PDB Short entry for 2EXG HEADER CELL ADHESION 08-NOV-05 2EXG TITLE MAKING PROTEIN-PROTEIN INTERACTIONS DRUGABLE: DISCOVERY OF LOW- TITLE 2 MOLECULAR-WEIGHT LIGANDS FOR THE AF6 PDZ DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: AFADIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PDZ DOMAIN (RESIDUES 985-1079); COMPND 5 SYNONYM: AF-6 PROTEIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS INHIBITORS OF PROTEIN-PROTEIN INTERACTIONS, LOW-MOLECULAR-WEIGHT KEYWDS 2 LIGANDS, PROTEIN STRUCTURE, NMR SCREENING, PDZ DOMAINS, CELL KEYWDS 3 ADHESION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.JOSHI,C.VARGAS,P.BOISGUERIN,G.KRAUSE,M.SCHADE,H.OSCHKINAT REVDAT 3 09-MAR-22 2EXG 1 REMARK SEQADV REVDAT 2 24-FEB-09 2EXG 1 VERSN REVDAT 1 17-OCT-06 2EXG 0 JRNL AUTH M.JOSHI,C.VARGAS,P.BOISGUERIN,A.DIEHL,G.KRAUSE,P.SCHMIEDER, JRNL AUTH 2 K.MOELLING,V.HAGEN,M.SCHADE,H.OSCHKINAT JRNL TITL DISCOVERY OF LOW-MOLECULAR-WEIGHT LIGANDS FOR THE AF6 PDZ JRNL TITL 2 DOMAIN. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 45 3790 2006 JRNL REFN ESSN 0570-0833 JRNL PMID 16671149 JRNL DOI 10.1002/ANIE.200503965 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DIANA 1.0.6, DIANA 1.0.6 REMARK 3 AUTHORS : GUENTERT, P. (DIANA), GUENTERT, P. (DIANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2EXG COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JAN-06. REMARK 100 THE DEPOSITION ID IS D_1000035212. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 295; 295 REMARK 210 PH : 6.5; 6.5 REMARK 210 IONIC STRENGTH : 20 MM PHOSPHATE, 50 MM NACL; 20 REMARK 210 MM PHOSPHATE, 50 MM NACL REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1.5 MM PDZ DOMAIN U-15N, 20MM REMARK 210 PHOSPHATE BUFFER, 50MM SODIUM REMARK 210 CHLORIDE, 90%H2O, 10% D2O; 1.5 REMARK 210 MM PDZ DOMAIN U-15N, 13C, 1.5 MM REMARK 210 5F, 20MM PHOSPHATE BUFFER, 50MM REMARK 210 SODIUM CHLORIDE, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 750 MHZ REMARK 210 SPECTROMETER MODEL : DRX; DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 3.5, SPARKY 3.1 REMARK 210 METHOD USED : TORSIONAL ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL 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 HG SER A 65 OE1 GLU A 93 1.59 REMARK 500 REMARK 500 REMARK: NULL 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 ARG A 69 CZ ARG A 69 NH1 0.132 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 1 ARG A 56 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 ARG A 85 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES 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 A 5 -62.44 -155.19 REMARK 500 1 LEU A 17 49.52 -80.13 REMARK 500 1 LYS A 18 -36.80 -36.36 REMARK 500 1 GLN A 20 -13.04 52.24 REMARK 500 1 ASN A 21 46.35 -71.05 REMARK 500 1 LEU A 38 175.01 54.02 REMARK 500 1 LEU A 64 -37.15 -133.30 REMARK 500 1 SER A 70 65.47 -62.81 REMARK 500 1 VAL A 72 -1.95 45.80 REMARK 500 1 ALA A 79 -50.85 -146.24 REMARK 500 1 SER A 87 -17.62 58.61 REMARK 500 1 SER A 88 -40.82 -143.18 REMARK 500 1 LYS A 96 109.60 -56.60 REMARK 500 2 LEU A 3 117.65 -167.98 REMARK 500 2 SER A 5 -57.06 -138.29 REMARK 500 2 LEU A 6 123.87 -173.22 REMARK 500 2 LYS A 8 82.77 -70.00 REMARK 500 2 GLU A 11 -174.46 176.15 REMARK 500 2 MET A 23 -54.90 162.92 REMARK 500 2 LYS A 37 65.62 -100.14 REMARK 500 2 LEU A 38 105.48 68.62 REMARK 500 2 SER A 44 173.34 156.69 REMARK 500 2 VAL A 46 -31.11 -39.49 REMARK 500 2 LYS A 47 27.74 86.51 REMARK 500 2 LEU A 64 -37.02 -147.72 REMARK 500 2 VAL A 72 -6.36 77.01 REMARK 500 2 ALA A 79 -74.45 -48.75 REMARK 500 2 ALA A 80 -67.85 -22.48 REMARK 500 2 GLU A 81 -70.68 -41.29 REMARK 500 2 ARG A 85 59.41 -67.37 REMARK 500 2 SER A 87 74.41 26.32 REMARK 500 2 SER A 88 -65.23 153.71 REMARK 500 2 LYS A 96 150.49 -47.19 REMARK 500 2 GLN A 97 152.69 166.84 REMARK 500 2 ALA A 99 -176.63 -172.27 REMARK 500 2 ILE A 100 -74.31 -48.41 REMARK 500 3 SER A 5 -79.21 -105.21 REMARK 500 3 GLU A 11 -149.49 -178.62 REMARK 500 3 ASN A 21 36.07 -91.35 REMARK 500 3 MET A 23 -76.43 165.41 REMARK 500 3 ASP A 36 -31.65 -38.03 REMARK 500 3 LEU A 38 142.83 -39.43 REMARK 500 3 SER A 44 176.21 177.44 REMARK 500 3 LYS A 47 32.06 74.22 REMARK 500 3 LEU A 64 -43.54 -140.57 REMARK 500 3 VAL A 72 -5.57 79.14 REMARK 500 3 GLU A 77 -79.79 -42.41 REMARK 500 3 ALA A 79 -86.71 -45.13 REMARK 500 3 ALA A 80 -84.90 1.66 REMARK 500 3 ARG A 85 59.46 -65.97 REMARK 500 REMARK 500 THIS ENTRY HAS 411 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL 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 ASP A 36 LYS A 37 1 -143.42 REMARK 500 SER A 44 VAL A 45 1 148.49 REMARK 500 VAL A 90 THR A 91 1 148.47 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 1 TYR A 41 0.07 SIDE CHAIN 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 STF A 102 DBREF 2EXG A 6 101 UNP P55196 AFAD_HUMAN 985 1079 SEQADV 2EXG GLY A 1 UNP P55196 CLONING ARTIFACT SEQADV 2EXG PRO A 2 UNP P55196 CLONING ARTIFACT SEQADV 2EXG LEU A 3 UNP P55196 CLONING ARTIFACT SEQADV 2EXG GLY A 4 UNP P55196 CLONING ARTIFACT SEQADV 2EXG SER A 5 UNP P55196 CLONING ARTIFACT SEQADV 2EXG VAL A 53 UNP P55196 CLONING ARTIFACT SEQRES 1 A 101 GLY PRO LEU GLY SER LEU ARG LYS GLU PRO GLU ILE ILE SEQRES 2 A 101 THR VAL THR LEU LYS LYS GLN ASN GLY MET GLY LEU SER SEQRES 3 A 101 ILE VAL ALA ALA LYS GLY ALA GLY GLN ASP LYS LEU GLY SEQRES 4 A 101 ILE TYR VAL LYS SER VAL VAL LYS GLY GLY ALA ALA ASP SEQRES 5 A 101 VAL ASP GLY ARG LEU ALA ALA GLY ASP GLN LEU LEU SER SEQRES 6 A 101 VAL ASP GLY ARG SER LEU VAL GLY LEU SER GLN GLU ARG SEQRES 7 A 101 ALA ALA GLU LEU MET THR ARG THR SER SER VAL VAL THR SEQRES 8 A 101 LEU GLU VAL ALA LYS GLN GLY ALA ILE TYR HET STF A 102 26 HETNAM STF (5R)-2-SULFANYL-5-[4-(TRIFLUOROMETHYL)BENZYL]-1,3- HETNAM 2 STF THIAZOL-4-ONE FORMUL 2 STF C11 H8 F3 N O S2 HELIX 1 1 GLY A 49 ARG A 56 1 8 HELIX 2 2 SER A 75 ARG A 78 5 4 HELIX 3 3 ALA A 79 THR A 84 1 6 SHEET 1 A 3 GLU A 11 THR A 16 0 SHEET 2 A 3 VAL A 89 ALA A 95 -1 O VAL A 90 N VAL A 15 SHEET 3 A 3 GLN A 62 VAL A 66 -1 N LEU A 64 O GLU A 93 SHEET 1 B 2 LEU A 25 ALA A 30 0 SHEET 2 B 2 GLY A 39 VAL A 45 -1 O GLY A 39 N ALA A 30 SITE 1 AC1 6 MET A 23 GLY A 24 LEU A 25 SER A 26 SITE 2 AC1 6 ILE A 27 MET A 83 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