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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN PL KINASE WITH BOUND THEOPHYLLINE
 
Authors :  M. K. Safo, A. K. Gandhi, F. N. Musayev
Date :  14 Apr 12  (Deposition) - 02 May 12  (Release) - 22 Aug 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. K. Gandhi, J. V. Desai, M. S. Ghatge, M. L. Di Salvo, S. Di Biase, R. Danso-Danquah, F. N. Musayev, R. Contestabile, V. Schirch, M. K. Safo
Crystal Structures Of Human Pyridoxal Kinase In Complex Wit The Neurotoxins, Ginkgotoxin And Theophylline: Insights Int Pyridoxal Kinase Inhibition.
Plos One V. 7 40954 2012
PubMed-ID: 22879864  |  Reference-DOI: 10.1371/JOURNAL.PONE.0040954

(-) Compounds

Molecule 1 - PYRIDOXAL KINASE
    Chains: A, B
    EC Number: 2.7.1.35
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: ROSETTA(DE3)PLYSS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PDXK, C21ORF124, C21ORF97, PKH, PNK, PRED79
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PL KINASE, PYRIDOXINE KINASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 25)

Asymmetric/Biological Unit (4, 25)
No.NameCountTypeFull Name
1MPD14Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2NA2Ligand/IonSODIUM ION
3SO47Ligand/IonSULFATE ION
4TEP2Ligand/IonTHEOPHYLLINE

(-) Sites  (25, 25)

Asymmetric Unit (25, 25)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:153 , HOH A:536 , HOH A:537 , HOH A:538 , HOH A:539 , HOH A:645BINDING SITE FOR RESIDUE NA A 401
02AC2SOFTWARESER A:12 , GLY A:20 , VAL A:231 , ASP A:235 , HOH A:546 , HOH A:631 , HOH A:633BINDING SITE FOR RESIDUE TEP A 402
03AC3SOFTWARESER A:12 , PHE A:43 , HIS A:46 , THR A:47 , HOH A:647BINDING SITE FOR RESIDUE MPD A 403
04AC4SOFTWARETHR A:186 , GLY A:234 , LEU A:263BINDING SITE FOR RESIDUE MPD A 404
05AC5SOFTWARELYS A:76 , TYR A:77 , ASP A:78 , ASN A:105 , HOH A:636BINDING SITE FOR RESIDUE MPD A 405
06AC6SOFTWAREILE A:223 , ARG A:224 , VAL A:226 , HIS A:264 , HOH A:541BINDING SITE FOR RESIDUE MPD A 406
07AC7SOFTWARECYS A:5 , LEU A:31 , GLY A:32 , LYS A:247BINDING SITE FOR RESIDUE MPD A 407
08AC8SOFTWARELEU A:156 , LYS A:161BINDING SITE FOR RESIDUE SO4 A 408
09AC9SOFTWAREARG A:70 , MET A:93 , GLU A:100BINDING SITE FOR RESIDUE SO4 A 409
10BC1SOFTWARESER A:40 , VAL A:56 , THR A:85 , ARG A:86 , ASP A:87 , PHE A:90 , HOH A:600BINDING SITE FOR RESIDUE SO4 A 410
11BC2SOFTWAREGLU B:153 , HOH B:615 , HOH B:628 , HOH B:690 , HOH B:691BINDING SITE FOR RESIDUE NA B 401
12BC3SOFTWARESER B:12 , TYR B:84 , VAL B:231 , ASP B:235 , HOH B:630 , HOH B:660 , HOH B:693BINDING SITE FOR RESIDUE TEP B 402
13BC4SOFTWAREHIS B:46 , THR B:47 , TYR B:84 , MPD B:407BINDING SITE FOR RESIDUE MPD B 403
14BC5SOFTWAREASP B:181 , ARG B:208BINDING SITE FOR RESIDUE MPD B 404
15BC6SOFTWAREPRO B:193BINDING SITE FOR RESIDUE MPD B 405
16BC7SOFTWAREMET B:126 , GLU B:130 , LEU B:156 , HOH B:636BINDING SITE FOR RESIDUE MPD B 406
17BC8SOFTWARESER A:192 , PRO A:193 , PHE B:43 , TYR B:84 , ARG B:86 , MPD B:403BINDING SITE FOR RESIDUE MPD B 407
18BC9SOFTWARETHR B:186 , THR B:233BINDING SITE FOR RESIDUE MPD B 408
19CC1SOFTWAREVAL B:109 , THR B:245 , PRO B:249 , HOH B:514 , HOH B:572 , HOH B:678 , HOH B:684BINDING SITE FOR RESIDUE MPD B 409
20CC2SOFTWAREILE B:223 , ARG B:224 , VAL B:226 , HIS B:264 , LEU B:267BINDING SITE FOR RESIDUE MPD B 410
21CC3SOFTWAREILE B:223 , ARG B:224 , HIS B:264 , VAL B:306 , VAL B:307BINDING SITE FOR RESIDUE MPD B 411
22CC4SOFTWAREGLN B:63 , GLU B:100 , HOH B:689BINDING SITE FOR RESIDUE SO4 B 412
23CC5SOFTWAREGLU B:4 , CYS B:5 , ASP B:78 , HIS B:246 , HOH B:581 , HOH B:663BINDING SITE FOR RESIDUE SO4 B 413
24CC6SOFTWARECYS B:5 , LEU B:31 , GLY B:32 , PHE B:33 , HIS B:246 , LYS B:247BINDING SITE FOR RESIDUE SO4 B 414
25CC7SOFTWAREGLU B:155 , LEU B:156BINDING SITE FOR RESIDUE SO4 B 415

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4EOH)

(-) 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:303
                                                                                                                                                                                                                                                                                                                                               
               SCOP domains d4eoha_ A: automated matches                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee.....hhhhhhhhhhhh..eeeeeeeeee..........eee.hhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhhhhhhhh...eeee....eee....eee.....hhhhhhhhhhhhh.ee..hhhhhhhhhh....hhhhhhhhhhhhhhhh..eeee............eeeeeeeee...eeeeeeeee.......hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhh.......ee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eoh A   4 ECRVLSIQSHVIRGYVGNRAATFPLQVLGFEIDAVNSVQFSNHTGYAHWKGQVLNSDELQELYEGLRLNNMNKYDYVLTGYTRDKSFLAMVVDIVQELKQQNPRLVYVCDPVLGDKWDGEGSMYVPEDLLPVYKEKVVPLADIITPNQFEAELLSGRKIHSQEEALRVMDMLHSMGPDTVVITSSDLPSPQGSNYLIVLGSQRRVVMERIRMDIRKVDAVFVGTGDLFAAMLLAWTHKHPNNLKVACEKTVSTLHHVLQRTIQCAKAQAGEGVRPSPMQLELRMVQSKRDIEDPEIVVQATVL 312
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203   ||  219       229       239       249       259       269       279       289       299       309   
                                                                                                                                                                                                                                     207|                                                                                                  
                                                                                                                                                                                                                                      214                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:307
                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains d4eohb_ B: automated matches                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee.....hhhhhhhhhhhh..eeeeeeeeee..........eee.hhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhhhhhhhh...eeee....ee......ee..hhhhhhhhhhhhhhhh.ee..hhhhhhhhhh....hhhhhhhhhhhhhhhh..eeee............eeeeeeeeeee.....eeeeeeeeeee.......hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhh.......ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eoh B   4 ECRVLSIQSHVIRGYVGNRAATFPLQVLGFEIDAVNSVQFSNHTGYAHWKGQVLNSDELQELYEGLRLNNMNKYDYVLTGYTRDKSFLAMVVDIVQELKQQNPRLVYVCDPVLGDKWDGEGSMYVPEDLLPVYKEKVVPLADIITPNQFEAELLSGRKIHSQEEALRVMDMLHSMGPDTVVITSSDLPSPQGSNYLIVLGSQRRRNPAGSVVMERIRMDIRKVDAVFVGTGDLFAAMLLAWTHKHPNNLKVACEKTVSTLHHVLQRTIQCAKAQAGVRPSPMQLELRMVQSKRDIEDPEIVVQATVL 312
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273     ||285       295       305       
                                                                                                                                                                                                                                                                                                             279|                              
                                                                                                                                                                                                                                                                                                              282
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (23, 23)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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        PDXK_HUMAN | O00764: 2ajp 2f7k 2yxt 2yxu 3fhx 3fhy 3keu 4en4

(-) Related Entries Specified in the PDB File

3kbi 4en4