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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN PRPF4B KINASE DOMAIN IN COMPLEX WITH 4-{5-[(2-CHLORO-PYRIDIN-4-YLMETHYL)-CARBAMOYL]-THIOPHEN-2-YL}-BENZO[B]THIOPHENE-2-CARBOXYLIC ACID AMINE
 
Authors :  I. Mechin, K. Haas, X. Chen, Y. Zhang, L. Mclean
Date :  22 Dec 12  (Deposition) - 28 Aug 13  (Release) - 06 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Kinase, Transferase, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Q. Gao, I. Mechin, N. Kothari, Z. Guo, G. Deng, K. Haas, J. Mcmanus, D. Hoffmann, A. Wang, D. Wiederschain, J. Rocnik, W. Czechtizky, X. Chen, L. Mclean, H. Arlt, D. Harper, F. Liu, T. Majid, V. Patel, C. Lengauer, C. Garcia-Echeverria, B. Zhang, H. Cheng, M. Dorsch, S. M. Huang
Evaluation Of Cancer Dependence And Druggability Of Prp4 Kinase Using Cellular, Biochemical, And Structural Approaches.
J. Biol. Chem. V. 288 30125 2013
PubMed-ID: 24003220  |  Reference-DOI: 10.1074/JBC.M113.473348

(-) Compounds

Molecule 1 - SERINE/THREONINE-PROTEIN KINASE PRP4 HOMOLOG
    Chains: A, B
    EC Number: 2.7.11.1
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Plasmid: PFASTBAC1
    Expression System Strain: SF9
    Expression System Taxid: 7108
    Expression System Vector Type: PLASMID
    Fragment: KINASE DOMAIN
    Gene: KIAA0536, PRP4, PRP4H, PRP4K, PRPF4B
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PRP4 KINASE, PRP4 PRE-MRNA-PROCESSING FACTOR 4 HOMOLOG

 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, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
11EH2Ligand/Ion4-(5-{[(2-CHLOROPYRIDIN-4-YL)METHYL]CARBAMOYL}THIOPHEN-2-YL)-1-BENZOTHIOPHENE-2-CARBOXAMIDE
2PTR2Mod. Amino AcidO-PHOSPHOTYROSINE
3SO46Ligand/IonSULFATE ION
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
11EH1Ligand/Ion4-(5-{[(2-CHLOROPYRIDIN-4-YL)METHYL]CARBAMOYL}THIOPHEN-2-YL)-1-BENZOTHIOPHENE-2-CARBOXAMIDE
2PTR1Mod. Amino AcidO-PHOSPHOTYROSINE
3SO44Ligand/IonSULFATE ION
Biological Unit 2 (3, 4)
No.NameCountTypeFull Name
11EH1Ligand/Ion4-(5-{[(2-CHLOROPYRIDIN-4-YL)METHYL]CARBAMOYL}THIOPHEN-2-YL)-1-BENZOTHIOPHENE-2-CARBOXAMIDE
2PTR1Mod. Amino AcidO-PHOSPHOTYROSINE
3SO42Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:693 , VAL A:701 , ARG A:703 , ALA A:715 , LYS A:717 , GLU A:768 , LEU A:770 , SER A:771 , MET A:772 , GLU A:776 , LEU A:822 , HOH A:1233 , HOH A:1271BINDING SITE FOR RESIDUE 1EH A 1101
2AC2SOFTWAREARG A:686 , ARG A:709 , ARG B:709BINDING SITE FOR RESIDUE SO4 A 1102
3AC3SOFTWAREPTR A:849 , ARG A:853 , ARG A:856BINDING SITE FOR RESIDUE SO4 A 1103
4AC4SOFTWARELYS A:804 , ARG A:808 , LYS B:990BINDING SITE FOR RESIDUE SO4 A 1104
5AC5SOFTWARELYS A:747 , PHE A:748 , ARG A:808BINDING SITE FOR RESIDUE SO4 A 1105
6AC6SOFTWARETHR B:693 , VAL B:701 , ARG B:703 , ALA B:715 , LYS B:717 , LEU B:770 , SER B:771 , MET B:772 , GLU B:776 , LEU B:822BINDING SITE FOR RESIDUE 1EH B 1101
7AC7SOFTWAREPTR B:849 , ARG B:853 , ARG B:856 , HOH B:1213BINDING SITE FOR RESIDUE SO4 B 1102
8AC8SOFTWARELYS B:804 , ARG B:808BINDING SITE FOR RESIDUE SO4 B 1103

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gly A:696 -Val A:697
2Gln B:695 -Gly B:696
3Gly B:696 -Val B:697

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4IJP)

(-) 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:331
                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............ee...eeeeee........eeeeee.hhh..eeeeee...hhhhhhhhhhhhhhhhhhhhhh.........eeeeeee..eeeeee....eehhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee......eee......ee...........hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh..hhhhhhhh.hhhhh......eeeee.....eeeee.......hhhhhhh...hhhhhhhhhhhhhhhhhhh..hhhhh.hhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4ijp A  670 DAEGYYRVNIGEVLDKRYNVYGYTGQGVFSNVVRARDNARANQEVAVKIIRNNELMQKTGLKELEFLKKLNDADPDDKFHCLRLFRHFYHKQHLCLVFEPLSMNLREVLKKYGKDVGLHIKAVRSYSQQLFLALKLLKRCNILHADIKPDNILVNESKTILKLCDFGSASHVADNDITPyLVSRFYRAPEIIIGKSYDYGIDMWSVGCTLYELYTGKILFPGKTNNHMLKLAMDLKGKMPNKMIRKGVFKDQHFDQNLNFMYIEVDEREKVTVMSTINPTKDLLADLIQRLPEDQRKKVHQLKDLLDQILMLDPAKRISINQALQHAFIQE 1005
                                   679       689       699       709       719       729       739       749       759       769       779       789       799       809       819       829       839       849       859       869       879       889       899       909       919       929     ||942       952       964       974       984       994      1004 
                                                                                                                                                                                                             849-PTR                                                                               935|                  960|                                          
                                                                                                                                                                                                                                                                                                    939                   963                                          


Chain B from PDB  Type:PROTEIN  Length:334
                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............ee...eeeeeeee....eeeeeeee.hhh..eeeeeee..hhhhhhhhhhhhhhhhhhhhhh.........eeeeeee..eeeeee....eehhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee......eee......ee...........hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh..hhhhhhhh.hhhhhh.....eeee......eeee.......hhhhhhhh....hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4ijp B  668 WTDAEGYYRVNIGEVLDKRYNVYGYTGQGVFSNVVRARDNARANQEVAVKIIRNNELMQKTGLKELEFLKKLNDADPDDKFHCLRLFRHFYHKQHLCLVFEPLSMNLREVLKKYGKDVGLHIKAVRSYSQQLFLALKLLKRCNILHADIKPDNILVNESKTILKLCDFGSASHVADNDITPyLVSRFYRAPEIIIGKSYDYGIDMWSVGCTLYELYTGKILFPGKTNNHMLKLAMDLKGKMPNKMIRKGVFKDQHFDQNLNFMYIEVDREKVTVMSTINPTKDLLADLIGCQRLPEDQRKKVHQLKDLLDQILMLDPAKRISINQALQHAFIQE 1005
                                   677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847 |     857       867       877       887       897       907       917       927       941       951       961       971       981       991      1001    
                                                                                                                                                                                                               849-PTR                                                                               935|                                                                 
                                                                                                                                                                                                                                                                                                      940
   Legend:   → Mismatch (orange background)
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    → 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 4IJP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 17)

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  PRP4B_HUMAN | Q13523
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 Related Entries

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

UniProtKB/Swiss-Prot
        PRP4B_HUMAN | Q13523: 4ian 4ifc 4iir

(-) Related Entries Specified in the PDB File

4ian 4ifc 4iir