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(-) Description

Title :  YEAST ALCOHOL DEHYDROGENASE WITH BOUND COENZYME
 
Authors :  B. V. Plapp, H. A. Charlier Jr. , S. Ramaswamy
Date :  09 Nov 15  (Deposition) - 25 Nov 15  (Release) - 20 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Tetramer, Rossmann, Nad, Alcohol, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. V. Plapp, H. A. Charlier, S. Ramaswamy
Mechanistic Implications From Structures Of Yeast Alcohol Dehydrogenase Complexed With Coenzyme And An Alcohol.
Arch. Biochem. Biophys. V. 591 35 2015
PubMed-ID: 26743849  |  Reference-DOI: 10.1016/J.ABB.2015.12.009
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ALCOHOL DEHYDROGENASE 1
    Chains: A, B
    EC Number: 1.1.1.1
    Engineered: YES
    Expression System: SACCHAROMYCES CEREVISIAE
    Expression System Plasmid: YEP13
    Expression System Strain: ATC 204508
    Expression System Taxid: 559292
    Gene: ADH1, ADC1, YOL086C, O0947
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 / S288C)
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: ALCOHOL DEHYDROGENASE I,YADH-1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1ETF2Ligand/IonTRIFLUOROETHANOL
2NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
3ZN4Ligand/IonZINC ION
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1ETF4Ligand/IonTRIFLUOROETHANOL
2NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
3ZN-1Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:43 , THR A:45 , HIS A:66 , CYS A:153 , NAD A:403 , ETF A:404binding site for residue ZN A 401
2AC2SOFTWARECYS A:97 , CYS A:100 , CYS A:103 , CYS A:111binding site for residue ZN A 402
3AC3SOFTWAREHIS A:44 , THR A:45 , HIS A:48 , TRP A:54 , THR A:157 , SER A:176 , GLY A:177 , ALA A:179 , GLY A:180 , GLY A:181 , LEU A:182 , ASP A:201 , LYS A:206 , PHE A:221 , SER A:246 , VAL A:268 , GLY A:269 , MET A:270 , SER A:293 , VAL A:295 , ARG A:340 , ZN A:401 , ETF A:404 , HOH A:508 , VAL B:284binding site for residue NAD A 403
4AC4SOFTWARETHR A:45 , TRP A:54 , HIS A:66 , TRP A:92 , CYS A:153 , MET A:270 , TYR A:294 , ZN A:401 , NAD A:403binding site for residue ETF A 404
5AC5SOFTWARECYS B:43 , HIS B:66 , GLU B:67 , CYS B:153 , ETF B:404binding site for residue ZN B 401
6AC6SOFTWARECYS B:97 , CYS B:100 , CYS B:103 , CYS B:111binding site for residue ZN B 402
7AC7SOFTWAREVAL A:284 , HIS B:44 , GLY B:177 , GLY B:180 , GLY B:181 , LEU B:182 , ILE B:200 , ASP B:201 , LYS B:206 , PHE B:221 , VAL B:245 , SER B:246 , VAL B:247 , ALA B:251 , VAL B:268 , MET B:270 , SER B:293 , TYR B:294 , VAL B:295 , ETF B:404binding site for residue NAD B 403
8AC8SOFTWARETHR B:45 , HIS B:66 , TRP B:92 , CYS B:153 , TYR B:294 , ZN B:401 , NAD B:403binding site for residue ETF B 404

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:277 -B:277

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Leu A:60 -Pro A:61
2Leu B:60 -Pro B:61

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5ENV)

(-) 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 ....eeeeee........eeeeee.......eeeeeeeeee.hhhhhhhhh................eeeeeeee...........eeee..eee....hhhhhh.hhhhh...ee...........eeeee....eee....hhhhhhhhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhhh..eeeeee...hhhhhhhhh...eeee.....hhhhhhhhhhh..eeeeee...hhhhhhhhhhheeeeeeeee.......eeeeehhhhhhh..eeee....hhhhhhhhhhhhhh......eeeee..hhhhhhhhhh......eeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5env 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 ....eeeee..........eeeee.......eeeeeeeeee..hhhhhhhhh...............eeeeeeee...........eeee..eee......hhhhhhhhhh...ee...........eeeee....eee....hhhhhhhhhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhhh..eeeeee...hhhhhhhh....eeee.....hhhhhhhhhhh..eeeeee...hhhhhhhhhhheeeeeeeee.......eeeeehhhhhhh..eeee....hhhhhhhhhhhhhh......eeeee..hhhhhhhhhhhh....eeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5env 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
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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 5ENV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

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        ADH1_YEAST | P00330: 4w6z

(-) Related Entries Specified in the PDB File

5c1k THE NEW DEPOSITION IS A RE-REFINEMENT, WITH 2 FEWER WATERS AND MORE APPROPRIATE B FACTORS. (PREVIOUS, 5C1K, HAD SOME B FACTORS HITTING THE MINIMUM, PRESUMABLY BECAUSE OF AN ERROR IN USING TLS, AND ADDING BACK THE TLS CONTRIBUTION TO THE RESIDUAL B FACTOR)