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(-) Description

Title :  CRYSTAL STRUCTURE OF AN INHIBITOR-BOUND SYK
 
Authors :  S. J. Lee, J. Choi, B. G. Han, H. Song, J. S. Koh, B. I. Lee
Date :  30 Dec 14  (Deposition) - 30 Dec 15  (Release) - 19 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Syk Kinase, Inhibitor, Spleen Tyrosine Kinase, Transferase- Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. J. Lee, J. S. Choi, B. G. Han, H. S. Kim, H. J. Song, J. Lee, S. Nam, S. H. Goh, J. H. Kim, J. S. Koh, B. I. Lee
Crystal Structures Of Spleen Tyrosine Kinase In Complex Wit Novel Inhibitors: Structural Insights For Design Of Anticancer Drugs
Febs J. V. 283 3613 2016
PubMed-ID: 27504936  |  Reference-DOI: 10.1111/FEBS.13831

(-) Compounds

Molecule 1 - TYROSINE-PROTEIN KINASE SYK
    Chains: A, B
    EC Number: 2.7.10.2
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Plasmid: PVL1393
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Fragment: PROTEIN KINASE DOMAIN, RESIDUES 356-635
    Gene: SYK
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SPLEEN TYROSINE KINASE,P72-SYK

 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  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1X3G2Ligand/Ion4-{[5-FLUORO-4-(3-{[(3R)-3-HYDROXYPYRROLIDIN-1-YL]METHYL}-4-METHYL-1H-PYRROL-1-YL)PYRIMIDIN-2-YL]AMINO}-2,6-DIMETHYLPHENYL METHANESULFONATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1X3G1Ligand/Ion4-{[5-FLUORO-4-(3-{[(3R)-3-HYDROXYPYRROLIDIN-1-YL]METHYL}-4-METHYL-1H-PYRROL-1-YL)PYRIMIDIN-2-YL]AMINO}-2,6-DIMETHYLPHENYL METHANESULFONATE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1X3G1Ligand/Ion4-{[5-FLUORO-4-(3-{[(3R)-3-HYDROXYPYRROLIDIN-1-YL]METHYL}-4-METHYL-1H-PYRROL-1-YL)PYRIMIDIN-2-YL]AMINO}-2,6-DIMETHYLPHENYL METHANESULFONATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:377 , VAL A:385 , ALA A:400 , VAL A:433 , MET A:448 , GLU A:449 , MET A:450 , ALA A:451 , GLY A:454 , PRO A:455 , ARG A:498 , LEU A:501 , ASP A:512binding site for residue X3G A 701
2AC2SOFTWARELEU B:377 , VAL B:385 , ALA B:400 , VAL B:433 , MET B:448 , GLU B:449 , MET B:450 , ALA B:451 , GLU B:452 , GLY B:454 , PRO B:455 , LYS B:458 , ARG B:498 , ASN B:499 , LEU B:501 , ASP B:512binding site for residue X3G B 701

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4XG3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4XG3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4XG3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4XG3)

(-) Exons   (0, 0)

(no "Exon" information available for 4XG3)

(-) 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:262
                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhh.eeeeeee...eeeeeeee..eeeeeeeee...hhhhhhhhhhhhhhh........eeeeee...eeeeee....eehhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eeeee..eeee......ee.......ee.......hhhhhhhhhhhhheehhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh.ee.......hhhhhhhhhhhh........hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xg3 A 363 VYLDRKLLTLEDKELGTVKKGYYQMKKVVKTVAVKILKPALKDELLAEANVMQQLDNPYIVRMIGICEAESWMLVMEMAELGPLNKYLQQNRHVKDKNIIELVHQVSMGMKYLEESNFVHRDLAARNVLLVTQHYAKISDFGLSKALRADENYYKAQTHGKWPVKWYAPECINYYKFSSKSDVWSFGVLMWEAFSYGQKPYRGMKGSEVTAMLEKGERMGCPAGCPREMYDLMNLCWTYDVENRPGFAAVELRLRNYYYDVV 634
                                   372    || 387       397       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632  
                                        377|                   405|                                                                                                                                                                                                                               
                                         383                    411                                                                                                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:267
                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhh.eeeeeeeeeee..eeeeeeeee....eeeeeeeee......hhhhhhhhhhhhhhhhh.......eeeeee...eeeeee....eehhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eeeee..eeee......ee.......ee...hhhhhhhhhhhhheehhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh........hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xg3 B 363 VYLDRKLLTLEDKELGSGNFGTVKKGYYQMKKVVKTVAVKILKNEANDPALKDELLAEANVMQQLDNPYIVRMIGICEAESWMLVMEMAELGPLNKYLQQNRHVKDKNIIELVHQVSMGMKYLEESNFVHRDLAARNVLLVTQHYAKISDFGLSKALRADENYYKAKWPVKWYAPECINYYKFSSKSDVWSFGVLMWEAFSYGQKPYRGMKGSEVTAMLEKGERMGCPAGCPREMYDLMNLCWTYDVENRPGFAAVELRLRNYYYDV 633
                                   372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522     ||536       546       556       566       576       586       596       606       616       626       
                                                                                                                                                                                               528|                                                                                                    
                                                                                                                                                                                                533
   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 4XG3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4XG3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4XG3)

(-) Gene Ontology  (87, 87)

Asymmetric Unit(hide GO term definitions)

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  4xg3
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  KSYK_HUMAN | P43405
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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
        KSYK_HUMAN | P43405: 1a81 1csy 1csz 1xba 1xbb 1xbc 3buw 3emg 3fqe 3fqh 3fqs 3srv 3tub 3tuc 3tud 3vf8 3vf9 4dfl 4dfn 4f4p 4fl1 4fl2 4fl3 4fyn 4fyo 4fz6 4fz7 4gfg 4i0r 4i0s 4i0t 4puz 4pv0 4px6 4rss 4rx7 4rx8 4rx9 4wnm 4xg2 4xg4 4xg6 4xg7 4xg8 4xg9 4yjo 4yjp 4yjq 4yjr 4yjs 4yjt 4yju 4yjv 5c26 5c27 5cxh 5cxz 5cy3 5ghv 5lma 5lmb 5t68 5tiu 5tr6 5tt7

(-) Related Entries Specified in the PDB File

4xg2 4xg4 4xg5 4xg6 4xg7 4xg8 4xg9