PDB Short entry for 2DKP HEADER SIGNALING PROTEIN 13-APR-06 2DKP TITLE SOLUTION STRUCTURE OF THE PH DOMAIN OF PLECKSTRIN HOMOLOGY DOMAIN- TITLE 2 CONTAINING PROTEIN FAMILY A MEMBER 5 FROM HUMAN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PLECKSTRIN HOMOLOGY DOMAIN-CONTAINING FAMILY A MEMBER 5; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PH DOMAIN; COMPND 5 SYNONYM: PHOSPHOINOSITOL 3-PHOSPHATE-BINDING PROTEIN 2, PEPP-2; 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 GENE: PLEKHA5, KIAA1686, PEPP2; SOURCE 6 EXPRESSION_SYSTEM: CELL FREE SYNTHESIS; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: P051025-03; SOURCE 9 OTHER_DETAILS: CELL-FREE PROTEIN SYNTHESIS KEYWDS PH DOMAIN, PLECKSTRIN HOMOLOGY DOMAIN-CONTAINING PROTEIN FAMILY A KEYWDS 2 MEMBER 5, STRUCTURAL GENOMICS, NPPSFA, NATIONAL PROJECT ON PROTEIN KEYWDS 3 STRUCTURAL AND FUNCTIONAL ANALYSES, RIKEN STRUCTURAL KEYWDS 4 GENOMICS/PROTEOMICS INITIATIVE, RSGI, SIGNALING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR H.LI,T.TOMIZAWA,S.KOSHIBA,M.INOUE,T.KIGAWA,S.YOKOYAMA,RIKEN AUTHOR 2 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 3 09-MAR-22 2DKP 1 REMARK SEQADV REVDAT 2 24-FEB-09 2DKP 1 VERSN REVDAT 1 13-OCT-06 2DKP 0 JRNL AUTH H.LI,T.TOMIZAWA,S.KOSHIBA,M.INOUE,T.KIGAWA,S.YOKOYAMA JRNL TITL SOLUTION STRUCTURE OF THE PH DOMAIN OF PLECKSTRIN HOMOLOGY JRNL TITL 2 DOMAIN-CONTAINING PROTEIN FAMILY A MEMBER 5 FROM HUMAN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 3.5, CYANA 2.0.17 REMARK 3 AUTHORS : BRUKER (XWINNMR), GUNTERT, P. (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2DKP COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-APR-06. REMARK 100 THE DEPOSITION ID IS D_1000025529. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 296 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 120MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.14MM PH DOMAIN U-15N,13C; 20MM REMARK 210 D-TRIS-HCL(PH 7.0); 100MM NACL; REMARK 210 1MM D-DTT; 0.02% NAN3; 90% H2O, REMARK 210 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 20030801, NMRVIEW 5.0.4, REMARK 210 KUJIRA 0.932, CYANA 2.0.17 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION,STRUCTURES WITH REMARK 210 THE LEAST RESTRAINT VIOLATIONS 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: 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 ASN A 11 83.25 -69.96 REMARK 500 1 ALA A 19 102.17 -41.58 REMARK 500 1 PRO A 20 106.37 -45.16 REMARK 500 1 LEU A 48 29.97 47.23 REMARK 500 1 LEU A 75 160.22 -49.34 REMARK 500 1 ASP A 79 48.65 -92.87 REMARK 500 1 GLU A 106 -27.84 -39.28 REMARK 500 1 LEU A 119 -33.64 -39.04 REMARK 500 1 VAL A 120 142.42 -37.35 REMARK 500 1 GLN A 121 61.87 -107.94 REMARK 500 2 LEU A 75 156.22 -49.57 REMARK 500 2 ASP A 79 132.52 -35.09 REMARK 500 2 HIS A 80 34.72 -95.82 REMARK 500 2 ASN A 82 42.36 -109.50 REMARK 500 2 GLN A 121 79.93 -109.65 REMARK 500 2 PRO A 125 23.81 -79.78 REMARK 500 3 SER A 5 140.14 -37.10 REMARK 500 3 ALA A 19 103.40 -43.85 REMARK 500 3 MET A 35 134.43 -34.20 REMARK 500 3 GLU A 58 50.97 34.56 REMARK 500 3 LEU A 74 151.19 -49.53 REMARK 500 3 HIS A 80 46.23 -81.04 REMARK 500 3 TYR A 85 53.09 34.41 REMARK 500 3 LEU A 119 -26.64 -39.78 REMARK 500 3 SER A 127 97.32 -51.67 REMARK 500 4 ASN A 11 -62.36 -99.01 REMARK 500 4 SER A 12 177.27 -59.47 REMARK 500 4 ALA A 19 142.11 -33.92 REMARK 500 4 TRP A 26 97.71 -62.95 REMARK 500 4 THR A 33 118.92 -37.00 REMARK 500 4 LEU A 75 165.42 -45.77 REMARK 500 4 LYS A 112 -39.19 -38.91 REMARK 500 4 GLN A 121 76.46 -114.26 REMARK 500 5 SER A 2 41.97 39.29 REMARK 500 5 SER A 12 170.92 -56.54 REMARK 500 5 ALA A 19 102.36 -37.81 REMARK 500 5 ARG A 23 131.31 -172.27 REMARK 500 5 TRP A 26 86.59 -67.56 REMARK 500 5 LEU A 74 150.01 -49.99 REMARK 500 5 HIS A 80 42.80 -83.19 REMARK 500 5 ASN A 82 40.05 -94.91 REMARK 500 5 GLU A 106 -18.20 -49.75 REMARK 500 5 LYS A 112 -39.57 -34.28 REMARK 500 5 GLN A 121 63.41 -100.36 REMARK 500 5 PRO A 125 46.30 -75.00 REMARK 500 6 SER A 2 106.23 -58.65 REMARK 500 6 ALA A 19 102.16 -33.98 REMARK 500 6 ARG A 23 140.39 -171.09 REMARK 500 6 LYS A 36 49.74 -86.06 REMARK 500 6 LEU A 48 40.53 35.81 REMARK 500 REMARK 500 THIS ENTRY HAS 169 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR DETERMINED REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: HSK002101658.1 RELATED DB: TARGETDB DBREF 2DKP A 8 122 UNP Q9HAU0 PKHA5_HUMAN 156 271 SEQADV 2DKP GLY A 1 UNP Q9HAU0 CLONING ARTIFACT SEQADV 2DKP SER A 2 UNP Q9HAU0 CLONING ARTIFACT SEQADV 2DKP SER A 3 UNP Q9HAU0 CLONING ARTIFACT SEQADV 2DKP GLY A 4 UNP Q9HAU0 CLONING ARTIFACT SEQADV 2DKP SER A 5 UNP Q9HAU0 CLONING ARTIFACT SEQADV 2DKP SER A 6 UNP Q9HAU0 CLONING ARTIFACT SEQADV 2DKP GLY A 7 UNP Q9HAU0 CLONING ARTIFACT SEQADV 2DKP SER A 123 UNP Q9HAU0 CLONING ARTIFACT SEQADV 2DKP GLY A 124 UNP Q9HAU0 CLONING ARTIFACT SEQADV 2DKP PRO A 125 UNP Q9HAU0 CLONING ARTIFACT SEQADV 2DKP SER A 126 UNP Q9HAU0 CLONING ARTIFACT SEQADV 2DKP SER A 127 UNP Q9HAU0 CLONING ARTIFACT SEQADV 2DKP GLY A 128 UNP Q9HAU0 CLONING ARTIFACT SEQRES 1 A 128 GLY SER SER GLY SER SER GLY LYS ARG SER ASN SER ILE SEQRES 2 A 128 LYS ARG ASN PRO ASN ALA PRO VAL VAL ARG ARG GLY TRP SEQRES 3 A 128 LEU TYR LYS GLN ASP SER THR GLY MET LYS LEU TRP LYS SEQRES 4 A 128 LYS ARG TRP PHE VAL LEU SER ASP LEU CYS LEU PHE TYR SEQRES 5 A 128 TYR ARG ASP GLU LYS GLU GLU GLY ILE LEU GLY SER ILE SEQRES 6 A 128 LEU LEU PRO SER PHE GLN ILE ALA LEU LEU THR SER GLU SEQRES 7 A 128 ASP HIS ILE ASN ARG LYS TYR ALA PHE LYS ALA ALA HIS SEQRES 8 A 128 PRO ASN MET ARG THR TYR TYR PHE CYS THR ASP THR GLY SEQRES 9 A 128 LYS GLU MET GLU LEU TRP MET LYS ALA MET LEU ASP ALA SEQRES 10 A 128 ALA LEU VAL GLN THR SER GLY PRO SER SER GLY HELIX 1 1 GLY A 104 LEU A 119 1 16 SHEET 1 A 7 ILE A 61 ILE A 65 0 SHEET 2 A 7 CYS A 49 TYR A 53 -1 N LEU A 50 O ILE A 65 SHEET 3 A 7 TRP A 38 SER A 46 -1 N VAL A 44 O PHE A 51 SHEET 4 A 7 ARG A 23 GLN A 30 -1 N LYS A 29 O LYS A 39 SHEET 5 A 7 TYR A 97 CYS A 100 -1 O TYR A 98 N GLN A 30 SHEET 6 A 7 ALA A 86 ALA A 90 -1 N PHE A 87 O PHE A 99 SHEET 7 A 7 GLN A 71 LEU A 74 -1 N ALA A 73 O LYS A 88 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