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(-) Description

Title :  YEAST ALCOHOL DEHYDROGENASE I, SACCHAROMYCES CEREVISIAE FERMENTATIVE ENZYME
 
Authors :  B. V. Plapp, B. R. Savarimuthu, S. Ramaswamy
Date :  21 Aug 14  (Deposition) - 03 Sep 14  (Release) - 01 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (2x)
Biol. Unit 2:  C,D  (2x)
Keywords :  Tetramer Of Asymmetric Dimers, Zinc Coordination, Intramolecular Disulfide Bonds, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. B. Raj, S. Ramaswamy, B. V. Plapp
Yeast Alcohol Dehydrogenase Structure And Catalysis.
Biochemistry V. 53 5791 2014
PubMed-ID: 25157460  |  Reference-DOI: 10.1021/BI5006442
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ALCOHOL DEHYDROGENASE 1
    ChainsA, B, C, D
    EC Number1.1.1.1
    EngineeredYES
    Expression SystemSACCHAROMYCES CEREVISIAE
    Expression System CommonBAKER'S YEAST
    Expression System PlasmidYEP13
    Expression System Strain302-21#2 (ADH1-11, ADH2, LEU2, TRP2)
    Expression System Taxid4932
    Expression System Vector TypePLASMID
    GeneADH1, ADC1, YOL086C, O0947
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid559292
    StrainATCC 204508 / S288C
    SynonymALCOHOL DEHYDROGENASE I,YADH-1

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (2x)AB  
Biological Unit 2 (2x)  CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 14)

Asymmetric Unit (3, 14)
No.NameCountTypeFull Name
18ID2Ligand/IonNICOTINAMIDE-8-IODO-ADENINE-DINUCLEOTIDE
2ETF4Ligand/IonTRIFLUOROETHANOL
3ZN8Ligand/IonZINC ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
18ID2Ligand/IonNICOTINAMIDE-8-IODO-ADENINE-DINUCLEOTIDE
2ETF4Ligand/IonTRIFLUOROETHANOL
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
18ID2Ligand/IonNICOTINAMIDE-8-IODO-ADENINE-DINUCLEOTIDE
2ETF4Ligand/IonTRIFLUOROETHANOL
3ZN-1Ligand/IonZINC ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:43 , THR A:45 , HIS A:66 , CYS A:153 , 8ID A:403 , ETF A:404binding site for residue ZN A 401
02AC2SOFTWARECYS A:97 , MET A:98 , CYS A:100 , CYS A:103 , CYS A:111binding site for residue ZN A 402
03AC3SOFTWARECYS A:43 , HIS A:44 , THR A:45 , HIS A:48 , TRP A:54 , CYS A:153 , THR A:157 , GLY A:177 , ALA A:179 , GLY A:180 , GLY A:181 , LEU A:182 , ILE A:200 , ASP A:201 , LYS A:206 , PHE A:221 , VAL A:245 , SER A:246 , SER A:248 , ALA A:251 , VAL A:268 , GLY A:269 , MET A:270 , SER A:293 , TYR A:294 , VAL A:295 , ARG A:340 , ZN A:401 , ETF A:404 , HOH A:515 , HOH A:516 , VAL B:284binding site for residue 8ID A 403
04AC4SOFTWARECYS A:43 , THR A:45 , TRP A:54 , HIS A:66 , TRP A:92 , CYS A:153 , MET A:270 , TYR A:294 , ZN A:401 , 8ID A:403binding site for residue ETF A 404
05AC5SOFTWARECYS B:43 , HIS B:66 , GLU B:67 , CYS B:153 , ETF B:404binding site for residue ZN B 401
06AC6SOFTWARECYS B:97 , CYS B:100 , CYS B:103 , CYS B:111binding site for residue ZN B 402
07AC7SOFTWARETHR B:45 , HIS B:66 , CYS B:153 , MET B:270 , VAL B:295 , ZN B:401binding site for residue ETF B 404
08AC8SOFTWARECYS C:43 , THR C:45 , HIS C:66 , CYS C:153 , 8ID C:403 , ETF C:404binding site for residue ZN C 401
09AC9SOFTWARECYS C:97 , CYS C:100 , CYS C:103 , CYS C:111binding site for residue ZN C 402
10AD1SOFTWARECYS C:43 , HIS C:44 , THR C:45 , HIS C:48 , TRP C:54 , CYS C:153 , THR C:157 , GLY C:177 , ALA C:179 , GLY C:180 , GLY C:181 , LEU C:182 , ILE C:200 , ASP C:201 , LYS C:206 , PHE C:221 , VAL C:245 , SER C:246 , SER C:248 , ALA C:251 , VAL C:268 , GLY C:269 , MET C:270 , SER C:293 , TYR C:294 , VAL C:295 , ARG C:340 , ZN C:401 , ETF C:404 , HOH C:513 , HOH C:514 , VAL D:284binding site for residue 8ID C 403
11AD2SOFTWARECYS C:43 , THR C:45 , TRP C:54 , HIS C:66 , TRP C:92 , CYS C:153 , MET C:270 , TYR C:294 , ZN C:401 , 8ID C:403binding site for residue ETF C 404
12AD3SOFTWARECYS D:43 , HIS D:66 , GLU D:67 , CYS D:153 , ETF D:404binding site for residue ZN D 401
13AD4SOFTWARECYS D:97 , MET D:98 , CYS D:100 , CYS D:103 , CYS D:111binding site for residue ZN D 402
14AD5SOFTWARETHR D:45 , HIS D:66 , CYS D:153 , VAL D:295 , ZN D:401 , HOH D:526binding site for residue ETF D 404

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:277 -B:277
2C:277 -D:277

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Leu A:60 -Pro A:61
2Leu B:60 -Pro B:61
3Leu C:60 -Pro C:61
4Leu D:60 -Pro D:61

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4W6Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4W6Z)

(-) Exons   (0, 0)

(no "Exon" information available for 4W6Z)

(-) 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:347
                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee.......eeeeee.......eeeeeeeeee.hhhhhhhhhh.........ee...eeeeeeeee...........eeee..eee....hhhhhh.hhhhh...ee...........eeeee....eee....hhhhhhhhhhhhhhhhhhhhh.......eeeee.....hhhhhhhhhhhhh.eeeeee...hhhhhhhhh...eeee.....hhhhhhhhhh...eeeeee...hhhhhhhhhhheeeeeeeee.......eeeeehhhhhhh..eeee....hhhhhhhhhhhhhh......eeeee..hhhhhhhhhhh.....eeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w6z A   1 SIPETQKGVIFYESHGKLEYKDIPVPKPKANELLINVKYSGVCHTDLHAWHGDWPLPVKLPLVGGHEGAGVVVGMGENVKGWKIGDYAGIKWLNGSCMACEYCELGNESNCPHADLSGYTHDGSFQQYATADAVQAAHIPQGTDLAQVAPILCAGITVYKALKSANLMAGHWVAISGAAGGLGSLAVQYAKAMGYRVLGIDGGEGKEELFRSIGGEVFIDFTKEKDIVGAVLKATDGGAHGVINVSVSEAAIEASTRYVRANGTTVLVGMPAGAKCCSDVFNQVVKSISIVGSYVGNRADTREALDFFARGLVKSPIKVVGLSTLPEIYEKMEKGQIVGRYVVDTSK 347
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       

Chain B from PDB  Type:PROTEIN  Length:347
                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee.......eeeeee.......eeeeeeeeee..hhhhhhhhh.........ee....eeeeeeee...........eeee..eee....hhhhhhhhhhhh...ee...........eeeee....eee....hhhhhhhhhhhhhhhhhhhhhh......eeeee....hhhhhhhhhhhhh..eeeeee...hhhhhhhhh...eeee.....hhhhhhhhhh...eeeeee...hhhhhhhhhhheeeeeeeee.......eeeeehhhhhhh..eeee....hhhhhhhhhhhhhh.......eeee..hhhhhhhhhhh......eeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w6z B   1 SIPETQKGVIFYESHGKLEYKDIPVPKPKANELLINVKYSGVCHTDLHAWHGDWPLPVKLPLVGGHEGAGVVVGMGENVKGWKIGDYAGIKWLNGSCMACEYCELGNESNCPHADLSGYTHDGSFQQYATADAVQAAHIPQGTDLAQVAPILCAGITVYKALKSANLMAGHWVAISGAAGGLGSLAVQYAKAMGYRVLGIDGGEGKEELFRSIGGEVFIDFTKEKDIVGAVLKATDGGAHGVINVSVSEAAIEASTRYVRANGTTVLVGMPAGAKCCSDVFNQVVKSISIVGSYVGNRADTREALDFFARGLVKSPIKVVGLSTLPEIYEKMEKGQIVGRYVVDTSK 347
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       

Chain C from PDB  Type:PROTEIN  Length:347
                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee.......eeeeee.......eeeeeeeeee.hhhhhhhhhh.........ee....eeeeeeee...........eeee..eee....hhhhhh.hhhhh...ee...........eeeee....eee....hhhhhhhhhhhhhhhhhhhhhh......eeeee.....hhhhhhhhhhhh..eeeeee...hhhhhhhhh...eeee.....hhhhhhhhhh...eeeeee...hhhhhhhhhhheeeeeeeee.......eeeeehhhhhhh..eeee....hhhhhhhhhhhhhh......eeeee..hhhhhhhhhhh.....eeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w6z C   1 SIPETQKGVIFYESHGKLEYKDIPVPKPKANELLINVKYSGVCHTDLHAWHGDWPLPVKLPLVGGHEGAGVVVGMGENVKGWKIGDYAGIKWLNGSCMACEYCELGNESNCPHADLSGYTHDGSFQQYATADAVQAAHIPQGTDLAQVAPILCAGITVYKALKSANLMAGHWVAISGAAGGLGSLAVQYAKAMGYRVLGIDGGEGKEELFRSIGGEVFIDFTKEKDIVGAVLKATDGGAHGVINVSVSEAAIEASTRYVRANGTTVLVGMPAGAKCCSDVFNQVVKSISIVGSYVGNRADTREALDFFARGLVKSPIKVVGLSTLPEIYEKMEKGQIVGRYVVDTSK 347
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       

Chain D from PDB  Type:PROTEIN  Length:347
                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee.......eeeeee.......eeeeeeeeeee.hhhhhhhhh.........ee....eeeeeeee...........eeee..eee....hhhhhhhhhhhh...ee...........eeeee....eee........hhhhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhhh..eeeeee...hhhhhhhhh...eeee.....hhhhhhhhhhh..eeeeee...hhhhhhhhhhheeeeeeeee.......eeeeehhhhhhh..eeee....hhhhhhhhhhhhhh.......eeee..hhhhhhhhhhhh.....eeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w6z D   1 SIPETQKGVIFYESHGKLEYKDIPVPKPKANELLINVKYSGVCHTDLHAWHGDWPLPVKLPLVGGHEGAGVVVGMGENVKGWKIGDYAGIKWLNGSCMACEYCELGNESNCPHADLSGYTHDGSFQQYATADAVQAAHIPQGTDLAQVAPILCAGITVYKALKSANLMAGHWVAISGAAGGLGSLAVQYAKAMGYRVLGIDGGEGKEELFRSIGGEVFIDFTKEKDIVGAVLKATDGGAHGVINVSVSEAAIEASTRYVRANGTTVLVGMPAGAKCCSDVFNQVVKSISIVGSYVGNRADTREALDFFARGLVKSPIKVVGLSTLPEIYEKMEKGQIVGRYVVDTSK 347
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       

   Legend:   → Mismatch (orange background)
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  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 4W6Z)

(-) CATH Domains  (0, 0 ; only for superseded entry 2HCY: 2,8)

(no "CATH Domain" information available for 4W6Z, only for superseded entry 2HCY replaced by 4W6Z)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4W6Z)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)

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