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(-) Description

Title :  CRYSTAL STRUCTURE OF THE TERNARY HUMAN PL KINASE-GINKGOTOXIN-MGATP COMPLEX
 
Authors :  M. K. Safo, F. N. Musayev, A. K. Gandhi
Date :  12 Apr 12  (Deposition) - 02 May 12  (Release) - 22 Aug 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
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: PYRIDOXINE KINASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 24)

Asymmetric/Biological Unit (7, 24)
No.NameCountTypeFull Name
1ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2GT02Ligand/Ion5-(HYDROXYMETHYL)-4-(METHOXYMETHYL)-2-METHYLPYRIDIN-3-OL
3GT12Ligand/Ion[5-HYDROXY-4-(METHOXYMETHYL)-6-METHYLPYRIDIN-3-YL]METHYL DIHYDROGEN PHOSPHATE
4MG4Ligand/IonMAGNESIUM ION
5MPD6Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
6NA2Ligand/IonSODIUM ION
7SO46Ligand/IonSULFATE ION

(-) Sites  (24, 24)

Asymmetric Unit (24, 24)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:118 , ATP A:404 , MPD A:406 , HOH A:589 , HOH A:590BINDING SITE FOR RESIDUE MG A 401
02AC2SOFTWAREASP A:113 , THR A:148 , PRO A:149 , ASN A:150 , THR A:186 , ATP A:404 , HOH A:518BINDING SITE FOR RESIDUE NA A 402
03AC3SOFTWAREASP A:235 , ATP A:404 , GT0 A:405 , GT1 A:410BINDING SITE FOR RESIDUE MG A 403
04AC4SOFTWAREASP A:113 , ASP A:118 , ASN A:150 , GLU A:153 , THR A:186 , SER A:187 , VAL A:201 , ARG A:224 , LYS A:225 , VAL A:226 , ALA A:228 , THR A:233 , GLY A:234 , PHE A:237 , LEU A:267 , MG A:401 , NA A:402 , MG A:403 , MPD A:406 , GT1 A:410 , HOH A:509 , HOH A:515 , HOH A:595 , HOH A:596BINDING SITE FOR RESIDUE ATP A 404
05AC5SOFTWARESER A:12 , GLY A:20 , HIS A:46 , THR A:47 , TYR A:84 , VAL A:231 , ASP A:235 , MG A:403 , HOH A:501BINDING SITE FOR RESIDUE GT0 A 405
06AC6SOFTWAREASP A:118 , TRP A:120 , LEU A:199 , MG A:401 , ATP A:404 , HOH A:589 , HOH A:590 , HOH A:594BINDING SITE FOR RESIDUE MPD A 406
07AC7SOFTWAREGLN A:63 , ARG A:70 , MET A:93 , GLU A:100BINDING SITE FOR RESIDUE SO4 A 407
08AC8SOFTWAREGLY A:159 , LYS A:161BINDING SITE FOR RESIDUE SO4 A 408
09AC9SOFTWARELEU A:31 , GLY A:32 , HIS A:246 , LYS A:247BINDING SITE FOR RESIDUE SO4 A 409
10BC1SOFTWARESER A:12 , THR A:47 , TYR A:84 , VAL A:231 , GLY A:232 , THR A:233 , GLY A:234 , ASP A:235 , MG A:403 , ATP A:404 , HOH A:590BINDING SITE FOR RESIDUE GT1 A 410
11BC2SOFTWAREASP B:118 , ATP B:404 , MPD B:407 , HOH B:505 , HOH B:506BINDING SITE FOR RESIDUE MG B 401
12BC3SOFTWAREASP B:113 , THR B:148 , PRO B:149 , THR B:186 , ATP B:404 , HOH B:507BINDING SITE FOR RESIDUE NA B 402
13BC4SOFTWAREVAL B:115 , ASP B:235 , ATP B:404 , GT1 B:405 , GT0 B:414BINDING SITE FOR RESIDUE MG B 403
14BC5SOFTWAREASP B:113 , ASP B:118 , ASN B:150 , GLU B:153 , THR B:186 , SER B:187 , LEU B:199 , VAL B:201 , ARG B:224 , LYS B:225 , VAL B:226 , ALA B:228 , THR B:233 , GLY B:234 , LEU B:263 , LEU B:267 , MG B:401 , NA B:402 , MG B:403 , GT1 B:405 , MPD B:407 , HOH B:506 , HOH B:546 , HOH B:576 , HOH B:577 , HOH B:626BINDING SITE FOR RESIDUE ATP B 404
15BC6SOFTWARESER B:12 , THR B:47 , TYR B:84 , VAL B:231 , GLY B:232 , THR B:233 , GLY B:234 , ASP B:235 , MG B:403 , ATP B:404 , HOH B:506BINDING SITE FOR RESIDUE GT1 B 405
16BC7SOFTWAREASP B:181 , ARG B:207 , ARG B:208 , MPD B:410BINDING SITE FOR RESIDUE MPD B 406
17BC8SOFTWAREASP B:118 , MG B:401 , ATP B:404 , HOH B:505 , HOH B:547 , HOH B:605BINDING SITE FOR RESIDUE MPD B 407
18BC9SOFTWAREASP B:173 , SER B:177 , ARG B:206 , LEU B:312 , HOH B:633BINDING SITE FOR RESIDUE MPD B 408
19CC1SOFTWAREGLN B:165 , PRO B:193BINDING SITE FOR RESIDUE MPD B 409
20CC2SOFTWAREGLY B:179 , ASP B:181 , MPD B:406 , HOH B:528 , HOH B:529 , HOH B:602BINDING SITE FOR RESIDUE MPD B 410
21CC3SOFTWAREGLY B:159BINDING SITE FOR RESIDUE SO4 B 411
22CC4SOFTWAREARG B:70 , GLU B:100BINDING SITE FOR RESIDUE SO4 B 412
23CC5SOFTWARELEU B:31 , GLY B:32 , LYS B:247BINDING SITE FOR RESIDUE SO4 B 413
24CC6SOFTWARESER B:12 , VAL B:19 , PHE B:43 , HIS B:46 , THR B:47 , VAL B:231 , ASP B:235 , MG B:403BINDING SITE FOR RESIDUE GT0 B 414

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4EN4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4EN4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4EN4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4EN4)

(-) Exons   (0, 0)

(no "Exon" information available for 4EN4)

(-) 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:310
                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains d4en4a_ A: automated matches                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee.....hhhhhhhhhhhh..eeeeeeeeee..........eee.hhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhhhhhhhh...eeee....eeee..eeee....hhhhhhhhhhhhhh.ee..hhhhhhhhhh....hhhhhhhhhhhhhhh...eeee............eeeeeeeeeee.....eeeeeeeeeee.......hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhh..hhhhhhhhhh.......ee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4en4 A   3 EECRVLSIQSHVIRGYVGNRAATFPLQVLGFEIDAVNSVQFSNHTGYAHWKGQVLNSDELQELYEGLRLNNMNKYDYVLTGYTRDKSFLAMVVDIVQELKQQNPRLVYVCDPVLGDKWDGEGSMYVPEDLLPVYKEKVVPLADIITPNQFEAELLSGRKIHSQEEALRVMDMLHSMGPDTVVITSSDLPSPQGSNYLIVLGSQRRRNPAGSVVMERIRMDIRKVDAVFVGTGDLFAAMLLAWTHKHPNNLKVACEKTVSTLHHVLQRTIQCAKAQAGEGVRPSPMQLELRMVQSKRDIEDPEIVVQATVL 312
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312


Chain B from PDB  Type:PROTEIN  Length:310
                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains d4en4b_ B: automated matches                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee.....hhhhhhhhhhhh..eeeeeeeeee..........eee.hhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhhhhhhhh...eeee....eeee..eeee..hhhhhhhhhhhhhhhh.ee..hhhhhhhhhh....hhhhhhhhhhhhhhhh..eeee............eeeeeeeeeee.....eeeeeeeeeee.......hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhh.......eee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4en4 B   3 EECRVLSIQSHVIRGYVGNRAATFPLQVLGFEIDAVNSVQFSNHTGYAHWKGQVLNSDELQELYEGLRLNNMNKYDYVLTGYTRDKSFLAMVVDIVQELKQQNPRLVYVCDPVLGDKWDGEGSMYVPEDLLPVYKEKVVPLADIITPNQFEAELLSGRKIHSQEEALRVMDMLHSMGPDTVVITSSDLPSPQGSNYLIVLGSQRRRNPAGSVVMERIRMDIRKVDAVFVGTGDLFAAMLLAWTHKHPNNLKVACEKTVSTLHHVLQRTIQCAKAQAGEGVRPSPMQLELRMVQSKRDIEDPEIVVQATVL 312
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312
   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 4EN4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4EN4)

(-) Gene Ontology  (23, 23)

Asymmetric/Biological Unit(hide GO term definitions)

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

(-) Related Entries Specified in the PDB File

2yxu 4eoh