HEADER SIGNALING PROTEIN 16-FEB-17 5N6R TITLE SOLUTION STRUCTURE OF THE DBL-HOMOLOGY DOMAIN OF BCR-ABL COMPND MOL_ID: 1; COMPND 2 MOLECULE: BREAKPOINT CLUSTER REGION PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DH DOMAIN, UNP RESIDUES 487-702; COMPND 5 SYNONYM: RENAL CARCINOMA ANTIGEN NY-REN-26; COMPND 6 EC: 2.7.11.1; COMPND 7 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: BCR, BCR1, D22S11; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS DBL-HOMOLOGY, HELICAL BUNDLE, BCR-ABL, LEUKEMIA, TRANSFERASE, KEYWDS 2 SIGNALING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR S.RECKEL,F.LOHR,L.BUCHNER,P.GUNTERT,V.DOTSCH,O.HANTSCHEL REVDAT 4 14-JUN-23 5N6R 1 REMARK REVDAT 3 08-MAY-19 5N6R 1 REMARK REVDAT 2 17-JAN-18 5N6R 1 SOURCE REVDAT 1 27-DEC-17 5N6R 0 JRNL AUTH S.RECKEL,C.GEHIN,D.TARDIVON,S.GEORGEON,T.KUKENSHONER,F.LOHR, JRNL AUTH 2 A.KOIDE,L.BUCHNER,A.PANJKOVICH,A.REYNAUD,S.PINHO,B.GERIG, JRNL AUTH 3 D.SVERGUN,F.POJER,P.GUNTERT,V.DOTSCH,S.KOIDE,A.C.GAVIN, JRNL AUTH 4 O.HANTSCHEL JRNL TITL STRUCTURAL AND FUNCTIONAL DISSECTION OF THE DH AND PH JRNL TITL 2 DOMAINS OF ONCOGENIC BCR-ABL TYROSINE KINASE. JRNL REF NAT COMMUN V. 8 2101 2017 JRNL REFN ESSN 2041-1723 JRNL PMID 29235475 JRNL DOI 10.1038/S41467-017-02313-6 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA REMARK 3 AUTHORS : GUNTERT P. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5N6R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-FEB-17. REMARK 100 THE DEPOSITION ID IS D_1200003545. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 0.05 REMARK 210 PRESSURE : AMBIENT PA REMARK 210 SAMPLE CONTENTS : 0.85 MM [U-13C; U-15N] DH, 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 3D HNCO; 3D HN(CA)CO; REMARK 210 3D HNCACB; 3D HN(COCA)CB; 3D CCH- REMARK 210 TOCSY; 3D (H)CC(CO)NH-TOCSY; 3D REMARK 210 H(CCCO)NH-TOCSY; 3D HN(CA)HA; 3D REMARK 210 1H-13C NOESY; 3D 1H-15N NOESY; REMARK 210 2D 1H-1H COSY; 2D 1H-1H TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 700 MHZ; 800 MHZ; 900 REMARK 210 MHZ; 950 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY, FLYA, TOPSPIN REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 ONFORMERS, NUMBER CALCULATED : REMARK 210 NULL 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 488 OD1 ASP A 491 1.58 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 2 ARG A 567 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 3 ARG A 592 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 16 ARG A 625 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 20 ARG A 623 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 20 ARG A 679 NE - CZ - NH1 ANGL. DEV. = 3.7 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 534 -129.51 50.58 REMARK 500 1 GLN A 574 50.73 -166.62 REMARK 500 1 LEU A 622 107.96 -39.46 REMARK 500 1 LYS A 631 -14.16 -143.44 REMARK 500 1 THR A 634 -167.33 -72.48 REMARK 500 1 THR A 693 88.42 91.17 REMARK 500 2 ALA A 531 -9.52 -59.41 REMARK 500 2 GLN A 574 -11.04 -153.09 REMARK 500 2 ASN A 627 -8.99 111.84 REMARK 500 2 LYS A 628 -64.28 -126.84 REMARK 500 2 THR A 634 77.92 -114.10 REMARK 500 2 LYS A 636 111.60 -38.52 REMARK 500 2 ARG A 695 43.26 38.39 REMARK 500 2 THR A 700 -169.52 53.00 REMARK 500 3 SER A 534 -116.12 45.09 REMARK 500 3 PHE A 547 31.86 -93.05 REMARK 500 3 GLN A 574 46.57 -152.67 REMARK 500 3 ARG A 623 2.48 -59.88 REMARK 500 3 PRO A 633 -4.15 -59.31 REMARK 500 3 ARG A 695 -149.90 53.22 REMARK 500 4 SER A 534 -130.38 41.19 REMARK 500 4 ASN A 627 -73.47 -77.10 REMARK 500 4 THR A 634 42.75 -88.84 REMARK 500 4 SER A 698 -167.12 -165.58 REMARK 500 5 MET A 486 -162.64 61.30 REMARK 500 5 ALA A 531 -9.44 -59.82 REMARK 500 5 SER A 534 -107.30 18.74 REMARK 500 5 GLN A 535 96.10 -161.28 REMARK 500 5 LYS A 636 -169.48 -128.85 REMARK 500 5 THR A 693 72.61 57.69 REMARK 500 5 ARG A 695 69.18 36.36 REMARK 500 6 VAL A 537 -69.86 -123.52 REMARK 500 6 ALA A 624 -156.59 -70.43 REMARK 500 6 ASP A 632 151.44 -48.15 REMARK 500 7 MET A 486 -167.15 59.70 REMARK 500 7 ALA A 531 -9.52 -59.61 REMARK 500 7 SER A 534 -129.19 44.47 REMARK 500 7 GLN A 574 77.87 -169.90 REMARK 500 7 GLN A 575 112.76 -160.87 REMARK 500 7 ALA A 624 110.86 59.72 REMARK 500 7 ASN A 627 146.47 81.19 REMARK 500 7 THR A 635 -24.88 72.87 REMARK 500 7 LYS A 636 104.31 -58.93 REMARK 500 7 ARG A 696 -39.01 -148.26 REMARK 500 8 MET A 486 -53.32 -161.38 REMARK 500 8 SER A 534 -130.20 43.62 REMARK 500 8 GLN A 574 54.28 -144.85 REMARK 500 8 ASN A 621 27.86 -77.05 REMARK 500 8 ARG A 625 80.75 106.89 REMARK 500 8 LYS A 628 -70.24 -168.94 REMARK 500 REMARK 500 THIS ENTRY HAS 143 RAMACHANDRAN OUTLIERS. 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 598 0.07 SIDE CHAIN REMARK 500 1 ARG A 623 0.08 SIDE CHAIN REMARK 500 2 TYR A 598 0.07 SIDE CHAIN REMARK 500 2 TYR A 644 0.07 SIDE CHAIN REMARK 500 2 ARG A 649 0.09 SIDE CHAIN REMARK 500 2 ARG A 652 0.09 SIDE CHAIN REMARK 500 3 ARG A 592 0.09 SIDE CHAIN REMARK 500 3 TYR A 598 0.12 SIDE CHAIN REMARK 500 3 ARG A 695 0.08 SIDE CHAIN REMARK 500 4 TYR A 591 0.07 SIDE CHAIN REMARK 500 4 ARG A 592 0.10 SIDE CHAIN REMARK 500 4 ARG A 623 0.12 SIDE CHAIN REMARK 500 4 TYR A 644 0.07 SIDE CHAIN REMARK 500 5 ARG A 499 0.08 SIDE CHAIN REMARK 500 5 ARG A 592 0.16 SIDE CHAIN REMARK 500 5 ARG A 623 0.08 SIDE CHAIN REMARK 500 6 TYR A 513 0.10 SIDE CHAIN REMARK 500 6 TYR A 561 0.08 SIDE CHAIN REMARK 500 6 ARG A 649 0.09 SIDE CHAIN REMARK 500 6 ARG A 679 0.16 SIDE CHAIN REMARK 500 7 TYR A 513 0.07 SIDE CHAIN REMARK 500 7 ARG A 625 0.09 SIDE CHAIN REMARK 500 8 ARG A 576 0.08 SIDE CHAIN REMARK 500 8 ARG A 696 0.13 SIDE CHAIN REMARK 500 9 ARG A 592 0.10 SIDE CHAIN REMARK 500 10 ARG A 649 0.10 SIDE CHAIN REMARK 500 11 TYR A 591 0.10 SIDE CHAIN REMARK 500 11 TYR A 598 0.10 SIDE CHAIN REMARK 500 12 ARG A 696 0.09 SIDE CHAIN REMARK 500 13 TYR A 598 0.11 SIDE CHAIN REMARK 500 13 TYR A 644 0.08 SIDE CHAIN REMARK 500 14 TYR A 598 0.08 SIDE CHAIN REMARK 500 15 TYR A 598 0.08 SIDE CHAIN REMARK 500 15 ARG A 696 0.08 SIDE CHAIN REMARK 500 16 ARG A 499 0.10 SIDE CHAIN REMARK 500 16 ARG A 592 0.12 SIDE CHAIN REMARK 500 16 ARG A 679 0.08 SIDE CHAIN REMARK 500 17 TYR A 513 0.07 SIDE CHAIN REMARK 500 17 ARG A 592 0.09 SIDE CHAIN REMARK 500 18 ARG A 679 0.08 SIDE CHAIN REMARK 500 19 ARG A 499 0.14 SIDE CHAIN REMARK 500 19 TYR A 598 0.08 SIDE CHAIN REMARK 500 20 ARG A 649 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34101 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF THE DBL-HOMOLOGY DOMAIN OF BCR-ABL DBREF 5N6R A 487 702 UNP P11274 BCR_HUMAN 487 702 SEQADV 5N6R ALA A 485 UNP P11274 EXPRESSION TAG SEQADV 5N6R MET A 486 UNP P11274 EXPRESSION TAG SEQRES 1 A 218 ALA MET ALA SER GLU LEU ASP LEU GLU LYS GLY LEU GLU SEQRES 2 A 218 MET ARG LYS TRP VAL LEU SER GLY ILE LEU ALA SER GLU SEQRES 3 A 218 GLU THR TYR LEU SER HIS LEU GLU ALA LEU LEU LEU PRO SEQRES 4 A 218 MET LYS PRO LEU LYS ALA ALA ALA THR THR SER GLN PRO SEQRES 5 A 218 VAL LEU THR SER GLN GLN ILE GLU THR ILE PHE PHE LYS SEQRES 6 A 218 VAL PRO GLU LEU TYR GLU ILE HIS LYS GLU PHE TYR ASP SEQRES 7 A 218 GLY LEU PHE PRO ARG VAL GLN GLN TRP SER HIS GLN GLN SEQRES 8 A 218 ARG VAL GLY ASP LEU PHE GLN LYS LEU ALA SER GLN LEU SEQRES 9 A 218 GLY VAL TYR ARG ALA PHE VAL ASP ASN TYR GLY VAL ALA SEQRES 10 A 218 MET GLU MET ALA GLU LYS CYS CYS GLN ALA ASN ALA GLN SEQRES 11 A 218 PHE ALA GLU ILE SER GLU ASN LEU ARG ALA ARG SER ASN SEQRES 12 A 218 LYS ASP ALA LYS ASP PRO THR THR LYS ASN SER LEU GLU SEQRES 13 A 218 THR LEU LEU TYR LYS PRO VAL ASP ARG VAL THR ARG SER SEQRES 14 A 218 THR LEU VAL LEU HIS ASP LEU LEU LYS HIS THR PRO ALA SEQRES 15 A 218 SER HIS PRO ASP HIS PRO LEU LEU GLN ASP ALA LEU ARG SEQRES 16 A 218 ILE SER GLN ASN PHE LEU SER SER ILE ASN GLU GLU ILE SEQRES 17 A 218 THR PRO ARG ARG GLN SER MET THR VAL LYS HELIX 1 AA1 SER A 488 ALA A 531 1 44 HELIX 2 AA2 THR A 539 THR A 545 1 7 HELIX 3 AA3 LYS A 549 GLY A 563 1 15 HELIX 4 AA4 GLY A 563 GLN A 569 1 7 HELIX 5 AA5 GLY A 578 GLN A 587 1 10 HELIX 6 AA6 LEU A 588 ASP A 596 1 9 HELIX 7 AA7 ASN A 597 ASN A 612 1 16 HELIX 8 AA8 ASN A 612 ASN A 621 1 10 HELIX 9 AA9 SER A 638 THR A 664 1 27 HELIX 10 AB1 PRO A 669 SER A 687 1 19 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