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(-) Description

Title :  CRYSTAL STRUCTURE OF TRKA KINASE WITH LIGAND
 
Authors :  F. Noritaka
Date :  26 Oct 16  (Deposition) - 22 Feb 17  (Release) - 08 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Trka Inhibitor, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Furuya, T. Momose, K. Katsuno, N. Fushimi, H. Muranaka, C. Handa, T. Ozawa, T. Kinoshita
The Juxtamembrane Region Of Trka Kinase Is Critical For Inhibitor Selectivity
Bioorg. Med. Chem. Lett. V. 27 1233 2017
PubMed-ID: 28159414  |  Reference-DOI: 10.1016/J.BMCL.2017.01.056

(-) Compounds

Molecule 1 - HIGH AFFINITY NERVE GROWTH FACTOR RECEPTOR
    Chains: A
    EC Number: 2.7.10.1
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Taxid: 7111
    Expression System Vector Type: BACULOVIRUS
    Gene: NTRK1, MTC, TRK, TRKA
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: TRKA KINASE,NEUROTROPHIC TYROSINE KINASE RECEPTOR TYPE 1, TRK1-TRANSFORMING TYROSINE KINASE PROTEIN,TROPOMYOSIN-RELATED KINASE A,TYROSINE KINASE RECEPTOR,TYROSINE KINASE RECEPTOR A,TRK-A,GP140TRK, P140-TRKA

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
17HF1Ligand/Ion1-[(3S,4R)-4-[3,4-BIS(FLUORANYL)PHENYL]-1-(2-METHOXYETHYL)PYRROLIDIN-3-YL]-3-(5-ETHOXY-4-METHYL-2-PHENYL-PYRAZOL-3-YL)UREA
2DTT2Ligand/Ion2,3-DIHYDROXY-1,4-DITHIOBUTANE
3NA1Ligand/IonSODIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:486 , GLY A:488 , HIS A:489 , ILE A:490 , ASN A:493 , LYS A:544 , GLU A:560 , VAL A:573 , MET A:587 , PHE A:589 , VAL A:647 , HIS A:648 , GLY A:667 , ASP A:668 , GLY A:670 , HOH A:1156 , HOH A:1162binding site for residue 7HF A 1001
2AC2SOFTWAREARG A:507 , CYS A:579 , THR A:580 , GLU A:581 , GLY A:582 , ARG A:583 , PRO A:584binding site for residue DTT A 1002
3AC3SOFTWARETYR A:701 , ASP A:738 , CYS A:739 , GLN A:742 , ARG A:744binding site for residue DTT A 1003
4AC4SOFTWAREARG A:649 , PHE A:704 , SER A:708 , ASP A:709 , HOH A:1142binding site for residue NA A 1004

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5H3Q)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Arg A:583 -Pro A:584

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5H3Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5H3Q)

(-) Exons   (0, 0)

(no "Exon" information available for 5H3Q)

(-) 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:303
                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh............hhh.eeeeeeeeee..eeeeeeee...eeeeeeee...hhhhhhhhhhhh.........eeeee......eeeee....eehhhhhhhh..................hhhhhhhhhhhhhhhhhhhhhh.......hhh.eeee...eeee....hhhhhhhhhhee.....eehhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhh.........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhh.hhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5h3q A 484 SGLQGHIIENPQYFSDACVHHIKRRDIVLKWELGEGAFGKVFLAECHNKMLVAVKALKEARQDFQREAELLTMLQHQHIVRFFGVCTEGRPLLMVFEYMRHGDLNRFLRSHGPDAKLLAGGEDVAPGPLGLGQLLAVASQVAAGMVYLAGLHFVHRDLATRNCLVGQGLVVKIGDFGMSRDIYSTDYYRVGGRTMLPIRWMPPESILYRKFTTESDVWSFGVVLWEIFTYGKQPWYQLSNTEAIDCITQGRELERPRACPPEVYAIMRGCWQREPQQRHSIKDVHARLQALAQAPPVYLDVLG 796
                                   493       503       513       523       539       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793   
                                                                         531|       548|                                                                                                                                                                                                                                                   
                                                                          538        553
   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 5H3Q)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5H3Q)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5H3Q)

(-) Gene Ontology  (88, 88)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Arg A:583 - Pro A:584   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        NTRK1_HUMAN | P04629: 1he7 1shc 1wwa 1www 2ifg 2n90 4aoj 4crp 4f0i 4gt5 4pmm 4pmp 4pms 4pmt 4yne 4yps 5jfs 5jfv 5jfw 5jfx 5kmi 5kmj 5kmk 5kml 5kmm 5kmn 5kmo

(-) Related Entries Specified in the PDB File

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