Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE ALCOHOL DEHYDROGENASE FROM THE HYPERTHERMOPHILIC ARCHAEON AEROPYRUM PERNIX AT 1.65A RESOLUTION
 
Authors :  J. E. Guy, M. N. Isupov, J. A. Littlechild
Date :  02 Aug 02  (Deposition) - 28 Aug 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.62
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Oxidoreductase, Archaea, Hyperthermophile, Alcohol Dehydrogenase Oxidoreductase, Zinc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. E. Guy, M. N. Isupov, J. A. Littlechild
The Structure Of An Alcohol Dehydrogenase From The Hyperthermophilic Archaeon Aeropyrum Pernix.
J. Mol. Biol. V. 331 1041 2003
PubMed-ID: 12927540  |  Reference-DOI: 10.1016/S0022-2836(03)00857-X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ALCOHOL DEHYDROGENASE
    Chains: A, B
    EC Number: 1.1.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTRC 99
    Expression System Strain: DH5
    Expression System Taxid: 562
    Organism Scientific: AEROPYRUM PERNIX
    Organism Taxid: 56636

 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, 9)

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
1NAJ2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE (ACIDICFORM)
2OCA2Ligand/IonOCTANOIC ACID (CAPRYLIC ACID)
3ZN5Ligand/IonZINC ION
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1NAJ4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE (ACIDICFORM)
2OCA4Ligand/IonOCTANOIC ACID (CAPRYLIC ACID)
3ZN-1Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:54 , THR A:56 , HIS A:79 , ASP A:168 , OCA A:1360 , NAJ A:1361BINDING SITE FOR RESIDUE ZN A1362
2AC2SOFTWAREASP A:332 , HIS A:334 , HOH A:2311 , GLU B:96BINDING SITE FOR RESIDUE ZN A1363
3AC3SOFTWAREASP A:109 , CYS A:112 , CYS A:115 , CYS A:123BINDING SITE FOR RESIDUE ZN A1364
4AC4SOFTWARECYS B:54 , HIS B:79 , ASP B:168 , OCA B:1360 , NAJ B:1361BINDING SITE FOR RESIDUE ZN B1362
5AC5SOFTWAREASP B:109 , CYS B:112 , CYS B:115 , CYS B:123BINDING SITE FOR RESIDUE ZN B1363
6AC6SOFTWARECYS A:54 , THR A:56 , HIS A:79 , PHE A:128 , LEU A:131 , ASP A:168 , ARG A:277 , SER A:299 , NAJ A:1361 , ZN A:1362BINDING SITE FOR RESIDUE OCA A1360
7AC7SOFTWARECYS A:54 , HIS A:55 , THR A:56 , HIS A:59 , ASP A:168 , THR A:172 , GLY A:194 , VAL A:195 , GLY A:196 , GLY A:197 , LEU A:198 , ASP A:218 , VAL A:219 , LYS A:223 , ALA A:238 , PHE A:261 , VAL A:262 , THR A:267 , TYR A:270 , VAL A:284 , GLY A:285 , TYR A:286 , ILE A:298 , SER A:307 , LEU A:308 , VAL A:309 , LEU A:346 , ARG A:354 , OCA A:1360 , ZN A:1362 , HOH A:2206 , HOH A:2225 , HOH A:2305 , HOH A:2306 , HOH A:2307 , HOH A:2308 , HOH A:2309 , HOH A:2310BINDING SITE FOR RESIDUE NAJ A1361
8AC8SOFTWARECYS B:54 , THR B:56 , HIS B:79 , PHE B:128 , ASP B:168 , NAJ B:1361 , ZN B:1362BINDING SITE FOR RESIDUE OCA B1360
9AC9SOFTWARECYS B:54 , HIS B:55 , THR B:56 , HIS B:59 , ASP B:168 , THR B:172 , GLY B:194 , VAL B:195 , GLY B:196 , GLY B:197 , LEU B:198 , ASP B:218 , VAL B:219 , LYS B:223 , ALA B:238 , PHE B:261 , VAL B:262 , THR B:267 , TYR B:270 , VAL B:284 , GLY B:285 , TYR B:286 , ILE B:298 , SER B:307 , LEU B:308 , VAL B:309 , LEU B:346 , ARG B:354 , OCA B:1360 , ZN B:1362 , HOH B:2241 , HOH B:2271 , HOH B:2344 , HOH B:2345 , HOH B:2346 , HOH B:2347 , HOH B:2348 , HOH B:2349BINDING SITE FOR RESIDUE NAJ B1361

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:115 -A:123
2B:115 -B:123

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Leu A:73 -Pro A:74
2Leu B:73 -Pro B:74

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1H2B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1H2B)

(-) Exons   (0, 0)

(no "Exon" information available for 1H2B)

(-) 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:343
 aligned with Q9Y9P9_AERPE | Q9Y9P9 from UniProtKB/TrEMBL  Length:344

    Alignment length:343
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341   
         Q9Y9P9_AERPE     2 KAARLHEYNKPLRIEDVDYPRLEGRFDVIVRIAGAGVCHTDLHLVQGMWHELLQPKLPYTLGHENVGYIEEVAEGVEGLEKGDPVILHPAVTDGTCLACRAGEDMHCENLEFPGLNIDGGFAEFMRTSHRSVIKLPKDISREKLVEMAPLADAGITAYRAVKKAARTLYPGAYVAIVGVGGLGHIAVQLLKVMTPATVIALDVKEEKLKLAERLGADHVVDARRDPVKQVMELTRGRGVNVAMDFVGSQATVDYTPYLLGRMGRLIIVGYGGELRFPTIRVISSEVSFEGSLVGNYVELHELVTLALQGKVRVEVDIHKLDEINDVLERLEKGEVLGRAVLIP 344
               SCOP domains d1h2ba1 A:17-154,A:327-359 Alcohol dehydrogenase                                                                                          d1h2ba2 A:155-326 Alcohol dehydrogenase                                                                                                                                     d1h2ba1 A:17-154,A:327-359        SCOP domains
               CATH domains 1h2bA01 A:17-168,A:309-359 Medium-chain alcohol dehydrogenases, catalytic domain                                                                        1h2bA02 A:169-308 NAD(P)-binding Rossmann-like Domain                                                                                       1h2bA01 A:17-168,A:309-359                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.......eee............eeeeeeeee.hhhhhhhhhh.hhhhhh....ee....eeeeeeee...........eeee........hhhhhh.hhhhh................eeeehhh.eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee..hhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhh...eeee...hhhhhhhhhh....eeeeee...hhhhhhhh...eeeeeeeee.........hhhhhhhh..eeee....hhhhhhhhhhhhhh......eeeee..hhhhhhhhhhh.....eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1h2b A  17 KAARLHEYNKPLRIEDVDYPRLEGRFDVIVRIAGAGVCHTDLHLVQGMWHELLQPKLPYTLGHENVGYIEEVAEGVEGLEKGDPVILHPAVTDGTCLACRAGEDMHCENLEFPGLNIDGGFAEFMRTSHRSVIKLPKDISREKLVEMAPLADAGITAYRAVKKAARTLYPGAYVAIVGVGGLGHIAVQLLKVMTPATVIALDVKEEKLKLAERLGADHVVDARRDPVKQVMELTRGRGVNVAMDFVGSQATVDYTPYLLGRMGRLIIVGYGGELRFPTIRVISSEVSFEGSLVGNYVELHELVTLALQGKVRVEVDIHKLDEINDVLERLEKGEVLGRAVLIP 359
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356   


Chain B from PDB  Type:PROTEIN  Length:344
 aligned with Q9Y9P9_AERPE | Q9Y9P9 from UniProtKB/TrEMBL  Length:344

    Alignment length:344
                                    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    
         Q9Y9P9_AERPE     1 MKAARLHEYNKPLRIEDVDYPRLEGRFDVIVRIAGAGVCHTDLHLVQGMWHELLQPKLPYTLGHENVGYIEEVAEGVEGLEKGDPVILHPAVTDGTCLACRAGEDMHCENLEFPGLNIDGGFAEFMRTSHRSVIKLPKDISREKLVEMAPLADAGITAYRAVKKAARTLYPGAYVAIVGVGGLGHIAVQLLKVMTPATVIALDVKEEKLKLAERLGADHVVDARRDPVKQVMELTRGRGVNVAMDFVGSQATVDYTPYLLGRMGRLIIVGYGGELRFPTIRVISSEVSFEGSLVGNYVELHELVTLALQGKVRVEVDIHKLDEINDVLERLEKGEVLGRAVLIP 344
               SCOP domains d1h2bb1 B:16-154,B:327-359 Alcohol dehydrogenase                                                                                           d1h2bb2 B:155-326 Alcohol dehydrogenase                                                                                                                                     d1h2bb1 B:16-154,B:327-359        SCOP domains
               CATH domains 1h2bB01 B:16-168,B:309-359 Medium-chain alcohol dehydrogenases, catalytic domain                                                                         1h2bB02 B:169-308 NAD(P)-binding Rossmann-like Domain                                                                                       1h2bB01 B:16-168,B:309-359                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.......eeee...........eeeeeeeee.hhhhhhhhh..hhhhhh....ee....eeeeeeee...........eeee........hhhhhh.hhhhh................eeeehhh.eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee..hhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhh...eeee...hhhhhhhhhh....eeeeee...hhhhhhhh...eeeeeeeee.........hhhhhhhhh.eeee....hhhhhhhhhhhhhh......eeeee..hhhhhhhhhhh.....eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1h2b B  16 LKAARLHEYNKPLRIEDVDYPRLEGRFDVIVRIAGAGVCHTDLHLVQGMWHELLQPKLPYTLGHENVGYIEEVAEGVEGLEKGDPVILHPAVTDGTCLACRAGEDMHCENLEFPGLNIDGGFAEFMRTSHRSVIKLPKDISREKLVEMAPLADAGITAYRAVKKAARTLYPGAYVAIVGVGGLGHIAVQLLKVMTPATVIALDVKEEKLKLAERLGADHVVDARRDPVKQVMELTRGRGVNVAMDFVGSQATVDYTPYLLGRMGRLIIVGYGGELRFPTIRVISSEVSFEGSLVGNYVELHELVTLALQGKVRVEVDIHKLDEINDVLERLEKGEVLGRAVLIP 359
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355
   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 Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1H2B)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q9Y9P9_AERPE | Q9Y9P9)
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:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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.

 Visualization

(-) Interactive Views

Asymmetric 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
    NAJ  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    OCA  [ 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 ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Leu A:73 - Pro A:74   [ RasMol ]  
    Leu B:73 - Pro B:74   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - 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
  1h2b
    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
  Q9Y9P9_AERPE | Q9Y9P9
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
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
  Q9Y9P9_AERPE | Q9Y9P9
    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 1H2B)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1H2B)