PDB Short entry for 2BOM HEADER SERINE PROTEASE INHIBITOR 12-APR-05 2BOM TITLE MODEL OF ALZHEIMER'S DISEASE AMYLOID-BETA PEPTIDE BASED ON TITLE 2 A RNA BINDING PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMYLOID BETA A4; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: AMYLOID BETA SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS KEYWDS ALTERNATIVE SPLICING, ALZHEIMERS DISEASE, AMYLOID BETA- KEYWDS 2 PEPTIDE, AMYLOID, DISEASE MUTATION, DOWN'S SYNDROME, KEYWDS 3 GLYCOPROTEIN, HELIX-KINK-HELIX, NEURONE, PROTEIN BINDING, KEYWDS 4 SERINE PROTEASE INHIBITOR, SIGNAL, TRANSMEMBRANE EXPDTA THEORETICAL MODEL AUTHOR V.S.MATHURA,D.PARIS,G.AIT-GHEZALA,A.QUADROS,N.S.PATEL, AUTHOR 2 D.N.KOLIPPAKKAM,C.H.VOLMAR,M.J.MULLAN REVDAT 2 25-MAY-05 2BOM 1 JRNL REVDAT 1 14-APR-05 2BOM 0 JRNL AUTH V.S.MATHURA,D.PARIS,G.AIT-GHEZALA,A.QUADROS, JRNL AUTH 2 N.S.PATEL,D.N.KOLIPPAKKAM,C.H.VOLMAR,M.J.MULLAN JRNL TITL MODEL OF ALZHEIMER'S DISEASE AMYLOID-BETA PEPTIDE JRNL TITL 2 BASED ON A RNA BINDING PROTEIN. JRNL REF BIOCHEM.BIOPHYS.RES.COMM. V. 332 585 2005 JRNL REFN ASTM BBRCA US ISSN 0006-291X REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NULL REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS CAN BE FOUND IN REMARK 3 THE JRNL CITATION ABOVE. REMARK 4 REMARK 4 2BOM COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY EBI ON 12-APR-2005. REMARK 100 THE EBI ID CODE IS EBI-23617. REMARK 220 REMARK 220 EXPERIMENTAL DETAILS REMARK 220 EXPERIMENT TYPE : THEORETICAL MODELLING REMARK 220 REMARK 220 REMARK: NULL REMARK 225 REMARK 225 THEORETICAL MODEL REMARK 225 THE COORDINATES IN THIS ENTRY REPRESENT A MODEL STRUCTURE. REMARK 225 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT CRYST1 AND REMARK 225 SCALE RECORDS BE INCLUDED, BUT THE VALUES ON THESE REMARK 225 RECORDS ARE MEANINGLESS. REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 VAL A 24 GLY A 25 -145.17 REMARK 500 GLY A 25 SER A 26 149.79 REMARK 500 GLY A 33 LEU A 34 133.72 REMARK 500 VAL B 24 GLY B 25 -145.22 REMARK 500 GLY B 25 SER B 26 149.81 REMARK 500 GLY B 33 LEU B 34 133.65 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1AAP RELATED DB: PDB REMARK 900 RELATED ID: 1AMB RELATED DB: PDB REMARK 900 ALZHEIMER'S DISEASE AMYLOID BETA-PEPTIDE ( REMARK 900 RESIDUES 1 - 28) (NMR, MINIMIZED AVERAGE REMARK 900 STRUCTURE) REMARK 900 RELATED ID: 1AMC RELATED DB: PDB REMARK 900 ALZHEIMER'S DISEASE AMYLOID BETA-PEPTIDE ( REMARK 900 RESIDUES 1 - 28) (NMR, 5 STRUCTURES) REMARK 900 RELATED ID: 1AML RELATED DB: PDB REMARK 900 THE ALZHEIMER`S DISEASE AMYLOID A4 PEPTIDE REMARK 900 (RESIDUES 1-40) REMARK 900 RELATED ID: 1BA4 RELATED DB: PDB REMARK 900 THE SOLUTION STRUCTURE OF AMYLOID BETA- REMARK 900 PEPTIDE (1-40) IN A WATER-MICELLE REMARK 900 ENVIRONMENT. IS THE MEMBRANE-SPANNING DOMAIN REMARK 900 WHERE WE THINK IT IS? NMR, 10 STRUCTURES REMARK 900 RELATED ID: 1BA6 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE METHIONINE-OXIDIZED REMARK 900 AMYLOID BETA-PEPTIDE (1-40). DOES REMARK 900 OXIDATION AFFECT CONFORMATIONAL SWITCHING? NMR REMARK 900 , 10 STRUCTURES REMARK 900 RELATED ID: 1BJB RELATED DB: PDB REMARK 900 SOLUTION NMR STRUCTURE OF AMYLOID BETA[E16 REMARK 900 ], RESIDUES 1-28, 14 STRUCTURES REMARK 900 RELATED ID: 1BJC RELATED DB: PDB REMARK 900 SOLUTION NMR STRUCTURE OF AMYLOID BETA[F16 REMARK 900 ], RESIDUES 1-28, 15 STRUCTURES REMARK 900 RELATED ID: 1BRC RELATED DB: PDB REMARK 900 RELATED ID: 1CA0 RELATED DB: PDB REMARK 900 BOVINE CHYMOTRYPSIN COMPLEXED TO APPI REMARK 900 RELATED ID: 1HZ3 RELATED DB: PDB REMARK 900 ALZHEIMER'S DISEASE AMYLOID-BETA PEPTIDE ( REMARK 900 RESIDUES 10-35) REMARK 900 RELATED ID: 1IYT RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE ALZHEIMER'S REMARK 900 DISEASE AMYLOID BETA-PEPTIDE (1-42) REMARK 900 RELATED ID: 1MWP RELATED DB: PDB REMARK 900 N-TERMINAL DOMAIN OF THE AMYLOID PRECURSOR REMARK 900 PROTEIN REMARK 900 RELATED ID: 1O6N RELATED DB: PDB REMARK 900 ABETA(1-16) FRAGMENT OF THE AMYLOID REMARK 900 PEPTIDE REMARK 900 RELATED ID: 1OWT RELATED DB: PDB REMARK 900 STRUCTURE OF THE ALZHEIMER'S DISEASE AMYLOID REMARK 900 PRECURSORPROTEIN COPPER BINDING DOMAIN REMARK 900 RELATED ID: 1QCM RELATED DB: PDB REMARK 900 AMYLOID BETA PEPTIDE (25-35), NMR, 20 REMARK 900 STRUCTURES REMARK 900 RELATED ID: 1QWP RELATED DB: PDB REMARK 900 NMR ANALYSIS OF 25-35 FRAGMENT OF BETA REMARK 900 AMYLOID PEPTIDE REMARK 900 RELATED ID: 1QXC RELATED DB: PDB REMARK 900 NMR STRUCTURE OF THE FRAGMENT 25-35 OF REMARK 900 BETA AMYLOID PEPTIDEIN 20/80 V:V REMARK 900 HEXAFLUOROISOPROPANOL/WATER MIXTURE REMARK 900 RELATED ID: 1QYT RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF FRAGMENT (25-35) OF REMARK 900 BETA AMYLOIDPEPTIDE IN SDS MICELLAR SOLUTION REMARK 900 RELATED ID: 1TAW RELATED DB: PDB REMARK 900 BOVINE TRYPSIN COMPLEXED TO APPI REMARK 900 RELATED ID: 1TKN RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF CAPPD*, AN INDEPENDENTLY REMARK 900 FOLDEDEXTRACELLULAR DOMAIN OF HUMAN AMYLOID- REMARK 900 BETA PRECURSORPROTEIN REMARK 900 RELATED ID: 1UO7 RELATED DB: PDB REMARK 900 MOLECULAR DYNAMICS SIMULATION OF AMYLOID BETA REMARK 900 1-42 (PDB: 1IYT) IN WATER REMARK 900 RELATED ID: 1UO8 RELATED DB: PDB REMARK 900 AFTER 2NS REMARK 900 RELATED ID: 1UOA RELATED DB: PDB REMARK 900 AFTER 3NS REMARK 900 RELATED ID: 1UOI RELATED DB: PDB REMARK 900 AFTER 4NS REMARK 900 RELATED ID: 2BOM RELATED DB: PDB REMARK 900 MODEL OF ALZHEIMER'S DISEASE AMYLOID-SS REMARK 900 PEPTIDE BASED ON A RNA BINDING PROTEIN DBREF 2BOM A 10 42 UNP P05067 A4_HUMAN 781 813 DBREF 2BOM B 10 42 UNP P05067 A4_HUMAN 781 813 SEQRES 1 A 33 TYR GLU VAL HIS HIS GLN LYS LEU VAL PHE PHE ALA GLU SEQRES 2 A 33 ASP VAL GLY SER ASN LYS GLY ALA ILE ILE GLY LEU MET SEQRES 3 A 33 VAL GLY GLY VAL VAL ILE ALA SEQRES 1 B 33 TYR GLU VAL HIS HIS GLN LYS LEU VAL PHE PHE ALA GLU SEQRES 2 B 33 ASP VAL GLY SER ASN LYS GLY ALA ILE ILE GLY LEU MET SEQRES 3 B 33 VAL GLY GLY VAL VAL ILE ALA SHEET 1 AA 2 LYS A 16 PHE A 19 0 SHEET 2 AA 2 GLY A 38 ILE A 41 -1 O VAL A 39 N VAL A 18 SHEET 1 BA 2 LYS B 16 PHE B 19 0 SHEET 2 BA 2 GLY B 38 ILE B 41 -1 O VAL B 39 N VAL B 18 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 2 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 -0.000001 -0.000001 0.00000 SCALE2 0.000000 1.000000 -0.000001 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000