PDB Short entry for 1IYT HEADER PROTEIN BINDING 06-SEP-02 1IYT TITLE SOLUTION STRUCTURE OF THE ALZHEIMER'S DISEASE AMYLOID BETA-PEPTIDE (1- TITLE 2 42) COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALZHEIMER'S DISEASE AMYLOID; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: BETA-PEPTIDE; COMPND 5 SYNONYM: ALZHEIMER'S DISEASE AMYLOID A4 PROTEIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE PEPTIDE WAS PREPARED BY SOLID-PHASE SYNTHESIS. SOURCE 4 THE SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN HOMO SAPIENS SOURCE 5 (HUMAN). KEYWDS AMYLOID BETA-PEPTIDE, ALZHEIMERS DISEASE, HELIX-KINK-HELIX, PROTEIN KEYWDS 2 BINDING EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR O.CRESCENZI,S.TOMASELLI,R.GUERRINI,S.SALVADORI,A.M.D'URSI, AUTHOR 2 P.A.TEMUSSI,D.PICONE REVDAT 4 27-DEC-23 1IYT 1 REMARK REVDAT 3 23-FEB-22 1IYT 1 REMARK REVDAT 2 24-FEB-09 1IYT 1 VERSN REVDAT 1 11-FEB-03 1IYT 0 JRNL AUTH O.CRESCENZI,S.TOMASELLI,R.GUERRINI,S.SALVADORI,A.M.D'URSI, JRNL AUTH 2 P.A.TEMUSSI,D.PICONE JRNL TITL SOLUTION STRUCTURE OF THE ALZHEIMER AMYLOID BETA-PEPTIDE JRNL TITL 2 (1-42) IN AN APOLAR MICROENVIRONMENT. SIMILARITY WITH A JRNL TITL 3 VIRUS FUSION DOMAIN. JRNL REF EUR.J.BIOCHEM. V. 269 5642 2002 JRNL REFN ISSN 0014-2956 JRNL PMID 12423364 JRNL DOI 10.1046/J.1432-1033.2002.03271.X REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 1.3, AMBER 6 REMARK 3 AUTHORS : CASE, PEARLMAN ET AL. (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL OF REMARK 3 413 NOE-DERIVED, NON-REDUNDANT RESTRAINTS (130 INTRA-RESIDUE, REMARK 3 283 INTER-RESIDUE) REMARK 4 REMARK 4 1IYT COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-SEP-02. REMARK 100 THE DEPOSITION ID IS D_1000005419. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300 REMARK 210 PH : NULL REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2MM AMYLOID BETA-PEPTIDE (TFA REMARK 210 PRETREATED); 20% H2O, 80% REMARK 210 HEXAFLUOROISOPROPANOL-D2; 2.5MM REMARK 210 AMYLOID BETA-PEPTIDE (TFA REMARK 210 PRETREATED); 20% D2O, 80% REMARK 210 HEXAFLUOROISOPROPANOL-D2 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 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 : NMRPIPE 1.5, NMRVIEW 4.0.3, REMARK 210 DYANA 1.5 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS AND REMARK 210 RESTRAINED MINIMIZATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR REMARK 210 TECHNIQUES 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: 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 1 GLU A 3 CD GLU A 3 OE2 0.111 REMARK 500 1 GLU A 11 CD GLU A 11 OE2 0.107 REMARK 500 1 GLU A 22 CD GLU A 22 OE2 0.105 REMARK 500 2 GLU A 3 CD GLU A 3 OE2 0.106 REMARK 500 2 GLU A 11 CD GLU A 11 OE2 0.106 REMARK 500 2 GLU A 22 CD GLU A 22 OE2 0.108 REMARK 500 3 GLU A 3 CD GLU A 3 OE2 0.107 REMARK 500 3 GLU A 11 CD GLU A 11 OE2 0.108 REMARK 500 3 GLU A 22 CD GLU A 22 OE2 0.107 REMARK 500 4 GLU A 3 CD GLU A 3 OE2 0.105 REMARK 500 4 GLU A 11 CD GLU A 11 OE2 0.108 REMARK 500 4 GLU A 22 CD GLU A 22 OE2 0.105 REMARK 500 5 GLU A 3 CD GLU A 3 OE2 0.110 REMARK 500 5 GLU A 11 CD GLU A 11 OE2 0.106 REMARK 500 5 GLU A 22 CD GLU A 22 OE2 0.109 REMARK 500 6 GLU A 3 CD GLU A 3 OE2 0.106 REMARK 500 6 GLU A 11 CD GLU A 11 OE2 0.110 REMARK 500 6 GLU A 22 CD GLU A 22 OE2 0.105 REMARK 500 7 GLU A 3 CD GLU A 3 OE2 0.109 REMARK 500 7 GLU A 11 CD GLU A 11 OE2 0.108 REMARK 500 7 GLU A 22 CD GLU A 22 OE2 0.109 REMARK 500 8 GLU A 3 CD GLU A 3 OE2 0.109 REMARK 500 8 GLU A 11 CD GLU A 11 OE2 0.113 REMARK 500 8 GLU A 22 CD GLU A 22 OE2 0.110 REMARK 500 9 GLU A 3 CD GLU A 3 OE2 0.109 REMARK 500 9 GLU A 11 CD GLU A 11 OE2 0.110 REMARK 500 9 GLU A 22 CD GLU A 22 OE2 0.105 REMARK 500 10 GLU A 3 CD GLU A 3 OE2 0.110 REMARK 500 10 GLU A 11 CD GLU A 11 OE2 0.106 REMARK 500 10 GLU A 22 CD GLU A 22 OE2 0.109 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 ALA A 2 -72.13 -150.20 REMARK 500 1 ASP A 7 -60.46 -101.38 REMARK 500 1 VAL A 12 -80.52 -44.31 REMARK 500 1 LYS A 16 -37.62 -36.95 REMARK 500 1 SER A 26 30.11 -81.26 REMARK 500 1 ASN A 27 32.36 -156.60 REMARK 500 2 ALA A 2 -63.58 76.34 REMARK 500 2 PHE A 4 -50.41 77.83 REMARK 500 2 ASP A 7 31.43 -69.37 REMARK 500 2 VAL A 24 -60.40 -97.11 REMARK 500 2 SER A 26 35.44 -96.22 REMARK 500 2 ASN A 27 30.33 -152.37 REMARK 500 2 ILE A 32 -39.79 -32.40 REMARK 500 3 ALA A 2 -62.29 171.45 REMARK 500 3 PHE A 4 -24.75 69.03 REMARK 500 3 ARG A 5 -52.07 -122.54 REMARK 500 3 ASP A 7 -64.01 -172.52 REMARK 500 3 VAL A 12 -89.41 -49.65 REMARK 500 3 ASN A 27 34.03 -160.29 REMARK 500 3 ILE A 32 159.62 -47.09 REMARK 500 4 ALA A 2 -68.21 -158.75 REMARK 500 4 HIS A 6 -135.94 -89.09 REMARK 500 4 ASN A 27 48.47 -144.51 REMARK 500 4 ILE A 32 159.58 -36.44 REMARK 500 5 ALA A 2 -32.83 72.10 REMARK 500 5 VAL A 12 -72.84 -39.51 REMARK 500 5 ASN A 27 36.14 -159.94 REMARK 500 6 ALA A 2 68.03 -162.32 REMARK 500 6 GLU A 3 -2.17 66.31 REMARK 500 6 HIS A 6 43.27 -76.67 REMARK 500 6 ASP A 7 -73.13 -176.48 REMARK 500 6 VAL A 12 -85.64 -51.09 REMARK 500 6 SER A 26 32.30 -90.15 REMARK 500 6 ASN A 27 31.45 -153.45 REMARK 500 7 ASN A 27 39.69 -148.27 REMARK 500 8 ALA A 2 -82.64 -90.36 REMARK 500 8 GLU A 3 39.05 -154.79 REMARK 500 8 ASP A 7 25.42 -73.72 REMARK 500 8 ASN A 27 32.58 -140.75 REMARK 500 9 ALA A 2 103.03 71.75 REMARK 500 9 HIS A 6 -128.15 -95.06 REMARK 500 9 VAL A 12 -77.57 -38.04 REMARK 500 9 VAL A 18 -62.00 -97.30 REMARK 500 9 ASN A 27 39.71 -144.02 REMARK 500 10 ALA A 2 -63.24 -162.67 REMARK 500 10 PHE A 4 -12.37 65.97 REMARK 500 10 ARG A 5 -48.29 -130.77 REMARK 500 10 TYR A 10 -70.79 -71.22 REMARK 500 10 ASN A 27 37.33 -153.46 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 3 TYR A 10 0.08 SIDE CHAIN REMARK 500 4 TYR A 10 0.10 SIDE CHAIN REMARK 500 5 TYR A 10 0.08 SIDE CHAIN REMARK 500 8 TYR A 10 0.07 SIDE CHAIN REMARK 500 10 TYR A 10 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1IYT A 1 42 UNP P05067 A4_HUMAN 672 713 SEQRES 1 A 42 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 A 42 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 3 A 42 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 A 42 VAL ILE ALA HELIX 1 1 ASP A 7 SER A 26 1 20 HELIX 2 2 ASN A 27 VAL A 40 1 14 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