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(-) Description

Title :  CRYSTAL STRUCTURE OF HCK IN COMPLEX WITH THE FLUORESCENT COMPOUND SKF86002
 
Authors :  L. J. Parker, A. Tanaka, N. Handa, K. Honda, Y. Tomabechi, M. Shirouzu, S
Date :  25 Jul 13  (Deposition) - 12 Feb 14  (Release) - 12 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.85
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Cocrystallization, Skf86002, Fluorescence, Inhibitor Screening, Kinase, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. J. Parker, S. Taruya, K. Tsuganezawa, N. Ogawa, J. Mikuni, K. Honda, T. Tomabechi, N. Handa, M. Shirouzu, S. Yokoyama, A. Tanaka
Kinase Crystal Identification And Atp-Competitive Inhibitor Screening Using The Fluorescent Ligand Skf86002
Acta Crystallogr. , Sect. D V. 70 392 2014
PubMed: search  |  Reference-DOI: 10.1107/S1399004713028654

(-) Compounds

Molecule 1 - TYROSINE-PROTEIN KINASE HCK
    Chains: A, B
    EC Number: 2.7.10.2
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Fragment: UNP RESIDUES 81-526
    Gene: HCK
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HEMATOPOIETIC CELL KINASE, HEMOPOIETIC CELL KINASE, P59- HCK/P60-HCK, P59HCK, P61HCK

 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  (5, 12)

Asymmetric Unit (5, 12)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION
2CL2Ligand/IonCHLORIDE ION
3GOL3Ligand/IonGLYCEROL
4PTR2Mod. Amino AcidO-PHOSPHOTYROSINE
5SK82Ligand/Ion6-(4-FLUOROPHENYL)-5-(PYRIDIN-4-YL)-2,3-DIHYDROIMIDAZO[2,1-B][1,3]THIAZOLE
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3GOL1Ligand/IonGLYCEROL
4PTR1Mod. Amino AcidO-PHOSPHOTYROSINE
5SK81Ligand/Ion6-(4-FLUOROPHENYL)-5-(PYRIDIN-4-YL)-2,3-DIHYDROIMIDAZO[2,1-B][1,3]THIAZOLE
Biological Unit 2 (3, 4)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3GOL2Ligand/IonGLYCEROL
4PTR1Mod. Amino AcidO-PHOSPHOTYROSINE
5SK81Ligand/Ion6-(4-FLUOROPHENYL)-5-(PYRIDIN-4-YL)-2,3-DIHYDROIMIDAZO[2,1-B][1,3]THIAZOLE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:490 , GLU B:524 , PTR B:527BINDING SITE FOR RESIDUE CA A 601
02AC2SOFTWAREGLU A:524 , PTR A:527 , GLU A:529 , HOH A:726 , GLU B:490BINDING SITE FOR RESIDUE CA A 602
03AC3SOFTWARELEU A:273 , VAL A:281 , ALA A:293 , LYS A:295 , ILE A:336 , THR A:338 , GLU A:339 , PHE A:340 , MET A:341 , SER A:345 , LEU A:393BINDING SITE FOR RESIDUE SK8 A 603
04AC4SOFTWARETYR A:92 , GLU A:145 , GLU A:147 , PHE A:150 , PHE A:151 , SER A:248BINDING SITE FOR RESIDUE GOL A 604
05AC5SOFTWAREARG A:85 , ARG A:123 , ARG A:128BINDING SITE FOR RESIDUE CL A 605
06AC6SOFTWARELEU B:273 , VAL B:281 , ALA B:293 , LYS B:295 , ILE B:336 , THR B:338 , GLU B:339 , PHE B:340 , MET B:341 , SER B:345 , LEU B:393 , ASP B:404 , GOL B:605BINDING SITE FOR RESIDUE SK8 B 601
07AC7SOFTWAREASN B:391 , ASP B:404 , HOH B:733 , HOH B:749BINDING SITE FOR RESIDUE CA B 602
08AC8SOFTWAREARG B:123 , ARG B:128BINDING SITE FOR RESIDUE CL B 603
09AC9SOFTWARETYR B:92 , GLU B:145 , PHE B:150 , PHE B:151BINDING SITE FOR RESIDUE GOL B 604
10BC1SOFTWAREALA B:275 , GLY B:276 , GLY B:279 , VAL B:281 , LYS B:295 , SK8 B:601 , HOH B:717 , HOH B:750BINDING SITE FOR RESIDUE GOL B 605

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Glu A:332 -Pro A:333
2Pro A:469 -Glu A:470
3Glu B:332 -Pro B:333

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4LUD)

(-) 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:422
                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains d4luda1 A:85-146 Hemapoetic cell kinase Hck                d4luda2 A:147-249 Hemopoetic cell kinase Hck                                                         d4luda3 A:250-531 Haemopoetic cell kinase Hck                                                                                                                                                                                                                          SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..................eeeeeeee..eeeeee.....eeeee...ee.......ee...hhhhhhhhhh........eeeee.......eeeeeeeee...eeeeeeeeeee...ee.....ee.hhhhhhhhhh..............................hhh.eeeeeeeee...eeeeeeee...eeeeeeee...hhhhhhhhhhhh.........eeeee....eeeeee.....hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh...........eee.....eee...hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh..........................hhhhhhhhhhhh..hhhhh.hhhhhhhhhhh...hhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lud A  85 RIIVVALYDYEAIHHEDLSFQKGDQMVVLEESGEWWKARSLATRKEGYIPSNYVARLETEEWFFKGISRKDAERQLLAPGNMLGSFMIRDSETTKGSYSLSVRDYDPRQGDTVKHYKIRTLDGFYISPRSTFSTLQELVDHYKKGNDGLCQKLSVPCMSSKPQKPWEKDAWEIPRESLKLEKKLGAGQFGEVWMATYNKHTKVAVKTMKPSVEAFLAEANVMKTLQHDKLVKLHAVVTKEPIYIITEFMAKGSLLDFLKSDEGSKQPLPKLIDFSAQIAEGMAFIEQRNYIHRDLRAANILVSASLVCKIADFGLARVIPIKWTAPEAINFGSFTIKSDVWSFGILLMEIVTYGRIPYPGMSNPELERGYRMPRPENCPEELYNIMMRCWKNRPEERPTFEYIQSVLDDFYTATESQyEEIP 531
                                    94       104       114       124       134     ||147       157       167       177       187       197       207 ||    219       229       239       249       259       269       279       289       299|      312       322       332       342       352       362       372       382       392       402       425       435       445       455       465    || 479       489       499       509       519       529  
                                                                                 140|                                                              209|                                                                                    299|                                                                                                         411|                                          470|                                                 527-PTR
                                                                                  144                                                               212                                                                                     303                                                                                                          425                                           475                                                        


Chain B from PDB  Type:PROTEIN  Length:410
                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains d4ludb1 B:85-146 Hemapoetic cell kinase Hck                   d4ludb2 B:147-249 Hemopoetic cell kinase Hck                                       d4ludb3 B:250-529 Haemopoetic cell kinase Hck                                                                                                                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..................eeeeeeee..eeeeee.....eeeee...eee.........ee...hhhhhhhhhhh.......eeeee....eeeeeeeee...eeeeeeee..hhhhhhhhh..............................hhh.eeeeeeeee...eeeeeeee...eeeeeeee.....hhhhhhhhhhh.........eeeee....eeeeee.....hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh...........eee.....eee...hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhh...hhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lud B  85 RIIVVALYDYEAIHHEDLSFQKGDQMVVLEESGEWWKARSLATRKEGYIPSNYVARVDSLETEEWFFKGISRKDAERQLLAPGNMLGSFMIRDSETSYSLSVRDYDPRQGDTVKHYKITLQELVDHYKKGNDGLCQKLSVPCMSSKPQKPWEKDAWEIPRESLKLEKKLGAGQFGEVWMATYNKHTKVAVKTMKPGSVEAFLAEANVMKTLQHDKLVKLHAVVTKEPIYIITEFMAKGSLLDFLKSDEGSKQPLPKLIDFSAQIAEGMAFIEQRNYIHRDLRAANILVSASLVCKIADFGLARVIPIKWTAPEAINFGSFTIKSDVWSFGILLMEIVTYGRIPYPGMSNPEVIRALERGYRMPRPENCPEELYNIMMRCWKNRPEERPTFEYIQSVLDDFYTATESQyEE 529
                                    94       104       114       124       134       144       154       164       174     ||187       197       224       234       244       254       264       274       284       294     ||306       316       326       336       346       356       366       376       386       396       406    || 429       439       449       459       469       479       489       499       509       519       529
                                                                                                                         180|                  205|                                                                          300|                                                                                                         411|                                                                                                   527-PTR
                                                                                                                          184                   223                                                                           303                                                                                                          425
   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  (3, 6)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (59, 59)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Glu A:332 - Pro A:333   [ RasMol ]  
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  HCK_HUMAN | P08631
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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
        HCK_HUMAN | P08631: 1ad5 1bu1 1qcf 2c0i 2c0o 2c0t 2hck 2hk5 2oi3 2oj2 3hck 3nhn 3rbb 3rea 3reb 3vry 3vrz 3vs0 3vs1 3vs2 3vs3 3vs4 3vs5 3vs6 3vs7 4hck 4lue 4orz 4u5w 5hck

(-) Related Entries Specified in the PDB File

4ll5 CRYSTAL STRUCTURE OF PIM1 IN COMPLEX WITH THE FLUORESCENT COMPOUND SKF86002
4lm5 CRYSTAL STRUCTURE OF PIM1 IN COMPLEX WITH 2-{4-[(3- AMINOPROPYL) AMINO]QUINAZOLIN-2-YL}PHENOL (RESULTING FROM DISPLACEMENT OF SKF86002)
4lmu CRYSTAL STRUCTURE OF PIM1 IN COMPLEX WITH THE INHIBITOR QUERCETIN (RESULTING FROM DISPLACEMENT OF SKF86002)
4lue CRYSTAL STRUCTURE OF HCK IN COMPLEX WITH 7-[TRANS-4-(4- METHYLPIPERAZIN-1-YL)CYCLOHEXYL]-5-(4-PHENOXYPHENYL)-7H- PYRROLO[2,3-D]PYRIMIDIN-4-AMINE (RESULTING FROM DISPLACEMENT OF SKF86002)