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(-) Description

Title :  CRYSTAL STRUCTURE OF ARABIDOPSIS THALIANA DJ-1D
 
Authors :  D. Choi, J. Kim, K. -S. Ryu, C. Park
Date :  15 Jan 14  (Deposition) - 15 Oct 14  (Release) - 24 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  Glyoxalase, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Choi, J. Kim, S. Ha, K. Kwon, E. H. Kim, H. Y. Lee, K. S. Ryu, C. Park
Stereospecific Mechanism Of Dj-1 Glyoxalases Inferred From Their Hemithioacetal-Containing Crystal Structures.
Febs J. V. 281 5447 2014
PubMed-ID: 25283443  |  Reference-DOI: 10.1111/FEBS.13085

(-) Compounds

Molecule 1 - PROTEIN DJ-1 HOMOLOG D
    Chains: A, B, C, D, E, F
    EC Number: 4.2.1.130
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: DJ1D, AT3G02720, F13E7.34
    Organism Common: MOUSE-EAR CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: ATDJ1D, LACTOYLGLUTATHIONE LYASE DJ1D

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABC   
Biological Unit 2 (1x):    DEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4OFW)

(-) Sites  (0, 0)

(no "Site" information available for 4OFW)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Asp A:351 -Pro A:352
2Asp B:351 -Pro B:352
3Asp C:351 -Pro C:352
4Asp D:351 -Pro D:352
5Asp E:351 -Pro E:352
6Asp F:351 -Pro F:352

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4OFW)

(-) 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:387
                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee....eehhhhhhhhhhhhhh..eeeee........ee.eeeee.......eeee...ee........hhhhh.eeee...hhhhhhh.hhhhhhhhhhhhhh...eeee..hhhhhhhh......ee..hhhhhhhhhh...ee........eeee..eeee.hhhhhhhhhhhhhhhh..eee....eeeee....eehhhhhhhhhhhhhhh.eeeee........ee.eeeee.......eeee...ee........hhhhh.eeee....hhhhhh.hhhhhhhhhhhhhh...eeee..hhhhhhhhh.....ee..hhhhhhhhhhhh.ee.........eee..eeee.hhhhhhhhhhhhhhh...eee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ofw A   3 NSRTVLILCGDYMEDYEVMVPFQALQAFGITVHTVCPGKKAGDSCPTAVHDFCGHQTYFESRGHNFTLNATFDEVDLSKYDGLVIPGGRAPEYLALTASVVELVKEFSRSGKPIASICHGQLILAAADTVNGRKCTAYATVGPSLVAAGAKWVEPITPDVCVVDGSLITAATYEGHPEFIQLFVKALGGKITGANKRILFLCGDYMEDYEVKVPFQSLQALGCQVDAVCPEKKAGERCPTAIHDFEGDQTYSEKPGHTFALTTNFDDLVSSSYDALVIPGGRAPEYLALNEHVLNIVKEFMNSEKPVASICHGQQILAAAGVLKGRKCTAYPAVKLNVVLGGGTWLEPDPIDRCFTDGNLVTGAAWPGHPEFVSQLMALLGIQVSFH 389
                                    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       322       332       342       352       362       372       382       


Chain B from PDB  Type:PROTEIN  Length:387
                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....eehhhhhhhhhhhhhh.eeeeee........eeeeeeee.......eeeeeeeee...hhhhhhhhhh.eeee...hhhhhhh.hhhhhhhhhhhhhh...eeee..hhhhhhhh......ee..hhhhhhhhhhh..ee........eeee..eeee.hhhhhhhhhhhhhhhh..eee....eeeee....eehhhhhhhhhhhhhhh.eeeee........ee.eeeee.......eeee...ee........hhhhh.eeee...hhhhhhh.hhhhhhhhhhhhhh...eeee..hhhhhhhh.....eee..hhhhhhhhhhh.eee.........eee..eeee.hhhhhhhhhhhhhhhhh.eee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ofw B   3 NSRTVLILCGDYMEDYEVMVPFQALQAFGITVHTVCPGKKAGDSCPTAVHDFCGHQTYFESRGHNFTLNATFDEVDLSKYDGLVIPGGRAPEYLALTASVVELVKEFSRSGKPIASICHGQLILAAADTVNGRKCTAYATVGPSLVAAGAKWVEPITPDVCVVDGSLITAATYEGHPEFIQLFVKALGGKITGANKRILFLCGDYMEDYEVKVPFQSLQALGCQVDAVCPEKKAGERCPTAIHDFEGDQTYSEKPGHTFALTTNFDDLVSSSYDALVIPGGRAPEYLALNEHVLNIVKEFMNSEKPVASICHGQQILAAAGVLKGRKCTAYPAVKLNVVLGGGTWLEPDPIDRCFTDGNLVTGAAWPGHPEFVSQLMALLGIQVSFH 389
                                    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       322       332       342       352       362       372       382       


Chain C from PDB  Type:PROTEIN  Length:387
                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....eehhhhhhhhhhhhh..eeeeee........ee.eeeee.......eeee...ee...hhhhhhhhhh.eeee...hhhhhhh.hhhhhhhhhhhhhh...eeee..hhhhhhhh......ee..hhhhhhhhhhh..ee........eeee..eeee.hhhhhhhhhhhhhhh...eee....eeeee....eehhhhhhhhhhhhhh..eeeee........ee.eeeee.......eeee...ee..............eeee...hhhhhhh.hhhhhhhhhhhhhhh..eeee..hhhhhhhh......ee..hhhhhhhhhhh..ee.........eee..eeee.hhhhhhhhhhhhhhhhh.eee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ofw C   3 NSRTVLILCGDYMEDYEVMVPFQALQAFGITVHTVCPGKKAGDSCPTAVHDFCGHQTYFESRGHNFTLNATFDEVDLSKYDGLVIPGGRAPEYLALTASVVELVKEFSRSGKPIASICHGQLILAAADTVNGRKCTAYATVGPSLVAAGAKWVEPITPDVCVVDGSLITAATYEGHPEFIQLFVKALGGKITGANKRILFLCGDYMEDYEVKVPFQSLQALGCQVDAVCPEKKAGERCPTAIHDFEGDQTYSEKPGHTFALTTNFDDLVSSSYDALVIPGGRAPEYLALNEHVLNIVKEFMNSEKPVASICHGQQILAAAGVLKGRKCTAYPAVKLNVVLGGGTWLEPDPIDRCFTDGNLVTGAAWPGHPEFVSQLMALLGIQVSFH 389
                                    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       322       332       342       352       362       372       382       


Chain D from PDB  Type:PROTEIN  Length:387
                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee....eehhhhhhhhhhhhhh..eeeee........ee.eeeee.......eeee...ee........hhhhh.eeee...hhhhhhh.hhhhhhhhhhhhhh...eeee..hhhhhhhh......ee..hhhhhhhhhh...ee........eeee..eeee.hhhhhhhhhhhhhhh...eee....eeeee....eehhhhhhhhhhhhhhh.eeeee........ee.eeeee.......eeee...ee..............eeee....hhhhhh.hhhhhhhhhhhhhh...eeee..hhhhhhhh......ee..hhhhhhhhhhh..ee.........eee..eeee.hhhhhhhhhhhhhhhhh.eee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ofw D   3 NSRTVLILCGDYMEDYEVMVPFQALQAFGITVHTVCPGKKAGDSCPTAVHDFCGHQTYFESRGHNFTLNATFDEVDLSKYDGLVIPGGRAPEYLALTASVVELVKEFSRSGKPIASICHGQLILAAADTVNGRKCTAYATVGPSLVAAGAKWVEPITPDVCVVDGSLITAATYEGHPEFIQLFVKALGGKITGANKRILFLCGDYMEDYEVKVPFQSLQALGCQVDAVCPEKKAGERCPTAIHDFEGDQTYSEKPGHTFALTTNFDDLVSSSYDALVIPGGRAPEYLALNEHVLNIVKEFMNSEKPVASICHGQQILAAAGVLKGRKCTAYPAVKLNVVLGGGTWLEPDPIDRCFTDGNLVTGAAWPGHPEFVSQLMALLGIQVSFH 389
                                    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       322       332       342       352       362       372       382       


Chain E from PDB  Type:PROTEIN  Length:387
                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....eehhhhhhhhhhhhhh.eeeeee........ee.eeeee.......eeee...ee...hhhhhhhhhh.eeee...hhhhhhh.hhhhhhhhhhhhhh...eeee..hhhhhhhh......ee..hhhhhhhhhhh..ee........eeee..eeee.hhhhhhhhhhhhhhh...eee....eeeee....eehhhhhhhhhhhhhhh.eeeee........ee.eeeee.......eeee...ee..............eeee....hhhhhh.hhhhhhhhhhhhhh...eeee..hhhhhhhh......ee..hhhhhhhhhhh..ee.........eee..eeee.hhhhhhhhhhhhhhhhh.eee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ofw E   3 NSRTVLILCGDYMEDYEVMVPFQALQAFGITVHTVCPGKKAGDSCPTAVHDFCGHQTYFESRGHNFTLNATFDEVDLSKYDGLVIPGGRAPEYLALTASVVELVKEFSRSGKPIASICHGQLILAAADTVNGRKCTAYATVGPSLVAAGAKWVEPITPDVCVVDGSLITAATYEGHPEFIQLFVKALGGKITGANKRILFLCGDYMEDYEVKVPFQSLQALGCQVDAVCPEKKAGERCPTAIHDFEGDQTYSEKPGHTFALTTNFDDLVSSSYDALVIPGGRAPEYLALNEHVLNIVKEFMNSEKPVASICHGQQILAAAGVLKGRKCTAYPAVKLNVVLGGGTWLEPDPIDRCFTDGNLVTGAAWPGHPEFVSQLMALLGIQVSFH 389
                                    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       322       332       342       352       362       372       382       


Chain F from PDB  Type:PROTEIN  Length:387
                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee....eehhhhhhhhhhhhhh..eeeee........ee.eeeee.......eeee...ee...hhhhh......eeee...hhhhhhh.hhhhhhhhhhhhhh...eeee..hhhhhhhhh.....ee..hhhhhhhhhhh..ee........eeee..eeee.hhhhhhhhhhhhhhhh..eee....eeeee....eehhhhhhhhhhhhhh..eeeee........eeeeeeee.......eeeeeeeee..............eeee...hhhhhhh.hhhhhhhhhhhhhhh..eeee..hhhhhhhh......ee..hhhhhhhhhhh..ee.........eee..eeee.hhhhhhhhhhhhhhhhh.eee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ofw F   3 NSRTVLILCGDYMEDYEVMVPFQALQAFGITVHTVCPGKKAGDSCPTAVHDFCGHQTYFESRGHNFTLNATFDEVDLSKYDGLVIPGGRAPEYLALTASVVELVKEFSRSGKPIASICHGQLILAAADTVNGRKCTAYATVGPSLVAAGAKWVEPITPDVCVVDGSLITAATYEGHPEFIQLFVKALGGKITGANKRILFLCGDYMEDYEVKVPFQSLQALGCQVDAVCPEKKAGERCPTAIHDFEGDQTYSEKPGHTFALTTNFDDLVSSSYDALVIPGGRAPEYLALNEHVLNIVKEFMNSEKPVASICHGQQILAAAGVLKGRKCTAYPAVKLNVVLGGGTWLEPDPIDRCFTDGNLVTGAAWPGHPEFVSQLMALLGIQVSFH 389
                                    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       322       332       342       352       362       372       382
   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 4OFW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

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    Asp A:351 - Pro A:352   [ RasMol ]  
    Asp B:351 - Pro B:352   [ RasMol ]  
    Asp C:351 - Pro C:352   [ RasMol ]  
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 Related Entries

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        DJ1D_ARATH | Q9M8R4: 3uk7 4ogg

(-) Related Entries Specified in the PDB File

4ogf 4ogg