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(-) Description

Title :  CRYSTAL STRUCTURE OF BRAF (R509H) KINASE DOMAIN BOUND TO AZ628
 
Authors :  Y. Wu, E. Gavathiotis
Date :  24 Dec 14  (Deposition) - 10 Aug 16  (Release) - 10 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.49
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A  (1x)
Biol. Unit 3:  B  (1x)
Keywords :  Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Karoulia, Y. Wu, T. A. Ahmed, X. Qisheng, J. Bollard, C. Krepler, X. Wu, C. Zhang, G. Bollag, M. Herlym, J. A. Fagin, A. Lujambio, E. Gavathiotis, P. I. Poulikakos
An Integrated Model Of Raf Inhibitor Action Predicts Inhibitor Activity Against Oncogenic Braf Signaling
Cancer Cell V. 30 1 2016
PubMed: search

(-) 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
    Fragment: PROTEIN KINASE DOMAIN RESIDUES 443-723
    Gene: BRAF, BRAF1, RAFB1
    Mutation: YES
    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 Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (1x): A 
Biological Unit 3 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
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
Biological Unit 1 (1, 2)
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
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1B1E1Ligand/Ion3-(2-CYANOPROPAN-2-YL)-N-{4-METHYL-3-[(3-METHYL-4-OXO-3,4-DIHYDROQUINAZOLIN-6-YL)AMINO]PHENYL}BENZAMIDE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1B1E1Ligand/Ion3-(2-CYANOPROPAN-2-YL)-N-{4-METHYL-3-[(3-METHYL-4-OXO-3,4-DIHYDROQUINAZOLIN-6-YL)AMINO]PHENYL}BENZAMIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:481 , LYS A:483 , GLU A:501 , LEU A:514 , THR A:529 , GLN A:530 , TRP A:531 , CYS A:532 , HIS A:574 , ILE A:592 , GLY A:593 , ASP A:594 , PHE A:595BINDING SITE FOR RESIDUE B1E A 801
2AC2SOFTWAREALA B:481 , LYS B:483 , GLU B:501 , LEU B:505 , ILE B:527 , THR B:529 , GLN B:530 , CYS B:532 , ILE B:592 , GLY B:593 , ASP B:594 , PHE B:595BINDING SITE FOR RESIDUE B1E B 801

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4RZW)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Asn B:631 -Pro B:632

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4RZW)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4RZW)

(-) Exons   (0, 0)

(no "Exon" information available for 4RZW)

(-) 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:251
                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhheeeeeee.....eeeeee...eeeeee......hhhhhhhhhhhhhhhh.........eeeee.....eeeee...eeehhhhhh......hhhhhhhhhhhhhhhhhhhhhh.......hhh.eeee...eeee..........hhhhhh...hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhh.....hhhhh....hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rzw A 448 DDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDVAVKMLNVTAPTPQQLQAFKNEVGVLRKTHHVNILLFMGYSTKPQLAIVTQWCEGSSLYHHLHASETKFEMKKLIDIARQTARGMDYLHAKSIIHRDLKSNNIFLHEDNTVKIGDFGGSILWMAPEVIRNPYSFQSDVYAFGIVLYELMTGQLPYSNINNRDQIIEMVGRGSLSPDLSKVRSNCPKRMKRLMAECLKKKRDERPSFPRILAEIEELARE 720
                                   457       467       477       487       497       507       517       527       537       547       557       567       577       587       615       625||     639       649       659       669       679       689       699       709       719 
                                                                                                                                                                              596|        626|                                                                                         
                                                                                                                                                                               615         631                                                                                         


Chain B from PDB  Type:PROTEIN  Length:252
                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..............eeee....eeeeee...eeeeee......hhhhhhhhhhhhhhhh.........eeeee.....eeeee.....hhhhhhh......hhhhhhhhhhhhhhhhhhhhhh...........eeeehhheeee.........hhhhhh....hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh....hhhhh....hhhhhhhhhhhh........hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4rzw B 448 DDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDVAVKMLNVTAPTPQQLQAFKNEVGVLRKTHHVNILLFMGYSTKPQLAIVTQWCEGSSLYHHLHASETKFEMKKLIDIARQTARGMDYLHAKSIIHRDLKSNNIFLHEDNTVKIGDFGSILWMAPEVIRMNPYSFQSDVYAFGIVLYELMTGQLPYSNINNRDQIIEMVGRGSLSPDLSKVRSNCPKRMKRLMAECLKKKRDERPSFPRILAEIEELAREL 721
                                   457       467       477       487       497       507       517       527       537       547       557       567       577       587       616       626||     639       649       659       669       679       689       699       709       719  
                                                                                                                                                                             595|         627|                                                                                          
                                                                                                                                                                              615          631
   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 4RZW)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4RZW)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4RZW)

(-) Gene Ontology  (64, 64)

Asymmetric Unit(hide GO term definitions)

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  4rzw
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  BRAF_HUMAN | P15056
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  2.7.11.1
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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 4wo5 4xv1 4xv2 4xv3 4xv9 4yht 5c9c 5csw 5csx 5ct7 5fd2 5hi2 5hid 5hie 5ita 5j17 5j18 5j2r 5jrq 5jsm 5jt2 5val 5vam

(-) Related Entries Specified in the PDB File

4rzv