARK 465 GLY C 9 REMARK 465 TYR C 10 REMARK 465 GLU C 11 REMARK 465 VAL C 12 REMARK 465 HIS C 13 REMARK 465 HIS C 14 REMARK 465 GLN C 15 REMARK 465 GLY E -10 REMARK 465 SER E -9 REMARK 465 SER E -8 REMARK 465 HIS E -7 REMARK 465 HIS E -6 REMARK 465 HIS E -5 REMARK 465 HIS E -4 REMARK 465 HIS E -3 REMARK 465 HIS E -2 REMARK 465 LEU E -1 REMARK 465 GLN E 0 REMARK 465 VAL E 1 REMARK 465 ASP E 2 REMARK 465 ASN E 3 REMARK 465 LYS E 4 REMARK 465 PHE E 5 REMARK 465 ASN E 6 REMARK 465 LYS E 7 REMARK 465 GLU E 8 REMARK 465 MET E 9 REMARK 465 ALA E 10 REMARK 465 SER E 11 REMARK 465 ALA E 12 REMARK 465 GLY E 13 REMARK 465 PRO E 57 REMARK 465 LYS E 58 REMARK 465 VAL E 59 REMARK 465 ASP E 60 REMARK 465 GLY F -10 REMARK 465 SER F -9 REMARK 465 SER F -8 REMARK 465 HIS F -7 REMARK 465 HIS F -6 REMARK 465 HIS F -5 REMARK 465 HIS F -4 REMARK 465 HIS F -3 REMARK 465 HIS F -2 REMARK 465 LEU F -1 REMARK 465 GLN F 0 REMARK 465 VAL F 1 REMARK 465 ASP F 2 REMARK 465 ASN F 3 REMARK 465 LYS F 4 REMARK 465 PHE F 5 REMARK 465 ASN F 6 REMARK 465 LYS F 7 REMARK 465 GLU F 8 REMARK 465 MET F 9 REMARK 465 ALA F 10 REMARK 465 SER F 11 REMARK 465 ALA F 12 REMARK 465 GLY F 13 REMARK 465 PRO F 57 REMARK 465 LYS F 58 REMARK 465 VAL F 59 REMARK 465 ASP F 60 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 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 C 26 -167.33 53.57 REMARK 500 1 LEU F 19 72.56 -116.35 REMARK 500 2 SER C 26 28.22 49.57 REMARK 500 2 ASP E 37 95.83 -162.80 REMARK 500 3 SER C 26 28.39 48.78 REMARK 500 4 SER C 26 174.25 -56.72 REMARK 500 5 LYS C 28 -23.51 -145.55 REMARK 500 6 LEU F 19 72.26 -116.00 REMARK 500 7 SER C 26 47.60 -78.96 REMARK 500 7 LYS C 28 -1.31 -142.02 REMARK 500 8 SER C 26 28.30 49.36 REMARK 500 8 ASP E 37 75.27 -116.77 REMARK 500 8 LEU F 19 72.35 -117.36 REMARK 500 8 ASP F 37 84.47 -151.62 REMARK 500 9 LEU F 19 78.07 -117.76 REMARK 500 10 SER C 26 28.79 48.47 REMARK 500 11 SER C 26 35.73 38.00 REMARK 500 11 LEU F 19 72.11 -115.59 REMARK 500 13 LEU F 19 71.06 -117.70 REMARK 500 14 SER C 26 28.50 47.07 REMARK 500 14 ASN C 27 -5.38 69.94 REMARK 500 15 GLN E 55 -68.86 -91.00 REMARK 500 16 SER C 26 28.22 48.20 REMARK 500 17 SER C 26 43.49 -79.30 REMARK 500 17 LEU F 19 72.91 -116.86 REMARK 500 18 SER C 26 27.87 49.06 REMARK 500 18 LEU E 19 60.07 -118.36 REMARK 500 19 LEU F 19 74.38 -118.74 REMARK 500 20 LEU F 19 72.12 -116.61 REMARK 500 21 SER C 26 28.82 49.42 REMARK 500 22 SER C 26 -169.83 54.18 REMARK 500 24 LEU F 19 77.33 -118.49 REMARK 500 REMARK 500 REMARK: NULL REMARK 999 REMARK 999 SEQUENCE REMARK 999 FRAGMENTS E AND F IS A DIMER OF AN ENGINEERED BINDING REMARK 999 PROTEIN, DECRIBED IN THE GRONWALL ET AL (2007) J. REMARK 999 BIOTECHNOL. DBREF 2OTK C 1 40 UNP P05067 A4_HUMAN 672 711 DBREF 2OTK E -10 60 PDB 2OTK 2OTK -10 60 DBREF 2OTK F -10 60 PDB 2OTK 2OTK -10 60 SEQRES 1 C 40 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 C 40 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 3 C 40 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 C 40 VAL SEQRES 1 E 71 GLY SER SER HIS HIS HIS HIS HIS HIS LEU GLN VAL ASP SEQRES 2 E 71 ASN LYS PHE ASN LYS GLU MET ALA SER ALA GLY GLY GLU SEQRES 3 E 71 ILE VAL TYR LEU PRO ASN LEU ASN PRO ASP GLN LEU CYS SEQRES 4 E 71 ALA PHE ILE HIS SER LEU HIS ASP ASP PRO SER GLN SER SEQRES 5 E 71 ALA ASN LEU LEU ALA GLU ALA LYS LYS LEU ASN ASP ALA SEQRES 6 E 71 GLN ALA PRO LYS VAL ASP SEQRES 1 F 71 GLY SER SER HIS HIS HIS HIS HIS HIS LEU GLN VAL ASP SEQRES 2 F 71 ASN LYS PHE ASN LYS GLU MET ALA SER ALA GLY GLY GLU SEQRES 3 F 71 ILE VAL TYR LEU PRO ASN LEU ASN PRO ASP GLN LEU CYS SEQRES 4 F 71 ALA PHE ILE HIS SER LEU HIS ASP ASP PRO SER GLN SER SEQRES 5 F 71 ALA ASN LEU LEU ALA GLU ALA LYS LYS LEU ASN ASP ALA SEQRES 6 F 71 GLN ALA PRO LYS VAL ASP HELIX 1 1 SER C 26 LYS C 28 5 3 HELIX 2 2 ASN E 23 ASP E 37 1 15 HELIX 3 3 GLN E 40 GLN E 55 1 16 HELIX 4 4 ASN F 23 ASP F 37 1 15 HELIX 5 5 ASP F 37 GLN F 55 1 19 SHEET 1 A 4 GLU E 15 TYR E 18 0 SHEET 2 A 4 GLY C 29 VAL C 36 -1 N LEU C 34 O VAL E 17 SHEET 3 A 4 LEU C 17 GLY C 25 -1 N PHE C 20 O GLY C 33 SHEET 4 A 4 ILE F 16 LEU F 19 -1 O LEU F 19 N PHE C 19 SSBOND 1 CYS E 28 CYS F 28 1555 1555 2.02 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