PDB Short entry for 1QZK HEADER TRANSFERASE 17-SEP-03 1QZK TITLE MOLECULAR MODEL OF MUTATED D816V HUMAN C-KIT KINASE DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: MAST/STEM CELL GROWTH FACTOR RECEPTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: KINASE DOMAIN; COMPND 5 SYNONYM: SCFR, PROTO-ONCOGENE TYROSINE-PROTEIN KINASE KIT, COMPND 6 C-KIT, CD117 ANTIGEN; COMPND 7 EC: 2.7.1.112; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 GENE: KIT KEYWDS RECEPTOR TYROSINE KINASE, MASTOCYTOSIS, PROTO ONCOGENE C- KEYWDS 2 KIT, D816V MUTATION EXPDTA THEORETICAL MODEL AUTHOR J.VENDOME,M.LE BRET REVDAT 1 21-SEP-04 1QZK 0 JRNL AUTH J.VENDOME,M.LE BRET JRNL TITL MOLECULAR MODEL OF MUTATED D816V HUMAN C-KIT JRNL TITL 2 KINASE DOMAIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PROMOD, MORCAD REMARK 3 AUTHORS : PEITSCH, M.C. (PROMOD), LE BRET, M. AND GABARRO REMARK 3 -ARPA, J. (MORCAD) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HOMOLOGY MODELING AND MOLECULAR REMARK 3 DYNAMICS REMARK 4 REMARK 4 1QZK COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-SEP-2003. REMARK 100 THE RCSB ID CODE IS RCSB020261. REMARK 220 REMARK 220 EXPERIMENTAL DETAILS REMARK 220 EXPERIMENT TYPE : THEORETICAL MODELLING REMARK 220 REMARK 220 REMARK: THIS MODEL IS BASED UPON THE COORDINATES OF 1VR2 (X-RAY REMARK 220 DIFFRACTION), 1FGK (X-RAY DIFFRACTION), 1FGI (X-RAY REMARK 220 DIFFRACTION), 1AGW (X-RAY DIFFRACTION), 2FGI (X-RAY REMARK 220 DIFFRACTION), 1IEP (X-RAY DIFFRACTION), FOLLOWED BY REMARK 220 MODIFICATION WITH MORCAD AND REFINEMENT IN AN AMBER REMARK 220 FORCE FIELD, AND MOLECULAR DYNAMICS IN WATER. REMARK 225 REMARK 225 THEORETICAL MODEL REMARK 225 THE COORDINATES IN THIS ENTRY REPRESENT A MODEL STRUCTURE. REMARK 225 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT CRYST1 AND REMARK 225 SCALE RECORDS BE INCLUDED, BUT THE VALUES ON THESE REMARK 225 RECORDS ARE MEANINGLESS. 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 M RES CSSEQI PSI PHI REMARK 500 LEU A 702 -31.87 69.18 REMARK 500 LEU A 762 -39.21 72.16 REMARK 500 ASN A 822 13.13 110.73 REMARK 500 CYS A 844 -62.53 69.55 REMARK 500 GLU A 893 -54.35 68.74 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 LEU A 576 PRO A 577 73.58 REMARK 500 PRO A 577 TYR A 578 88.30 REMARK 500 GLU A 711 SER A 712 145.70 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1QZJ RELATED DB: PDB REMARK 900 RELATED ID: 1R01 RELATED DB: PDB DBREF 1QZK A 576 932 UNP P10721 KIT_HUMAN 576 932 SEQADV 1QZK VAL A 816 UNP P10721 ASP 816 ENGINEERED SEQRES 1 A 357 LEU PRO TYR ASP HIS LYS TRP GLU PHE PRO ARG ASN ARG SEQRES 2 A 357 LEU SER PHE GLY LYS THR LEU GLY ALA GLY ALA PHE GLY SEQRES 3 A 357 LYS VAL VAL GLU ALA THR ALA TYR GLY LEU ILE LYS SER SEQRES 4 A 357 ASP ALA ALA MET THR VAL ALA VAL LYS MET LEU LYS PRO SEQRES 5 A 357 SER ALA HIS LEU THR GLU ARG GLU ALA LEU MET SER GLU SEQRES 6 A 357 LEU LYS VAL LEU SER TYR LEU GLY ASN HIS MET ASN ILE SEQRES 7 A 357 VAL ASN LEU LEU GLY ALA CYS THR ILE GLY GLY PRO THR SEQRES 8 A 357 LEU VAL ILE THR GLU TYR CYS CYS TYR GLY ASP LEU LEU SEQRES 9 A 357 ASN PHE LEU ARG ARG LYS ARG ASP SER PHE ILE CYS SER SEQRES 10 A 357 LYS GLN GLU ASP HIS ALA GLU ALA ALA LEU TYR LYS ASN SEQRES 11 A 357 LEU LEU HIS SER LYS GLU SER SER CYS SER ASP SER THR SEQRES 12 A 357 ASN GLU TYR MET ASP MET LYS PRO GLY VAL SER TYR VAL SEQRES 13 A 357 VAL PRO THR LYS ALA ASP LYS ARG ARG SER VAL ARG ILE SEQRES 14 A 357 GLY SER TYR ILE GLU ARG ASP VAL THR PRO ALA ILE MET SEQRES 15 A 357 GLU ASP ASP GLU LEU ALA LEU ASP LEU GLU ASP LEU LEU SEQRES 16 A 357 SER PHE SER TYR GLN VAL ALA LYS GLY MET ALA PHE LEU SEQRES 17 A 357 ALA SER LYS ASN CYS ILE HIS ARG ASP LEU ALA ALA ARG SEQRES 18 A 357 ASN ILE LEU LEU THR HIS GLY ARG ILE THR LYS ILE CYS SEQRES 19 A 357 ASP PHE GLY LEU ALA ARG VAL ILE LYS ASN ASP SER ASN SEQRES 20 A 357 TYR VAL VAL LYS GLY ASN ALA ARG LEU PRO VAL LYS TRP SEQRES 21 A 357 MET ALA PRO GLU SER ILE PHE ASN CYS VAL TYR THR PHE SEQRES 22 A 357 GLU SER ASP VAL TRP SER TYR GLY ILE PHE LEU TRP GLU SEQRES 23 A 357 LEU PHE SER LEU GLY SER SER PRO TYR PRO GLY MET PRO SEQRES 24 A 357 VAL ASP SER LYS PHE TYR LYS MET ILE LYS GLU GLY PHE SEQRES 25 A 357 ARG MET LEU SER PRO GLU HIS ALA PRO ALA GLU MET TYR SEQRES 26 A 357 ASP ILE MET LYS THR CYS TRP ASP ALA ASP PRO LEU LYS SEQRES 27 A 357 ARG PRO THR PHE LYS GLN ILE VAL GLN LEU ILE GLU LYS SEQRES 28 A 357 GLN ILE SER GLU SER THR HELIX 1 1 PRO A 585 ASN A 587 5 3 HELIX 2 2 HIS A 630 GLY A 648 1 19 HELIX 3 3 ASP A 677 LYS A 685 1 9 HELIX 4 4 GLY A 727 VAL A 732 5 6 HELIX 5 5 LEU A 766 SER A 785 1 20 HELIX 6 6 ALA A 794 ARG A 796 5 3 HELIX 7 7 PRO A 838 ASN A 843 1 6 HELIX 8 8 THR A 847 SER A 864 1 18 HELIX 9 9 ASP A 876 GLY A 886 1 11 HELIX 10 10 MET A 899 TRP A 907 1 9 HELIX 11 11 THR A 916 GLU A 930 1 15 SHEET 1 A 5 LEU A 589 GLY A 598 0 SHEET 2 A 5 GLY A 601 TYR A 609 -1 O GLY A 601 N GLY A 598 SHEET 3 A 5 ALA A 617 MET A 624 -1 O MET A 618 N ALA A 608 SHEET 4 A 5 LEU A 667 THR A 670 -1 O THR A 670 N ALA A 621 SHEET 5 A 5 LEU A 656 CYS A 660 -1 N GLY A 658 O ILE A 669 SHEET 1 B 2 ILE A 798 LEU A 800 0 SHEET 2 B 2 THR A 806 ILE A 808 -1 O LYS A 807 N LEU A 799 CISPEP 1 TYR A 578 ASP A 579 0 -5.17 CISPEP 2 LEU A 764 ASP A 765 0 -8.25 CISPEP 3 ASP A 765 LEU A 766 0 -15.01 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