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 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
REMARK 3 AUTHORS : DOMINGUEZ, BOELENS, BONVIN
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 RCSB ID CODE IS RCSB100893.
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 BUFFER
REMARK 210 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: 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
(ATOM LINES ARE NOT SHOWN.)
END