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(-) Description

Title :  BRAF KINASE DOMAIN B3AC LOOP DELETION MUTANT IN COMPLEX WITH DABRAFENIB
 
Authors :  D. M. Whalen, S. A. Foster, A. Ozen, M. Wongchenko, J. Yin, G. Schaefer, J. Mayfield, J. Chmielecki, P. Stephens, L. Albacker, Y. Yan, K. Song, G. Hatzivassiliou, C. Eigenbrot, C. Yu, A. S. Shaw, G. Manning, N. J. Sk S. G. Hymowitz, S. Malek
Date :  11 Jan 16  (Deposition) - 06 Apr 16  (Release) - 03 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. A. Foster, D. M. Whalen, A. Ozen, M. J. Wongchenko, J. Yin, I. Yen, G. Schaefer, J. D. Mayfield, J. Chmielecki, P. J. Stephens, L. A. Albacker, Y. Yan, K. Song, G. Hatzivassiliou, C. Eigenbrot, C. Yu A. S. Shaw, G. Manning, N. J. Skelton, S. G. Hymowitz, S. Malek
Activation Mechanism Of Oncogenic Deletion Mutations In Braf, Egfr, And Her2.
Cancer Cell V. 29 477 2016
PubMed-ID: 26996308  |  Reference-DOI: 10.1016/J.CCELL.2016.02.010

(-) Compounds

Molecule 1 - SERINE/THREONINE-PROTEIN KINASE B-RAF
    ChainsA, B, C, D
    EC Number2.7.11.1
    EngineeredYES
    Expression SystemTRICHOPLUSIA NI
    Expression System Taxid7111
    GeneBRAF, BRAF1, RAFB1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPROTO-ONCOGENE B-RAF,P94,V-RAF MURINE SARCOMA VIRAL ONCOGENE HOMOLOG B1

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A   
Biological Unit 2 (1x) B  
Biological Unit 3 (1x)  C 
Biological Unit 4 (1x)   D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1P064Ligand/IonDABRAFENIB
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1P061Ligand/IonDABRAFENIB
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1P061Ligand/IonDABRAFENIB
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1P061Ligand/IonDABRAFENIB
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1P061Ligand/IonDABRAFENIB

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:464 , GLY A:466 , PHE A:468 , VAL A:471 , ALA A:481 , LYS A:483 , LEU A:505 , LEU A:514 , ILE A:527 , GLN A:530 , TRP A:531 , CYS A:532 , PHE A:583 , GLY A:593 , ASP A:594 , PHE A:595binding site for residue P06 A 801
2AC2SOFTWAREGLY B:464 , SER B:465 , GLY B:466 , PHE B:468 , VAL B:471 , ALA B:481 , LYS B:483 , PHE B:498 , LEU B:505 , LEU B:514 , ILE B:527 , THR B:529 , GLN B:530 , TRP B:531 , CYS B:532 , GLY B:593 , ASP B:594 , PHE B:595binding site for residue P06 B 801
3AC3SOFTWAREGLY C:464 , SER C:465 , GLY C:466 , PHE C:468 , VAL C:471 , ALA C:481 , LYS C:483 , VAL C:504 , LEU C:514 , ILE C:527 , THR C:529 , GLN C:530 , TRP C:531 , CYS C:532 , PHE C:583 , GLY C:593 , ASP C:594 , PHE C:595binding site for residue P06 C 801
4AC4SOFTWAREGLY D:464 , SER D:465 , GLY D:466 , PHE D:468 , VAL D:471 , ALA D:481 , LYS D:483 , LEU D:514 , PHE D:516 , ILE D:527 , THR D:529 , GLN D:530 , TRP D:531 , CYS D:532 , ASN D:580 , PHE D:583 , GLY D:593 , ASP D:594 , PHE D:595binding site for residue P06 D 801

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5HIE)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Lys A:522 -Pro A:523
2Lys B:522 -Pro B:523
3Lys C:522 -Pro C:523
4Lys D:522 -Pro D:523

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5HIE)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5HIE)

(-) Exons   (0, 0)

(no "Exon" information available for 5HIE)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:258
                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eeeeeeee....eeeeee...eeeeee.hhhhhhhhhhhhhhhhhh.......eeeee.....eeeee...eeehhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh...........eeee...eeee........ee.......hhhhhhh......hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhh.....hhhhh....hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5hie A 449 DWEIPDGQITVGQRIGSGSFGTVYKGKWHGDVAVKMLTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHHLHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATVKSRGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNINNRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARSLP 722
                                   458       468       478      |493       503       513       523       533       543       553       563       573       583       593       603|      624       634       644       654       664       674       684       694       704       714        
                                                              485|                                                                                                             603|                                                                                                           
                                                               491                                                                                                              615                                                                                                           

Chain B from PDB  Type:PROTEIN  Length:259
                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.....eeeeeeee....eeeeee...eeeeee.hhhhhhhhhhhh.............eeeee.....eeeee...eeehhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh...........eeee...eeee.......ee.........hhhhhhh......hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhh.....hhhhh....hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hie B 449 DWEIPDGQITVGQRIGSGSFGTVYKGKWHGDVAVKMLTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHHLHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATVKSRSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNINNRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARSLP 722
                                   458       468       478      |493       503       513       523       533       543       553       563       573       583       593       603|      623       633       643       653       663       673       683       693       703       713         
                                                              485|                                                                                                             603|                                                                                                            
                                                               491                                                                                                              614                                                                                                            

Chain C from PDB  Type:PROTEIN  Length:253
                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeee....eeeeee...eeeeee.hhhhhhhhhhhhhhhhhh.......eeeee.....eeeee...eeehhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh...........eeee...eeee............hhhhhhh......hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhh.....hhhhh....hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hie C 449 DWEIPDGQITVGQRIGSGSFGTVYKGKWHGDVAVKMLTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHHLHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNINNRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARSLP 722
                                   458       468       478      |493       503       513       523       533       543       553       563       573       583       593   ||  619       629       639       649       659       669       679       689       699       709       719   
                                                              485|                                                                                                       597|                                                                                                            
                                                               491                                                                                                        614                                                                                                            

Chain D from PDB  Type:PROTEIN  Length:253
                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeee....eeeeee...eeeeee.hhhhhhhhhhhhhhhhhh.......eeeee.....eeeee...eeehhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh...........eeee...eeee............hhhhhhh......hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhh.....hhhhh....hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hie D 449 DWEIPDGQITVGQRIGSGSFGTVYKGKWHGDVAVKMLTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHHLHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNINNRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARSLP 722
                                   458       468       478      |493       503       513       523       533       543       553       563       573       583       593   ||  619       629       639       649       659       669       679       689       699       709       719   
                                                              485|                                                                                                       597|                                                                                                            
                                                               491                                                                                                        614                                                                                                            

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5HIE)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5HIE)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5HIE)

(-) Gene Ontology  (64, 64)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        BRAF_HUMAN | P150561uwh 1uwj 2fb8 2l05 3c4c 3d4q 3idp 3ii5 3ny5 3og7 3ppj 3ppk 3prf 3pri 3psb 3psd 3q4c 3q96 3skc 3tv4 3tv6 4cqe 4dbn 4e26 4e4x 4ehe 4ehg 4fc0 4fk3 4g9c 4g9r 4h58 4jvg 4ksp 4ksq 4mbj 4mne 4mnf 4pp7 4r5y 4rzv 4rzw 4wo5 4xv1 4xv2 4xv3 4xv9 4yht 5c9c 5csw 5csx 5ct7 5fd2 5hi2 5hid 5ita 5j17 5j18 5j2r 5jrq 5jsm 5jt2 5val 5vam

(-) Related Entries Specified in the PDB File

5hi2 BRAF KINASE DOMAIN B3AC LOOP DELETION MUTANT IN COMPLEX WITH SORAFENIB
5hid BRAF KINASE DOMAIN B3AC LOOP DELETION MUTANT IN COMPLEX WITH AZ628