HEADER TRANSFERASE 17-DEC-07 2JYQ
TITLE NMR STRUCTURE OF THE APO V-SRC SH2 DOMAIN
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: TYROSINE-PROTEIN KINASE TRANSFORMING PROTEIN SRC;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: SH2 DOMAIN;
COMPND 5 SYNONYM: P60-SRC, V-SRC, PP60V-SRC;
COMPND 6 EC: 2.7.10.2;
COMPND 7 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: ROUS SARCOMA VIRUS;
SOURCE 3 ORGANISM_TAXID: 11886;
SOURCE 4 STRAIN: SCHMIDT-RUPPIN E;
SOURCE 5 GENE: V-SRC;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS;
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR;
SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET3A
KEYWDS PROTEIN, SRC, SH2, SRC HOMOLOGY 2, ATP-BINDING, KINASE, LIPOPROTEIN,
KEYWDS 2 MYRISTATE, NUCLEOTIDE-BINDING, ONCOGENE, PHOSPHOPROTEIN, SH2 DOMAIN,
KEYWDS 3 SH3 DOMAIN, TRANSFERASE, TYROSINE-PROTEIN KINASE
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR J.D.TAYLOR,A.ABABOU,M.A.WILLIAMS,J.E.LADBURY
REVDAT 4 16-MAR-22 2JYQ 1 REMARK
REVDAT 3 24-FEB-09 2JYQ 1 VERSN
REVDAT 2 25-NOV-08 2JYQ 1 JRNL
REVDAT 1 24-JUN-08 2JYQ 0
JRNL AUTH J.D.TAYLOR,A.ABABOU,R.R.FAWAZ,C.J.HOBBS,M.A.WILLIAMS,
JRNL AUTH 2 J.E.LADBURY
JRNL TITL STRUCTURE, DYNAMICS, AND BINDING THERMODYNAMICS OF THE V-SRC
JRNL TITL 2 SH2 DOMAIN: IMPLICATIONS FOR DRUG DESIGN
JRNL REF PROTEINS V. 73 929 2008
JRNL REFN ISSN 0887-3585
JRNL PMID 18536014
JRNL DOI 10.1002/PROT.22119
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : NMRPIPE, CNS 1.2
REMARK 3 AUTHORS : DELAGLIO, GRZESIEK, VUISTER, ZHU, PFEIFER, BAX
REMARK 3 (NMRPIPE), BRUNGER, ADAMS, CLORE, GROS, NILGES,
REMARK 3 READ (CNS)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: FINAL STRUCTURES REFINED IN SHELL OF
REMARK 3 WATER
REMARK 4
REMARK 4 2JYQ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-DEC-07.
REMARK 100 THE DEPOSITION ID IS D_1000100457.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 298
REMARK 210 PH : 6.0
REMARK 210 IONIC STRENGTH : 0.05
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : 0.5MM [U-100% 13C; U-100% 15N] V
REMARK 210 -SRC SH2 POLYPEPTIDE, 90% H2O/10%
REMARK 210 D2O; 0.5MM [U-100% 15N] V-SRC
REMARK 210 SH2 POLYPEPTIDE, 90% H2O/10% D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC;
REMARK 210 3D CBCA(CO)NH; 3D C(CO)NH; 3D
REMARK 210 HNCO; 3D HNCA; 3D HNCACB; 3D
REMARK 210 HNHA; 3D HNHB; 3D HCCH-TOCSY; 3D
REMARK 210 1H-15N NOESY; 3D 1H-15N TOCSY;
REMARK 210 3D 1H-13C NOESY
REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 800 MHZ
REMARK 210 SPECTROMETER MODEL : UNITYPLUS; INOVA
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : ANSIG, ARIA 2.2, CNS 1.2
REMARK 210 METHOD USED : SIMULATED ANNEALING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 120
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20
REMARK 210 CONFORMERS, SELECTION CRITERIA : BACK CALCULATED DATA AGREE WITH
REMARK 210 EXPERIMENTAL NOESY SPECTRUM
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
REMARK 210
REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING A COMBINATION OF NOE
REMARK 210 AND H BONDING DATA
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 OD2 ASP A 47 HZ1 LYS A 57 1.57
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 GLU A 4 -84.51 30.42
REMARK 500 1 LEU A 20 38.16 -78.01
REMARK 500 1 ALA A 51 -26.29 -165.51
REMARK 500 1 SER A 73 42.53 -74.69
REMARK 500 1 ARG A 74 -71.90 -125.95
REMARK 500 1 ASP A 92 -67.03 67.75
REMARK 500 1 LEU A 98 109.76 -56.83
REMARK 500 1 THR A 99 -60.09 -98.71
REMARK 500 1 SER A 105 33.09 -140.42
REMARK 500 2 ALA A 2 53.39 -177.90
REMARK 500 2 ASN A 50 49.83 -81.48
REMARK 500 2 ALA A 51 -41.87 -171.32
REMARK 500 2 SER A 66 14.43 -142.21
REMARK 500 2 ASP A 92 -81.71 62.90
REMARK 500 2 LEU A 98 106.59 -52.25
REMARK 500 3 LEU A 20 26.65 -77.52
REMARK 500 3 ALA A 51 -51.22 -120.21
REMARK 500 3 SER A 73 47.04 -78.91
REMARK 500 3 ARG A 74 -62.72 -125.44
REMARK 500 3 ASP A 92 -72.15 66.55
REMARK 500 3 ARG A 97 124.82 66.82
REMARK 500 3 THR A 99 -66.02 -96.02
REMARK 500 4 ALA A 2 50.88 176.82
REMARK 500 4 PRO A 22 23.66 -69.54
REMARK 500 4 PHE A 48 72.82 -101.84
REMARK 500 4 ALA A 51 -51.53 -162.22
REMARK 500 4 LEU A 64 -91.69 -70.10
REMARK 500 4 ASP A 65 -34.37 -134.16
REMARK 500 4 SER A 66 -31.13 -149.07
REMARK 500 4 ASP A 92 -73.74 70.11
REMARK 500 4 LEU A 98 85.68 -69.04
REMARK 500 4 THR A 104 -175.81 57.39
REMARK 500 4 SER A 105 -10.34 -154.97
REMARK 500 5 PRO A 22 14.39 -65.67
REMARK 500 5 THR A 36 -66.65 -103.21
REMARK 500 5 ARG A 74 -78.64 -126.34
REMARK 500 5 ASP A 92 -80.00 64.75
REMARK 500 5 LEU A 98 97.58 -60.33
REMARK 500 6 PRO A 22 8.48 -69.88
REMARK 500 6 ASP A 65 -66.26 63.91
REMARK 500 6 SER A 73 21.52 -76.06
REMARK 500 6 ASP A 92 -82.79 62.94
REMARK 500 6 SER A 105 69.41 63.37
REMARK 500 7 GLU A 4 -78.57 28.19
REMARK 500 7 LYS A 9 68.86 -100.14
REMARK 500 7 LYS A 38 38.75 -84.84
REMARK 500 7 ARG A 74 -71.60 -139.82
REMARK 500 7 LYS A 89 -38.32 -131.66
REMARK 500 7 ASP A 92 -82.41 62.19
REMARK 500 7 LEU A 98 107.30 -56.37
REMARK 500
REMARK 500 THIS ENTRY HAS 132 RAMACHANDRAN OUTLIERS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 6503 RELATED DB: BMRB
REMARK 900 1H, 13C, AND 15N COMPLETE CHEMICAL SHIFT ASSIGNMENTS FOR THE APO V-
REMARK 900 SRC SH2 DOMAIN
DBREF 2JYQ A 1 106 UNP P63185 SRC_RSVSE 144 249
SEQRES 1 A 106 GLN ALA GLU GLU TRP TYR PHE GLY LYS ILE THR ARG ARG
SEQRES 2 A 106 GLU SER GLU ARG LEU LEU LEU ASN PRO GLU ASN PRO ARG
SEQRES 3 A 106 GLY THR PHE LEU VAL ARG GLU SER GLU THR THR LYS GLY
SEQRES 4 A 106 ALA TYR CYS LEU SER VAL SER ASP PHE ASP ASN ALA LYS
SEQRES 5 A 106 GLY LEU ASN VAL LYS HIS TYR LYS ILE ARG LYS LEU ASP
SEQRES 6 A 106 SER GLY GLY PHE TYR ILE THR SER ARG THR GLN PHE SER
SEQRES 7 A 106 SER LEU GLN GLN LEU VAL ALA TYR TYR SER LYS HIS ALA
SEQRES 8 A 106 ASP GLY LEU CYS HIS ARG LEU THR ASN VAL CYS PRO THR
SEQRES 9 A 106 SER LYS
HELIX 1 1 THR A 11 LEU A 20 1 10
HELIX 2 2 SER A 79 SER A 88 1 10
SHEET 1 A 5 TYR A 6 GLY A 8 0
SHEET 2 A 5 THR A 28 GLU A 33 1 O GLU A 33 N GLY A 8
SHEET 3 A 5 TYR A 41 ASP A 49 -1 O SER A 46 N THR A 28
SHEET 4 A 5 GLY A 53 LYS A 63 -1 O LYS A 57 N VAL A 45
SHEET 5 A 5 PHE A 69 TYR A 70 -1 O TYR A 70 N ARG A 62
SHEET 1 B 3 TYR A 6 GLY A 8 0
SHEET 2 B 3 THR A 28 GLU A 33 1 O GLU A 33 N GLY A 8
SHEET 3 B 3 ASN A 100 VAL A 101 1 O ASN A 100 N PHE A 29
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
