HEADER SIGNALING PROTEIN 17-NOV-08 2KAW TITLE NMR STRUCTURE OF THE MDVL1 PDZ DOMAIN IN COMPLEX WITH ITS INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: SEGMENT POLARITY PROTEIN DISHEVELLED HOMOLOG DVL-1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 248-337, PDZ DOMAIN; COMPND 5 SYNONYM: DISHEVELLED-1, DSH HOMOLOG 1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: DVL1, DVL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL-21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET28 KEYWDS INHIBITOR OF PROTEIN-PROTEIN INTERACTIONS, PROTEIN STRUCTURE, PDZ KEYWDS 2 DOMAIN, WNT SIGNALING, DEVELOPMENTAL PROTEIN, WNT SIGNALING PATHWAY, KEYWDS 3 SIGNALING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR H.J.LEE,Y.SHAO,N.X.WANG,D.L.SHI,J.J.ZHENG REVDAT 3 01-MAY-24 2KAW 1 REMARK REVDAT 2 13-JUL-11 2KAW 1 VERSN REVDAT 1 15-SEP-09 2KAW 0 JRNL AUTH H.J.LEE,N.X.WANG,D.L.SHI,J.J.ZHENG JRNL TITL SULINDAC INHIBITS CANONICAL WNT SIGNALING BY BLOCKING THE JRNL TITL 2 PDZ DOMAIN OF THE PROTEIN DISHEVELLED. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 48 6448 2009 JRNL REFN ISSN 1433-7851 JRNL PMID 19637179 JRNL DOI 10.1002/ANIE.200902981 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : HADDOCK 1.2, HADDOCK 1.2 REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 (HADDOCK), DOMINGUEZ, BOELENS, BONVIN (HADDOCK) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NOE DISTANCE VIOLATION (<0.5A) REMARK 4 REMARK 4 2KAW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-NOV-08. REMARK 100 THE DEPOSITION ID IS D_1000100893. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 7.5 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM MDVL1 PDZ DOMAIN U-15N,13C, REMARK 210 10 MM SUZ, 100MM PHOSPHATE REMARK 210 BUFFER PH 7.5, 90% H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-F1_HALF_FILTERED_F2_EDIT; REMARK 210 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D CBCA(CO)NH; 3D HNCO; 3D HCCH- REMARK 210 TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; INOVA REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : HADDOCK 1.2, NMRPIPE, SPAKY 3.1 REMARK 210 METHOD USED : SIMULATED ANNEALING, HADDOCK REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 2000 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST ENERGY CONFORMATION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED WITH HADDOCK USING BASED ON A REMARK 210 TOTAL OF 55 RESTRAINTS: 45 INTERMOLECULAR DISTANCE CONTRAINTS, 7 REMARK 210 INTRAMOLECULAR DISTANCE CONTRAINTS FOR SMALL MOLECULE, AND 3 ARE REMARK 210 DISTANCE RESTRAINTS FROM 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: 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: 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 ASP A 45 -74.14 -95.18 REMARK 500 1 LEU A 55 -64.77 -103.92 REMARK 500 1 ASP A 59 -38.30 77.39 REMARK 500 2 ASP A 45 -69.03 -93.71 REMARK 500 2 LEU A 55 -65.23 -90.62 REMARK 500 2 ASN A 58 64.62 63.32 REMARK 500 2 ASP A 59 -48.04 76.46 REMARK 500 3 ASN A 24 -147.10 -142.05 REMARK 500 3 ARG A 26 -77.34 -74.47 REMARK 500 3 ASP A 45 -71.83 -93.06 REMARK 500 3 ASN A 58 67.83 61.64 REMARK 500 3 ASP A 59 -46.01 72.57 REMARK 500 4 ASP A 45 -70.60 -102.15 REMARK 500 4 ASP A 59 -18.68 74.36 REMARK 500 5 ASN A 24 -139.57 -100.45 REMARK 500 5 ASP A 45 -73.07 -77.76 REMARK 500 5 PRO A 50 106.91 -57.46 REMARK 500 5 LEU A 55 -78.80 -97.52 REMARK 500 5 ASN A 58 71.13 62.60 REMARK 500 5 ASP A 59 -52.35 74.12 REMARK 500 5 ASN A 64 56.66 -119.20 REMARK 500 6 ASN A 24 -92.89 -156.22 REMARK 500 6 ASP A 45 -70.29 -95.85 REMARK 500 6 LEU A 55 -67.75 -102.81 REMARK 500 6 ASN A 58 66.45 63.42 REMARK 500 6 ASP A 59 -44.36 74.91 REMARK 500 7 ASP A 45 -72.76 -100.96 REMARK 500 7 LEU A 55 -71.58 -102.35 REMARK 500 7 ASP A 59 -52.57 76.33 REMARK 500 7 THR A 81 74.88 -109.35 REMARK 500 8 ASN A 24 -92.87 -123.65 REMARK 500 8 ASP A 28 48.23 -82.02 REMARK 500 8 ASP A 45 -74.01 -101.15 REMARK 500 8 LEU A 55 -64.02 -102.97 REMARK 500 8 ASN A 58 75.58 57.98 REMARK 500 8 ASP A 59 -51.76 72.63 REMARK 500 9 ASN A 24 -170.05 -174.86 REMARK 500 9 ARG A 26 -70.09 -77.47 REMARK 500 9 ASP A 28 39.54 -83.25 REMARK 500 9 ASP A 45 -76.19 -96.83 REMARK 500 9 LEU A 55 -69.30 -94.75 REMARK 500 9 ASN A 58 74.52 51.86 REMARK 500 9 ASP A 59 -43.87 75.45 REMARK 500 10 ASN A 24 -160.94 -163.63 REMARK 500 10 ASP A 45 -73.93 -77.41 REMARK 500 10 LEU A 55 -74.79 -104.05 REMARK 500 10 ASN A 58 72.60 60.17 REMARK 500 10 ASP A 59 -45.63 72.90 REMARK 500 11 ASN A 24 -161.33 -174.61 REMARK 500 11 ASP A 28 47.36 -79.70 REMARK 500 REMARK 500 THIS ENTRY HAS 87 RAMACHANDRAN OUTLIERS. 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 SUZ A 91 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1MC7 RELATED DB: PDB REMARK 900 MDVL1 PDZ REMARK 900 RELATED ID: 1L6O RELATED DB: PDB REMARK 900 XDSH PDZ DBREF 2KAW A 1 90 UNP P51141 DVL1_MOUSE 248 337 SEQRES 1 A 90 ASN ILE ILE THR VAL THR LEU ASN MET GLU ARG HIS HIS SEQRES 2 A 90 PHE LEU GLY ILE SER ILE VAL GLY GLN SER ASN ASP ARG SEQRES 3 A 90 GLY ASP GLY GLY ILE TYR ILE GLY SER ILE MET LYS GLY SEQRES 4 A 90 GLY ALA VAL ALA ALA ASP GLY ARG ILE GLU PRO GLY ASP SEQRES 5 A 90 MET LEU LEU GLN VAL ASN ASP VAL ASN PHE GLU ASN MET SEQRES 6 A 90 SER ASN ASP ASP ALA VAL ARG VAL LEU ARG GLU ILE VAL SEQRES 7 A 90 SER GLN THR GLY PRO ILE SER LEU THR VAL ALA LYS HET SUZ A 91 41 HETNAM SUZ [(1Z)-5-FLUORO-2-METHYL-1-{4- HETNAM 2 SUZ [METHYLSULFINYL]BENZYLIDENE}-1H-INDEN-3-YL]ACETIC ACID HETSYN SUZ SULINDAC FORMUL 2 SUZ C20 H17 F O3 S HELIX 1 1 SER A 66 SER A 79 1 14 SHEET 1 A 4 ILE A 2 LEU A 7 0 SHEET 2 A 4 ILE A 84 ALA A 89 -1 O ILE A 84 N LEU A 7 SHEET 3 A 4 MET A 53 VAL A 57 -1 N LEU A 55 O THR A 87 SHEET 4 A 4 VAL A 60 ASN A 61 -1 O VAL A 60 N VAL A 57 SHEET 1 B 2 ILE A 17 GLY A 21 0 SHEET 2 B 2 ILE A 31 ILE A 36 -1 O TYR A 32 N VAL A 20 SITE 1 AC1 13 MET A 9 PHE A 14 LEU A 15 GLY A 16 SITE 2 AC1 13 ILE A 17 SER A 18 ILE A 19 ASP A 68 SITE 3 AC1 13 VAL A 71 ARG A 72 VAL A 73 LEU A 74 SITE 4 AC1 13 ARG A 75 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 MODEL 1