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(-) Description

Title :  CRYSTAL STRUCTURE OF AMPPNP-BOUND HUMAN PRPF4B KINASE DOMAIN
 
Authors :  I. Mechin, K. Haas, X. Chen, Y. Zhang, L. Mclean
Date :  20 Dec 12  (Deposition) - 28 Aug 13  (Release) - 06 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Kinase, Transferase (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  (4, 9)

Asymmetric Unit (4, 9)
No.NameCountTypeFull Name
1ANP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2MG1Ligand/IonMAGNESIUM ION
3PTR2Mod. Amino AcidO-PHOSPHOTYROSINE
4SO44Ligand/IonSULFATE ION
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1ANP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2MG-1Ligand/IonMAGNESIUM ION
3PTR1Mod. Amino AcidO-PHOSPHOTYROSINE
4SO41Ligand/IonSULFATE ION
Biological Unit 2 (3, 5)
No.NameCountTypeFull Name
1ANP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2MG-1Ligand/IonMAGNESIUM ION
3PTR1Mod. Amino AcidO-PHOSPHOTYROSINE
4SO43Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:693 , SER A:699 , VAL A:701 , ALA A:715 , LYS A:717 , LEU A:751 , PHE A:767 , GLU A:768 , LEU A:770 , ASN A:773 , ASP A:819 , ASN A:820 , LEU A:822 , ASP A:834 , MG A:1103 , HOH A:1211 , HOH A:1276 , HOH A:1327 , HOH A:1388BINDING SITE FOR RESIDUE ANP A 1101
2AC2SOFTWAREPTR A:849 , ARG A:853 , ARG A:856 , HOH A:1248 , HOH A:1285 , HOH A:1305BINDING SITE FOR RESIDUE SO4 A 1102
3AC3SOFTWAREANP A:1101 , HOH A:1331BINDING SITE FOR RESIDUE MG A 1103
4AC4SOFTWARETHR B:693 , SER B:699 , VAL B:701 , ALA B:715 , LYS B:717 , LEU B:751 , PHE B:767 , GLU B:768 , LEU B:770 , ASN B:773 , ASP B:819 , ASN B:820 , LEU B:822 , ASP B:834BINDING SITE FOR RESIDUE ANP B 1101
5AC5SOFTWAREARG A:709 , ARG B:686 , ARG B:709 , HOH B:1314 , HOH B:1322 , HOH B:1377BINDING SITE FOR RESIDUE SO4 B 1102
6AC6SOFTWAREPTR B:849 , ARG B:853 , ARG B:856 , HOH B:1228BINDING SITE FOR RESIDUE SO4 B 1103
7AC7SOFTWARELYS B:804 , ARG B:808 , HOH B:1258 , HOH B:1289BINDING SITE FOR RESIDUE SO4 B 1104

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4IIR)

(-) 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:326
                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............ee...eeeeeeee...eeeeeee.hhh..eeeeee....hhhhhhhhhhhhhhhhhhhhh.........eeeeeee..eeeeee....eehhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee......eee......ee...........hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh..hhhhhhhh............eeee....eeee.......hhhhhhh.hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4iir A  668 WTDAEGYYRVNIGEVLDKRYNVYGYTGQGSNVVRARDNARANQEVAVKIIRNNELMQKTGLKELEFLKKLNDADPDDKFHCLRLFRHFYHKQHLCLVFEPLSMNLREVLKKYGKDVGLHIKAVRSYSQQLFLALKLLKRCNILHADIKPDNILVNESKTILKLCDFGSASHVADNDITPyLVSRFYRAPEIIIGKSYDYGIDMWSVGCTLYELYTGKILFPGKTNNHMLKLAMDLKGKMPNKMIRKGVFKDQHFDQNLNFMYIEREKVTVMSTINPTKDLLADLILPEDQRKKVHQLKDLLDQILMLDPAKRISINQALQHAFIQE 1005
                                   677       687       699       709       719       729       739       749       759       769       779       789       799       809       819       829       839       849       859       869       879       889       899       909       919       929   ||  945       955    || 969       979       989       999      
                                                      696|                                                                                                                                                   849-PTR                                                                             933|                 960|                                        
                                                       699                                                                                                                                                                                                                                        940                  965                                        


Chain B from PDB  Type:PROTEIN  Length:328
                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............ee...eeeeeeee..eeeeeee.hhh..eeeeee...hhhhhhhhhhhhhhhhhhhhhh.........eeeeeee..eeeeee....eehhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee......eee......ee...........hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh..hhhhhhhh.hhhhh......eeeeee...eeeeee.......hhhhhhh....hhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4iir B  670 DAEGYYRVNIGEVLDKRYNVYGYTGQSNVVRARDNARANQEVAVKIIRNNELMQKTGLKELEFLKKLNDADPDDKFHCLRLFRHFYHKQHLCLVFEPLSMNLREVLKKYGKDVGLHIKAVRSYSQQLFLALKLLKRCNILHADIKPDNILVNESKTILKLCDFGSASHVADNDITPyLVSRFYRAPEIIIGKSYDYGIDMWSVGCTLYELYTGKILFPGKTNNHMLKLAMDLKGKMPNKMIRKGVFKDQHFDQNLNFMYIEVDEREKVTVMSTINPTKDLLADLIQRLPEDQRKKVHQLKDLLDQILMLDPAKRISINQALQHAFIQE 1005
                                   679       689     ||702       712       722       732       742       752       762       772       782       792       802       812       822       832       842      |852       862       872       882       892       902       912       922       932  ||   945       955    || 967       977       987       997        
                                                   695|                                                                                                                                                   849-PTR                                                                               935|                  960|                                          
                                                    699                                                                                                                                                                                                                                          939                   963
   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 4IIR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)

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  4iir
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  PRP4B_HUMAN | Q13523
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  2.7.11.1
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

4ian 4ifc 4ijp