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 :  V203A HORSE LIVER ALCOHOL DEHYDROGENASE E COMPLEXED WITH NAD+ AND 2,3, 4,5,6-PENTAFLUOROBENZYL ALCOHOL
 
Authors :  B. V. Plapp
Date :  01 Nov 13  (Deposition) - 13 Nov 13  (Release) - 26 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rossmann Fold, Dehydrogenase, Nad, Liver Cytosol, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Yahashiri, J. K. Rubach, B. V. Plapp
Effects Of Cavities At The Nicotinamide Binding Site Of Liver Alcohol Dehydrogenase On Structure, Dynamics And Catalysis.
Biochemistry V. 53 881 2014
PubMed-ID: 24437493  |  Reference-DOI: 10.1021/BI401583F

(-) Compounds

Molecule 1 - ALCOHOL DEHYDROGENASE E CHAIN
    Chains: A, B
    EC Number: 1.1.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBPP/EQADH E
    Expression System Strain: XL1-BLUE
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Common: DOMESTIC HORSE,EQUINE
    Organism Scientific: EQUUS CABALLUS
    Organism Taxid: 9796
    Strain: DOMESTIC HORSE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric/Biological Unit (4, 12)
No.NameCountTypeFull Name
1MRD4Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
2NAJ2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE (ACIDIC FORM)
3PFB2Ligand/Ion2,3,4,5,6-PENTAFLUOROBENZYL ALCOHOL
4ZN4Ligand/IonZINC ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:46 , HIS A:67 , CYS A:174 , NAJ A:377 , PFB A:378 , HOH A:995BINDING SITE FOR RESIDUE ZN A 375
02AC2SOFTWARECYS A:97 , CYS A:100 , CYS A:103 , CYS A:111BINDING SITE FOR RESIDUE ZN A 376
03AC3SOFTWAREARG A:47 , SER A:48 , HIS A:51 , CYS A:174 , THR A:178 , GLY A:199 , GLY A:201 , GLY A:202 , ALA A:203 , ASP A:223 , ILE A:224 , LYS A:228 , VAL A:268 , ILE A:269 , VAL A:292 , GLY A:293 , VAL A:294 , ALA A:317 , ILE A:318 , PHE A:319 , ARG A:369 , ZN A:375 , PFB A:378 , HOH A:406 , HOH A:430 , HOH A:439 , HOH A:517 , HOH A:588 , HOH A:647 , HOH A:664 , HOH A:686 , HOH A:711 , HOH A:994BINDING SITE FOR RESIDUE NAJ A 377
04AC4SOFTWARECYS A:46 , SER A:48 , LEU A:57 , HIS A:67 , PHE A:93 , PHE A:140 , LEU A:141 , CYS A:174 , VAL A:294 , ILE A:318 , ZN A:375 , NAJ A:377 , LEU B:309BINDING SITE FOR RESIDUE PFB A 378
05AC5SOFTWAREASP A:297 , GLN A:299 , LYS A:338 , LYS A:339 , PHE A:340 , HOH A:735 , HOH A:814 , HOH A:1019BINDING SITE FOR RESIDUE MRD A 379
06AC6SOFTWARETHR A:238 , GLU A:239 , HOH A:998 , ARG B:218 , THR B:238 , GLU B:239 , HOH B:930BINDING SITE FOR RESIDUE MRD A 380
07AC7SOFTWARELYS A:168 , ASP A:343 , ILE A:346 , THR A:347 , HOH A:852BINDING SITE FOR RESIDUE MRD A 381
08AC8SOFTWARECYS B:46 , HIS B:67 , CYS B:174 , NAJ B:377 , PFB B:378 , HOH B:995BINDING SITE FOR RESIDUE ZN B 375
09AC9SOFTWARECYS B:97 , CYS B:100 , CYS B:103 , CYS B:111BINDING SITE FOR RESIDUE ZN B 376
10BC1SOFTWAREARG B:47 , SER B:48 , HIS B:51 , CYS B:174 , THR B:178 , GLY B:199 , GLY B:201 , GLY B:202 , ALA B:203 , ASP B:223 , ILE B:224 , LYS B:228 , VAL B:268 , ILE B:269 , ARG B:271 , VAL B:292 , GLY B:293 , VAL B:294 , ALA B:317 , ILE B:318 , PHE B:319 , ARG B:369 , ZN B:375 , PFB B:378 , HOH B:403 , HOH B:443 , HOH B:449 , HOH B:514 , HOH B:574 , HOH B:649 , HOH B:664 , HOH B:689 , HOH B:879 , HOH B:907 , HOH B:994BINDING SITE FOR RESIDUE NAJ B 377
11BC2SOFTWARELEU A:309 , CYS B:46 , SER B:48 , LEU B:57 , HIS B:67 , PHE B:93 , LEU B:116 , PHE B:140 , LEU B:141 , CYS B:174 , VAL B:294 , ZN B:375 , NAJ B:377BINDING SITE FOR RESIDUE PFB B 378
12BC3SOFTWARELYS B:338 , LYS B:339BINDING SITE FOR RESIDUE MRD B 379

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4NG5)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Leu A:61 -Pro A:62
2Leu B:61 -Pro B:62

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4NG5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4NG5)

(-) Exons   (0, 0)

(no "Exon" information available for 4NG5)

(-) 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
                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains d4ng5a1 A:1-163,A:340-374 Alcohol dehydrogenase                                                                                                                    d4ng5a2 A:164-339 Alcohol dehydrogenase                                                                                                                                         d4ng5a1 A:1-163,A:340-374           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeee.......eeeeeee......eeeeeeeeee.hhhhhhhhh........ee....eeeeeeee...........eeee........hhhhhh........................eee..eee...........eeeee...eee.....hhhhhhhhhhhhhhhhhhhhh........eeeee..hhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhh..eeehhhhh..hhhhhhhhhh.....eeee...hhhhhhhhhhhh.....eeee.........eee.hhhhhh..eeee.hhhhhhhhhhhhhhhhhhhh....hhh.eeeeee..hhhhhhhhhhh....eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ng5 A   1 STAGKVIKCKAAVLWEEKKPFSIEEVEVAPPKAHEVRIKMVATGICRSDDHVVSGTLVTPLPVIAGHEAAGIVESIGEGVTTVRPGDKVIPLFTPQCGKCRVCKHPEGNFCLKNDLSMPRGTMQDGTSRFTCRGKPIHHFLGTSTFSQYTVVDEISVAKIDAASPLEKVCLIGCGFSTGYGSAVKVAKVTQGSTCAVFGLGGAGLSVIMGCKAAGAARIIGVDINKDKFAKAKEVGATECVNPQDYKKPIQEVLTEMSNGGVDFSFEVIGRLDTMVTALSCCQEAYGVSVIVGVPPDSQNLSMNPMLLLSGRTWKGAIFGGFKSKDSVPKLVADFMAKKFALDPLITHVLPFEKINEGFDLLRSGESIRTILTF 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
                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains d4ng5b1 B:1-163,B:340-374 Alcohol dehydrogenase                                                                                                                    d4ng5b2 B:164-339 Alcohol dehydrogenase                                                                                                                                         d4ng5b1 B:1-163,B:340-374           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeee........eeeeeee......eeeeeeeeee.hhhhhhhhh..............eeeeeeee...........eeee........hhhhhh........................eee..eee...........eeeee...eee.....hhhhhhhhhhhhhhhhhhhhh........eeeee..hhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhh..eeehhhhh..hhhhhhhhhh.....eeee...hhhhhhhhhhhh.....eeee.........eee.hhhhhh..eeee.hhhhhhhhhhhhhhhhhhhh....hhh.eeeeee..hhhhhhhhhhh....eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ng5 B   1 STAGKVIKCKAAVLWEEKKPFSIEEVEVAPPKAHEVRIKMVATGICRSDDHVVSGTLVTPLPVIAGHEAAGIVESIGEGVTTVRPGDKVIPLFTPQCGKCRVCKHPEGNFCLKNDLSMPRGTMQDGTSRFTCRGKPIHHFLGTSTFSQYTVVDEISVAKIDAASPLEKVCLIGCGFSTGYGSAVKVAKVTQGSTCAVFGLGGAGLSVIMGCKAAGAARIIGVDINKDKFAKAKEVGATECVNPQDYKKPIQEVLTEMSNGGVDFSFEVIGRLDTMVTALSCCQEAYGVSVIVGVPPDSQNLSMNPMLLLSGRTWKGAIFGGFKSKDSVPKLVADFMAKKFALDPLITHVLPFEKINEGFDLLRSGESIRTILTF 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  (0, 0)

(no "CATH Domain" information available for 4NG5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4NG5)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

 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
    MRD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAJ  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PFB  [ 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 ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Leu A:61 - Pro A:62   [ RasMol ]  
    Leu B:61 - Pro B:62   [ 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
  4ng5
    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
  ADH1E_HORSE | P00327
    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
  ADH1E_HORSE | P00327
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        ADH1E_HORSE | P00327: 1a71 1a72 1adb 1adc 1adf 1adg 1axe 1axg 1bto 1het 1heu 1hf3 1hld 1ju9 1lde 1ldy 1mg0 1mgo 1n8k 1n92 1p1r 1qlh 1qlj 1qv6 1qv7 1ye3 2jhf 2jhg 2ohx 2oxi 3bto 3oq6 4dwv 4dxh 4nfh 4nfs 4xd2 5adh 5cdg 5cds 5cdt 5cdu 5kcp 5kcz 5kj1 5kj6 5kjc 5kje 5kjf 5vj5 5vjg 5vkr 5vl0 5vn1 6adh 7adh 8adh

(-) Related Entries Specified in the PDB File

1a71 F93W:V203A HORSE LIVER ALCOHOL DEHYDROGENASE E COMPLEXED WITH NAD+ AND 2,2,2-TRIFLUOROETHANOL
1hld WILD-TYPE HORSE LIVER ALCOHOL DEHYDROGENASE E COMPLEXED WITH NAD+ AND 2,3,4,5,6-PENTAFLUOROBENZYL ALCOHOL AT 278K
3oq6 A317C HORSE LIVER ALCOHOL DEHYDROGENASE E COMPLEXED WITH NAD+ AND 2,3,4,5,6-PENTAFLUOROBENZYL ALCOHOL
4dwv WILD-TYPE HORSE LIVER ALCOHOL DEHYDROGENASE E COMPLEXED WITH NAD+ AND 2,3,4,5,6-PENTAFLUOROBENZYL ALCOHOL
4nfh V207A HORSE LIVER ALCOHOL DEHYDROGENASE E COMPLEXED WITH NAD+ AND 2,3,4,5,6-PENTAFLUOROBENZYL ALCOHOL
4nfs V203A HORSE LIVER ALCOHOL DEHYDROGENASE E COMPLEXED WITH NAD+ AND 2,2,2-TRIFLUOROETHANOL