Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  ALCOHOL DEHYDROGENASE (E.C.1.1.1.1) (EE ISOZYME) COMPLEXED WITH NICOTINAMIDE ADENINE DINUCLEOTIDE (NAD), AND ZINC
 
Authors :  H. Eklund
Date :  29 Sep 95  (Deposition) - 08 Mar 96  (Release) - 29 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Oxidoreductase, Oxidoreductase (Ch-Oh(D)-Nad(A)) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Ramaswamy, M. El Ahmad, O. Danielsson, H. Jornvall, H. Eklund
Crystal Structure Of Cod Liver Class I Alcohol Dehydrogenase: Substrate Pocket And Structurally Variable Segments.
Protein Sci. V. 5 663 1996
PubMed-ID: 8845755
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ALCOHOL DEHYDROGENASE
    Chains: A, B
    EC Number: 1.1.1.1
    Organ: LIVER
    Organism Common: BALTIC COD
    Organism Scientific: GADUS CALLARIAS
    Organism Taxid: 8053

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
2ZN4Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:46 , HIS A:68 , CYS A:175 , NAD A:375 , HOH A:1352BINDING SITE FOR RESIDUE ZN A 376
2AC2SOFTWARECYS A:98 , CYS A:101 , CYS A:104 , CYS A:112BINDING SITE FOR RESIDUE ZN A 377
3AC3SOFTWARECYS B:46 , HIS B:68 , CYS B:175 , NAD B:375 , HOH B:1253BINDING SITE FOR RESIDUE ZN B 376
4AC4SOFTWARECYS B:98 , CYS B:101 , CYS B:104 , CYS B:112BINDING SITE FOR RESIDUE ZN B 377
5AC5SOFTWAREHIS A:47 , THR A:48 , CYS A:175 , THR A:179 , GLY A:200 , GLY A:202 , ALA A:203 , VAL A:204 , VAL A:223 , ASP A:224 , LEU A:225 , LYS A:229 , CYS A:269 , VAL A:270 , GLY A:271 , VAL A:275 , VAL A:293 , TRP A:295 , SER A:317 , PHE A:319 , ARG A:369 , ZN A:376 , HOH A:849 , HOH A:952 , HOH A:1010 , HOH A:1213 , HOH A:1256 , HOH A:1257BINDING SITE FOR RESIDUE NAD A 375
6AC6SOFTWAREHIS B:47 , THR B:179 , GLY B:200 , GLY B:202 , ALA B:203 , VAL B:204 , ASP B:224 , LEU B:225 , LYS B:229 , CYS B:269 , VAL B:270 , VAL B:275 , VAL B:293 , GLY B:294 , TRP B:295 , SER B:317 , MET B:318 , PHE B:319 , ARG B:369 , ZN B:376 , HOH B:857 , HOH B:859 , HOH B:863 , HOH B:1117 , HOH B:1240 , HOH B:1253 , HOH B:1259 , HOH B:1341 , HOH B:1357 , HOH B:1385BINDING SITE FOR RESIDUE NAD B 375
7ZINUNKNOWNCYS A:46 , GLY A:174 , GLY A:67 , CYS B:46 , GLY B:174 , GLY B:67NULL

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1CDO)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Phe A:62 -Pro A:63
2Phe B:62 -Pro B:63

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1CDO)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADH_ZINCPS00059 Zinc-containing alcohol dehydrogenases signature.ADH1_GADMC67-81
 		  2A:67-81
B:67-81

(-) Exons   (0, 0)

(no "Exon" information available for 1CDO)

(-) 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:374
 aligned with ADH1_GADMC | P26325 from UniProtKB/Swiss-Prot  Length:375

    Alignment length:374
                                    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       350       360       370    
           ADH1_GADMC     1 ATVGKVIKCKAAVAWEANKPLVIEEIEVDVPHANEIRIKIIATGVCHTDLYHLFEGKHKDGFPVVLGHEGAGIVESVGPGVTEFQPGEKVIPLFISQCGECRFCQSPKTNQCVKGWANESPDVMSPKETRFTCKGRKVLQFLGTSTFSQYTVVNQIAVAKIDPSAPLDTVCLLGCGVSTGFGAAVNTAKVEPGSTCAVFGLGAVGLAAVMGCHSAGAKRIIAVDLNPDKFEKAKVFGATDFVNPNDHSEPISQVLSKMTNGGVDFSLECVGNVGVMRNALESCLKGWGVSVLVGWTDLHDVATRPIQLIAGRTWKGSMFGGFKGKDGVPKMVKAYLDKKVKLDEFITHRMPLESVNDAIDLMKHGKCIRTVLSL 374
               SCOP domains d1cdoa1 A:1-164,A:340-374 Alcohol dehydrogenase                                                                                                                     d1cdoa2 A:165-339 Alcohol dehydrogenase                                                                                                                                        d1cdoa1 A:1-164,A:340-374           SCOP domains
               CATH domains 1cdoA01 A:1-179,A:318-374 Medium-chain alcohol dehydrogenases, catalytic domain                                                                                                    1cdoA02 A:180-317 NAD(P)-binding Rossmann-like Domain                                                                                     1cdoA01 A:1-179,A:318-374                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeee........eeeeeee......eeeeee.eee..hhhhhhhh.................eeeeee............eee.........hhhh..........hhh............eee..eee..hhh......eeeeehhheee......hhhhhhhh.hhhhhhhhhh.........eeeee...hhhhhhhhhhhh....eeeee...hhhhhhhhh....eee.hhh....hhhhhhhhh.....eeee....hhhhhhhhh.......eeee.......eeeeehhhhh...eeee..hhh..hhhhhhhhhhhhh......hhheeeeeehhhhhhhhhhhhh....eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------ADH_ZINC       ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1cdo A   1 ATVGKVIKCKAAVAWEANKPLVIEEIEVDVPHANEIRIKIIATGVCHTDLYHLFEGKHKDGFPVVLGHEGAGIVESVGPGVTEFQPGEKVIPLFISQCGECRFCQSPKTNQCVKGWANESPDVMSPKETRFTCKGRKVLQFLGTSTFSQYTVVNQIAVAKIDPSAPLDTVCLLGCGVSTGFGAAVNTAKVEPGSTCAVFGLGAVGLAAVMGCHSAGAKRIIAVDLNPDKFEKAKVFGATDFVNPNDHSEPISQVLSKMTNGGVDFSLECVGNVGVMRNALESCLKGWGVSVLVGWTDLHDVATRPIQLIAGRTWKGSMFGGFKGKDGVPKMVKAYLDKKVKLDEFITHRMPLESVNDAIDLMKHGKCIRTVLSL 374
                                    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       350       360       370    


Chain B from PDB  Type:PROTEIN  Length:374
 aligned with ADH1_GADMC | P26325 from UniProtKB/Swiss-Prot  Length:375

    Alignment length:374
                                    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       350       360       370    
           ADH1_GADMC     1 ATVGKVIKCKAAVAWEANKPLVIEEIEVDVPHANEIRIKIIATGVCHTDLYHLFEGKHKDGFPVVLGHEGAGIVESVGPGVTEFQPGEKVIPLFISQCGECRFCQSPKTNQCVKGWANESPDVMSPKETRFTCKGRKVLQFLGTSTFSQYTVVNQIAVAKIDPSAPLDTVCLLGCGVSTGFGAAVNTAKVEPGSTCAVFGLGAVGLAAVMGCHSAGAKRIIAVDLNPDKFEKAKVFGATDFVNPNDHSEPISQVLSKMTNGGVDFSLECVGNVGVMRNALESCLKGWGVSVLVGWTDLHDVATRPIQLIAGRTWKGSMFGGFKGKDGVPKMVKAYLDKKVKLDEFITHRMPLESVNDAIDLMKHGKCIRTVLSL 374
               SCOP domains d1cdob1 B:1-164,B:340-374 Alcohol dehydrogenase                                                                                                                     d1cdob2 B:165-339 Alcohol dehydrogenase                                                                                                                                        d1cdob1 B:1-164,B:340-374           SCOP domains
               CATH domains 1cdoB01 B:1-179,B:318-374 Medium-chain alcohol dehydrogenases, catalytic domain                                                                                                    1cdoB02 B:180-317 NAD(P)-binding Rossmann-like Domain                                                                                     1cdoB01 B:1-179,B:318-374                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeee........eeeeeee......eeeeee.eee..hhhhhhhhh...hhh..........eeeeee............eee.......................hhhh.....................hhh......eeeeehhheee......hhhhhhhh.hhhhhhhhhh.........eeeee...hhhhhhhhhhhhh...eeeee...hhhhhhhhhh...eee.hhh....hhhhhhhhh.....eeee....hhhhhhhhh.......eeee.......eeeeehhhhh...eeee..hhh..hhhhhhhhhhhhh......hhheeeeeehhhhhhhhhhhh.....eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------ADH_ZINC       ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1cdo B   1 ATVGKVIKCKAAVAWEANKPLVIEEIEVDVPHANEIRIKIIATGVCHTDLYHLFEGKHKDGFPVVLGHEGAGIVESVGPGVTEFQPGEKVIPLFISQCGECRFCQSPKTNQCVKGWANESPDVMSPKETRFTCKGRKVLQFLGTSTFSQYTVVNQIAVAKIDPSAPLDTVCLLGCGVSTGFGAAVNTAKVEPGSTCAVFGLGAVGLAAVMGCHSAGAKRIIAVDLNPDKFEKAKVFGATDFVNPNDHSEPISQVLSKMTNGGVDFSLECVGNVGVMRNALESCLKGWGVSVLVGWTDLHDVATRPIQLIAGRTWKGSMFGGFKGKDGVPKMVKAYLDKKVKLDEFITHRMPLESVNDAIDLMKHGKCIRTVLSL 374
                                    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       350       360       370
   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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1CDO)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (ADH1_GADMC | P26325)
molecular function
    GO:0004022    alcohol dehydrogenase (NAD) activity    Catalysis of the reaction: an alcohol + NAD+ = an aldehyde or ketone + NADH + H+.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    NAD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    ZIN  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Phe A:62 - Pro A:63   [ RasMol ]  
    Phe B:62 - Pro B:63   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1cdo
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  ADH1_GADMC | P26325
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  1.1.1.1
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  ADH1_GADMC | P26325
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 1CDO)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1CDO)