HEADER PEPTIDE BINDING PROTEIN 14-SEP-00 1FU5
TITLE NMR STRUCTURE OF THE N-SH2 DOMAIN OF THE P85 SUBUNIT OF PI3-KINASE
TITLE 2 COMPLEXED TO A DOUBLY PHOSPHORYLATED PEPTIDE DERIVED FROM
TITLE 3 POLYOMAVIRUS MIDDLE T ANTIGEN
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PHOSPHATIDYLINOSITOL 3-KINASE REGULATORY ALPHA SUBUNIT;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: RESIDUES 321 TO 431 OF P85, N-SH2 (SRC HOMOLOGY 2) DOMAIN;
COMPND 5 SYNONYM: PI3-KINASE P85-ALPHA SUBUNIT, PTDINS-3-KINASE P85-ALPHA,
COMPND 6 PI3K;
COMPND 7 ENGINEERED: YES;
COMPND 8 MOL_ID: 2;
COMPND 9 MOLECULE: DOUBLY PHOSPHORYLATED MIDDLE T ANTIGEN;
COMPND 10 CHAIN: B;
COMPND 11 FRAGMENT: RESIDUES 312 TO 326 OF MT ANTIGEN, Y315 AND Y322
COMPND 12 PHOSPHORYLATED;
COMPND 13 SYNONYM: MT PEPTIDE;
COMPND 14 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS;
SOURCE 3 ORGANISM_COMMON: NORWAY RAT;
SOURCE 4 ORGANISM_TAXID: 10116;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 7 MOL_ID: 2;
SOURCE 8 SYNTHETIC: YES;
SOURCE 9 OTHER_DETAILS: MT PEPTIDE WAS SYNTHESIZED BY THE TUFTS PROTEIN
SOURCE 10 CHEMISTRY FACILITY
KEYWDS PROTEIN-PEPTIDE COMPLEX, PEPTIDE BINDING PROTEIN
EXPDTA SOLUTION NMR
AUTHOR T.WEBER,B.SCHAFFHAUSEN,Y.LIU,U.L.GUENTHER
REVDAT 5 13-NOV-24 1FU5 1 REMARK
REVDAT 4 23-FEB-22 1FU5 1 REMARK SEQADV LINK
REVDAT 3 24-FEB-09 1FU5 1 VERSN
REVDAT 2 01-APR-03 1FU5 1 JRNL
REVDAT 1 21-FEB-01 1FU5 0
JRNL AUTH T.WEBER,B.SCHAFFHAUSEN,Y.LIU,U.L.GUNTHER
JRNL TITL NMR STRUCTURE OF THE N-SH2 OF THE P85 SUBUNIT OF
JRNL TITL 2 PHOSPHOINOSITIDE 3-KINASE COMPLEXED TO A DOUBLY
JRNL TITL 3 PHOSPHORYLATED PEPTIDE REVEALS A SECOND PHOSPHOTYROSINE
JRNL TITL 4 BINDING SITE.
JRNL REF BIOCHEMISTRY V. 39 15860 2000
JRNL REFN ISSN 0006-2960
JRNL PMID 11123912
JRNL DOI 10.1021/BI001474D
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : NMRLAB, DISCOVER
REMARK 3 AUTHORS : ULRICH GUENTHER, CHRISTIAN LUDWIG AND HEINZ
REMARK 3 RUETERJANS (NMRLAB), MSI (DISCOVER)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE WITH THE LOWEST ENERGY IS
REMARK 3 PRESENTED
REMARK 4
REMARK 4 1FU5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-SEP-00.
REMARK 100 THE DEPOSITION ID IS D_1000011903.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 305
REMARK 210 PH : 6.8
REMARK 210 IONIC STRENGTH : 0.1MM
REMARK 210 PRESSURE : 1 BAR
REMARK 210 SAMPLE CONTENTS : 0.15MM N-SH2 15N, 13C; MT
REMARK 210 PEPTIDE; 0.1MM KCL; 95% H2O, 5%
REMARK 210 D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 3D_13C
REMARK 210 -SEPARATED_NOESY; 3D_15N-
REMARK 210 SEPARATED_NOESY; 13C{F1}-
REMARK 210 FILTERED 2D-NOESY
REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ
REMARK 210 SPECTROMETER MODEL : DMX
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : PRONTO, NMR2ST, DYANA
REMARK 210 METHOD USED : THE STRUCTURES WERE ENERGY
REMARK 210 MINIMIZED WITH MSI DISCOVER.
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 110
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1
REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH FAVORABLE NON
REMARK 210 -BOND ENERGY
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
REMARK 210
REMARK 210 REMARK: NOESY ASSIGNMENTS WERE OBTAINED BY A SEMI-AUTOMATIC
REMARK 210 PROCEDURE EMPLOYING A PROGRAM FROM PRISTOVSEK [PRISTOVSEK, P. &
REMARK 210 KIDRIC, J. (1997) BIOPOL. 42, 671-679)]. INITIAL CALCULATIONS
REMARK 210 INCLUDED ONLY INTRAMOLECULAR CONSTRAINTS. THE OBSERVED NOES
REMARK 210 DERIVED FROM 13C{F1}-FILTERED 2D-NOESY SPECTRA WERE INCORPORATED
REMARK 210 INTO THE STRUCTURE CALCULATION WHEN THE PROTEIN FOLD WAS ALREADY
REMARK 210 CORRECT.
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: DIMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B
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 HD22 LEU B 12 HXT LEU B 15 1.06
REMARK 500 HZ1 LYS A 26 HZ3 LYS A 110 1.24
REMARK 500 HB3 ASP A 67 HZ3 LYS A 69 1.26
REMARK 500 O LEU A 36 H THR A 51 1.55
REMARK 500 O LEU A 93 H GLN A 95 1.56
REMARK 500 H ASP A 47 O ILE A 63 1.57
REMARK 500 O GLU A 21 H ASN A 24 1.58
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 LEU B 15 C LEU B 15 OXT 0.151
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 ASN A 3 87.69 58.86
REMARK 500 MET A 6 139.89 -179.89
REMARK 500 SER A 7 154.39 62.20
REMARK 500 GLN A 9 40.07 34.23
REMARK 500 ASP A 10 31.83 -159.73
REMARK 500 GLU A 12 -73.92 65.24
REMARK 500 TYR A 14 34.40 -87.84
REMARK 500 ASP A 17 108.25 52.00
REMARK 500 SER A 19 103.52 76.53
REMARK 500 ARG A 20 -70.27 -30.12
REMARK 500 ASP A 29 39.58 175.70
REMARK 500 THR A 30 -77.66 -55.68
REMARK 500 THR A 34 45.72 -82.27
REMARK 500 PHE A 35 163.63 -42.98
REMARK 500 LEU A 36 155.86 177.95
REMARK 500 ARG A 38 -44.29 -137.31
REMARK 500 ASP A 39 147.06 57.01
REMARK 500 ALA A 40 -138.79 -177.42
REMARK 500 THR A 42 89.14 -54.68
REMARK 500 HIS A 45 71.35 -101.53
REMARK 500 TYR A 48 28.77 -158.95
REMARK 500 THR A 49 -176.16 47.82
REMARK 500 LEU A 50 145.00 178.90
REMARK 500 ASN A 58 119.69 60.90
REMARK 500 SER A 60 -47.41 168.91
REMARK 500 ILE A 61 141.32 57.27
REMARK 500 LYS A 62 143.71 174.57
REMARK 500 ARG A 66 -85.01 -138.93
REMARK 500 ASP A 67 61.81 -100.04
REMARK 500 TYR A 70 -165.98 -53.87
REMARK 500 PHE A 72 -31.83 -36.50
REMARK 500 ASP A 74 86.70 61.83
REMARK 500 THR A 77 44.96 152.61
REMARK 500 VAL A 81 38.51 -90.69
REMARK 500 ASN A 90 116.95 151.18
REMARK 500 GLU A 91 -18.51 154.99
REMARK 500 SER A 92 160.90 89.48
REMARK 500 ALA A 94 64.20 -65.37
REMARK 500 GLN A 95 -84.37 -66.53
REMARK 500 ASN A 97 148.35 -178.70
REMARK 500 PRO A 98 48.19 -75.00
REMARK 500 LEU A 100 -76.80 -125.30
REMARK 500 ASP A 101 66.06 30.35
REMARK 500 LYS A 103 164.55 78.26
REMARK 500 LEU A 104 27.24 -160.29
REMARK 500 LYS A 110 93.25 46.20
REMARK 500 GLU B 3 -121.99 -77.45
REMARK 500 MET B 7 152.39 169.34
REMARK 500 GLU B 8 -99.29 174.66
REMARK 500 ASP B 9 126.14 73.44
REMARK 500
REMARK 500 THIS ENTRY HAS 52 RAMACHANDRAN OUTLIERS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1FU6 RELATED DB: PDB
REMARK 900 1FU6 IS NMR STRUCTURE OF THE N-SH2 DOMAIN OF THE P85 SUBUNIT OF PI3-
REMARK 900 KINASE
DBREF 1FU5 A 1 111 UNP Q63787 P85A_RAT 321 431
DBREF 1FU5 B 1 15 UNP P03076 TAMI_POVM3 331 345
SEQADV 1FU5 SER A 60 UNP Q63787 LEU 380 CONFLICT
SEQADV 1FU5 PTR B 4 UNP P03076 TYR 334 MODIFIED RESIDUE
SEQADV 1FU5 PTR B 11 UNP P03076 TYR 341 MODIFIED RESIDUE
SEQRES 1 A 111 GLY MET ASN ASN ASN MET SER LEU GLN ASP ALA GLU TRP
SEQRES 2 A 111 TYR TRP GLY ASP ILE SER ARG GLU GLU VAL ASN GLU LYS
SEQRES 3 A 111 LEU ARG ASP THR ALA ASP GLY THR PHE LEU VAL ARG ASP
SEQRES 4 A 111 ALA SER THR LYS MET HIS GLY ASP TYR THR LEU THR LEU
SEQRES 5 A 111 ARG LYS GLY GLY ASN ASN LYS SER ILE LYS ILE PHE HIS
SEQRES 6 A 111 ARG ASP GLY LYS TYR GLY PHE SER ASP PRO LEU THR PHE
SEQRES 7 A 111 ASN SER VAL VAL GLU LEU ILE ASN HIS TYR ARG ASN GLU
SEQRES 8 A 111 SER LEU ALA GLN TYR ASN PRO LYS LEU ASP VAL LYS LEU
SEQRES 9 A 111 LEU TYR PRO VAL SER LYS TYR
SEQRES 1 B 15 GLU GLU GLU PTR MET PRO MET GLU ASP LEU PTR LEU ASP
SEQRES 2 B 15 ILE LEU
MODRES 1FU5 PTR B 4 TYR O-PHOSPHOTYROSINE
MODRES 1FU5 PTR B 11 TYR O-PHOSPHOTYROSINE
HET PTR B 4 25
HET PTR B 11 25
HETNAM PTR O-PHOSPHOTYROSINE
HETSYN PTR PHOSPHONOTYROSINE
FORMUL 2 PTR 2(C9 H12 N O6 P)
HELIX 1 1 SER A 19 LEU A 27 1 9
HELIX 2 2 VAL A 82 TYR A 88 1 7
LINK C GLU B 3 N PTR B 4 1555 1555 1.33
LINK C PTR B 4 N MET B 5 1555 1555 1.32
LINK C LEU B 10 N PTR B 11 1555 1555 1.33
LINK C PTR B 11 N LEU B 12 1555 1555 1.33
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