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(-) Description

Title :  THE CRYSTAL STRUCTURE OF HUMAN ABL1 T315I GATEKEEPER MUTANT KINASE DOMAIN IN COMPLEX WITH AXITINIB
 
Authors :  E. Johnson, M. Mctigue, C. N. Cronin
Date :  01 Jul 14  (Deposition) - 11 Feb 15  (Release) - 13 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Gatekeeper Mutant Kinase Domain Dfgin, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Pemovska, E. Johnson, M. Kontro, G. A. Repasky, J. Chen, P. Wells, C. N. Cronin, M. Mctigue, O. Kallioniemi, K. Porkka, B. W. Murray, K. Wennerberg
Axitinib Effectively Inhibits Bcr-Abl1(T315I) With A Distinct Binding Conformation.
Nature V. 519 102 2015
PubMed-ID: 25686603  |  Reference-DOI: 10.1038/NATURE14119

(-) Compounds

Molecule 1 - TYROSINE-PROTEIN KINASE ABL1
    Chains: A, B
    EC Number: 2.7.10.2
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Taxid: 7108
    Fragment: UNP RESIDUES 252-522
    Gene: ABL1, ABL, JTK7
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ABELSON MURINE LEUKEMIA VIRAL ONCOGENE HOMOLOG 1,ABELSON TYROSINE-PROTEIN KINASE 1,PROTO-ONCOGENE C-ABL,P150

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
1AXI2Ligand/IonAXITINIB
2NA3Ligand/IonSODIUM ION
3NI4Ligand/IonNICKEL (II) ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1AXI1Ligand/IonAXITINIB
2NA-1Ligand/IonSODIUM ION
3NI-1Ligand/IonNICKEL (II) ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1AXI1Ligand/IonAXITINIB
2NA-1Ligand/IonSODIUM ION
3NI-1Ligand/IonNICKEL (II) ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:248 , TYR A:253 , ALA A:269 , LYS A:271 , GLU A:316 , PHE A:317 , MET A:318 , THR A:319 , GLY A:321 , ASN A:368 , LEU A:370 , ASP A:381binding site for residue AXI A 601
2AC2SOFTWAREGLU A:352 , HIS A:490 , NI A:603 , HOH A:709 , HOH A:729 , HOH A:738binding site for residue NI A 602
3AC3SOFTWAREHIS A:490 , GLU A:494 , NI A:602binding site for residue NI A 603
4AC4SOFTWAREARG A:362 , HIS A:396binding site for residue NA A 604
5AC5SOFTWAREARG A:362 , HOH A:707 , HOH A:714binding site for residue NA A 605
6AC6SOFTWARETYR B:253 , ALA B:269 , LYS B:271 , GLU B:316 , PHE B:317 , MET B:318 , THR B:319 , GLY B:321 , ASN B:368 , LEU B:370 , ASP B:381binding site for residue AXI B 601
7AC7SOFTWAREGLU B:352 , HIS B:490 , GLU B:494 , HOH B:720binding site for residue NI B 602
8AC8SOFTWAREHIS B:490 , GLU B:494 , HOH B:705binding site for residue NI B 603
9AC9SOFTWAREGLU A:373 , ARG B:386 , TYR B:393binding site for residue NA B 604

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Pro A:309 -Pro A:310
2Pro B:309 -Pro B:310

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4TWP)

(-) 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:266
                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhh.eeeeee.hhhh...eeeeee....eeeeee...hhhhhhhhhhhhhh.......eeeee......eeeee.....hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhee....hhh.eee.hhh.eee......ee.....ee.......hhhhhhhhhhhhheehhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4twp A 233 DKWEMERTDITMKHKLGGGQYGEVYEGVWKKYSLTVAVKTLEVEEFLKEAAVMKEIKHPNLVQLLGVCTREPPFYIIIEFMTYGNLLDYLRECNRQEVNAVVLLYMATQISSAMEYLEKKNFIHRDLAARNCLVGENHLVKVADFGLSRLMTGDTYTAHAGAKFPIKWTAPESLAYNKFSIKSDVWAFGVLLWEIATYGMSPYPGIDLSQVYELLEKDYRMERPEGCPEKVYELMRACWQWNPSDRPSFAEIHQAFETMFQESSIS 503
                                   242       252       262       272||     287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497      
                                                                  273|                                                                                                                                                                                                                                
                                                                   279                                                                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:271
                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhheeeee.hhhh...eeeee.hhhh.eeeee.......hhhhhhhhhhhhhhh.......eeeee......eeeee.....hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhee....hhh.eee.hhh.eee.hhhhhee.....ee.......hhhhhhhhhhhhheehhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4twp B 233 DKWEMERTDITMKHKLGGGQYGEVYEGVWKKYSLTVAVKTLKEDTMEVEEFLKEAAVMKEIKHPNLVQLLGVCTREPPFYIIIEFMTYGNLLDYLRECNRQEVNAVVLLYMATQISSAMEYLEKKNFIHRDLAARNCLVGENHLVKVADFGLSRLMTGDTYTAHAGAKFPIKWTAPESLAYNKFSIKSDVWAFGVLLWEIATYGMSPYPGIDLSQVYELLEKDYRMERPEGCPEKVYELMRACWQWNPSDRPSFAEIHQAFETMFQESSIS 503
                                   242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502
   Legend:   → Mismatch (orange background)
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  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 4TWP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (125, 125)

Asymmetric Unit(hide GO term definitions)

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  4twp
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  ABL1_HUMAN | P00519
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  2.7.10.2
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 Related Entries

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

UniProtKB/Swiss-Prot
        ABL1_HUMAN | P00519: 1ab2 1abl 1awo 1bbz 1ju5 1opl 1zzp 2abl 2e2b 2f4j 2fo0 2g1t 2g2f 2g2h 2g2i 2gqg 2hiw 2hyy 2hz0 2hz4 2hzi 2o88 2v7a 3cs9 3eg0 3eg1 3eg2 3eg3 3egu 3k2m 3pyy 3qri 3qrj 3qrk 3t04 3ue4 3uyo 4j9b 4j9c 4j9d 4j9e 4j9f 4j9g 4j9h 4j9i 4jjb 4jjc 4jjd 4wa9 4xey 4yc8 4zog 5dc0 5dc4 5dc9 5hu9 5mo4 5oaz

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4TWP)