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(-) Description

Title :  PKA IN COMPLEX WITH A HALOGENATED PHTHALAZINONE FRAGMENT COMPOUND.
 
Authors :  D. Narayanan, K. A. Alam, R. A. Engh
Date :  08 Jun 15  (Deposition) - 14 Sep 16  (Release) - 14 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.89
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Inhibitor, Protein Kinase, Structure-Guided, Fragment-Based, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Narayanan, O. A. Gani, K. A. Alam, R. A. Engh
Pka Based Studies Of Ligand Interactions With A Methionine Gatekeeper.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - CAMP-DEPENDENT PROTEIN KINASE CATALYTIC SUBUNIT ALPHA
    Chains: A
    EC Number: 2.7.11.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28B
    Expression System Taxid: 469008
    Expression System Variant: PRAR
    Expression System Vector Type: PLASMID
    Gene: PRKACA, PKACA
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PKA C-ALPHA
 
Molecule 2 - CAMP-DEPENDENT PROTEIN KINASE INHIBITOR ALPHA
    Chains: B
    Engineered: YES
    Fragment: UNP RESIDUES 6-25
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: UNP RESIDUES 6-25
    Synonym: PKI-ALPHA,CAMP-DEPENDENT PROTEIN KINASE INHIBITOR, MUSCLE/BRAIN ISOFORM
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
14951Ligand/Ion4-CHLOROPHTHALAZIN-1(2H)-ONE
2MPD3Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3SEP2Mod. Amino AcidPHOSPHOSERINE
4TPO1Mod. Amino AcidPHOSPHOTHREONINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:70 , VAL A:104 , MET A:120 , GLU A:121 , TYR A:122 , VAL A:123 , LEU A:173 , THR A:183 , PHE A:327 , HOH A:667binding site for residue 495 A 401
2AC2SOFTWAREPHE A:18 , GLU A:155 , TYR A:306binding site for residue MPD A 402
3AC3SOFTWAREARG A:134 , ASN A:326 , PHE A:327 , ASP A:328 , MPD A:404binding site for residue MPD A 403
4AC4SOFTWAREHIS A:131 , ARG A:134 , PHE A:314 , MPD A:403 , HOH A:501binding site for residue MPD A 404

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5BX6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5BX6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5BX6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5BX6)

(-) Exons   (0, 0)

(no "Exon" information available for 5BX6)

(-) 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:346
                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhh......hhh.eeeeeeeee...eeeeeeee.....eeeeeeeehhhhhhh.hhhhhhhhhhhhh.........eeeeee...eeeeeee.....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee........eehhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh........hhhhhhhhhhhh..............hhhhhhhhhhh..hhhhhhh........................................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bx6 A   5 AAKKGsEQESVKEFLAKAKEDFLKKWESPAQNTAHLDQFERIKTLGTGSFGRVMLVKHKETGNHYAMKILDKQKVVKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYVPGGEMFSHLRRIGRFSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKGRTWtLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWFATTDWIAIYQRKVEAPFIPKFKGPGDTSNFDDYEEEEIRVsINEKCGKEFSEF 350
                                 |  14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194  |    204       214       224       234       244       254       264       274       284       294       304       314       324       334   |   344      
                                 |                                                                                                                                                                                        197-TPO                                                                                                                                      338-SEP        
                                10-SEP                                                                                                                                                                                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:20
                                                    
               SCOP domains -------------------- SCOP domains
               CATH domains -------------------- CATH domains
               Pfam domains -------------------- Pfam domains
         Sec.struct. author .hhhhhhh.........ee. Sec.struct. author
                 SAPs(SNPs) -------------------- SAPs(SNPs)
                    PROSITE -------------------- PROSITE
                 Transcript -------------------- Transcript
                 5bx6 B   5 TTYADFIASGRTGRRNAIHD  24
                                    14        24
   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 5BX6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5BX6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5BX6)

(-) Gene Ontology  (86, 89)

Asymmetric/Biological Unit(hide GO term definitions)

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  5bx6
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  IPKA_HUMAN | P61925
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  KAPCA_HUMAN | P17612
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  2.7.11.11
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 Related Entries

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

UniProtKB/Swiss-Prot
        IPKA_HUMAN | P61925: 1cdk 1cmk 1ctp 1jlu 1q24 1q61 1q62 1q8t 1q8u 1q8w 1smh 1stc 1sve 1svg 1svh 1veb 1xh4 1xh5 1xh6 1xh7 1xh8 1xh9 1xha 1ydr 1yds 1ydt 2c1a 2c1b 2f7e 2gni 2jds 2jdt 2jdv 2l1l 2uvx 2uvy 2uvz 2uw0 2uw3 2uw4 2uw5 2uw6 2uw7 2uw8 2vnw 2vny 2vo0 2vo3 2vo6 2vo7 3ama 3amb 3l9l 3l9m 3l9n 3mvj 3nx8 3oog 3ovv 3owp 3oxt 3p0m 3poo 3vqh 3wyg 3x2u 3x2v 3x2w 4axa 4iac 4iad 4iaf 4iai 4iak 4iay 4iaz 4ib0 4ib1 4ib3 4ie9 4ij9 4o21 4o22 4uj1 4uj2 4uj9 4uja 4ujb 4wb5 4wb6 4wb7 4wb8 4z83 4z84 5bx7 5dh9
        KAPCA_HUMAN | P17612: 2gu8 3agl 3agm 3ama 3amb 3l9l 3l9m 3l9n 3mvj 3nx8 3oog 3ovv 3owp 3oxt 3p0m 3poo 3vqh 4ae6 4ae9 4uj1 4uj2 4uj9 4uja 4ujb 4wb5 4wb6 4wb7 4wb8 5bx7 5izf 5izj 5j5x

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5BX6)