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(-) Description

Title :  BRAF KINASE DOMAIN B3AC LOOP DELETION MUTANT IN COMPLEX WITH AZ628
 
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 :  2.50
Chains :  Asym./Biol. Unit :  A,B
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
    Chains: A, B
    EC Number: 2.7.11.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: BRAF, BRAF1, RAFB1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PROTO-ONCOGENE B-RAF,P94,V-RAF MURINE SARCOMA VIRAL ONCOGENE HOMOLOG B1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1B1E2Ligand/Ion3-(2-CYANOPROPAN-2-YL)-N-{4-METHYL-3-[(3-METHYL-4-OXO-3,4-DIHYDROQUINAZOLIN-6-YL)AMINO]PHENYL}BENZAMIDE
2PEG2Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:463 , ALA A:481 , LYS A:483 , GLU A:501 , VAL A:504 , LEU A:514 , THR A:529 , GLN A:530 , CYS A:532 , ILE A:592 , GLY A:593 , ASP A:594 , PHE A:595 , TRP B:604binding site for residue B1E A 801
2AC2SOFTWAREGLN A:456 , LYS A:475 , TRP A:476 , HIS A:477 , GLY A:478 , HOH A:907 , LEU B:711 , GLU B:715binding site for residue PEG A 802
3AC3SOFTWAREILE B:463 , ALA B:481 , LYS B:483 , GLU B:501 , LEU B:514 , THR B:529 , GLN B:530 , TRP B:531 , CYS B:532 , HIS B:574 , ILE B:592 , GLY B:593 , ASP B:594 , PHE B:595binding site for residue B1E B 801
4AC4SOFTWAREGLN B:456 , TRP B:476 , HIS B:477 , GLY B:478 , HOH B:922binding site for residue PEG B 802

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Lys A:522 -Pro A:523
2Lys B:522 -Pro B:523

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5HID)

(-) Sequences/Alignments

Asymmetric/Biological 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:257
                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeee...eeeeeee...eeeeeee...hhhhhhhhhhhhh.........eeeee....eeeeee...eeehhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.......hhh.eeee...eeee...........hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhh.....hhhhh....hhhhhhhhhhhhh.hhhhh.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hid A 449 DWEIPDGQITVGQRIGSGSFGTVYKGKWHGDVAVKMLTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHHLHASETKFEMKKLIDIARQTARGMDYLHAKSIIHRDLKSNNIFLHEDNTVKIGDFGLAEQLSGSILWMAPEVIRMQDSNPYSFQSDVYAFGIVLYELMTGQLPYSNINNRDQIIEMVGRGSLSPDLSKVRSNCPKRMKRLMAECLKKKRDERPSFPRILAEIEELARELS 722
                                   458       468       478      |493       503       513       523       533       543       553       563       573       583       593    || 615       625       635       645       655       665       675       685       695       705       715       
                                                              485|                                                                                                        598|                                                                                                               
                                                               491                                                                                                         611                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:269
                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeee...eeeeeee...eeeeeee...hhhhhhhhhhhhh.........eeeee....eeeeee...eeehhhhhh......hhhhhhhhhhhhhhhhhhhhhh.......hhh.eeee...eeee.......................hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhh.....hhhhh....hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hid B 449 DWEIPDGQITVGQRIGSGSFGTVYKGKWHGDVAVKMLTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHHLHASETKFEMKKLIDIARQTARGMDYLHAKSIIHRDLKSNNIFLHEDNTVKIGDFGLATVKSRWSGSHQFEQLSGSILWMAPEVIRMQDSNPYSFQSDVYAFGIVLYELMTGQLPYSNINNRDQIIEMVGRGSLSPDLSKVRSNCPKRMKRLMAECLKKKRDERPSFPRILAEIEELARELS 722
                                   458       468       478      |493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713         
                                                              485|                                                                                                                                                                                                                                       
                                                               491
   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 5HID)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (64, 64)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        BRAF_HUMAN | P15056: 1uwh 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 5hie 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
5hie BRAF KINASE DOMAIN B3AC LOOP DELETION MUTANT IN COMPLEX WITH DABRAFENIB