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 :  SINAPYL ALCOHOL DEHYDROGENASE AT 2.5 ANGSTROM RESOLUTION
 
Authors :  E. K. Bomati, J. P. Noel
Date :  02 Feb 05  (Deposition) - 12 Jul 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Lignin Monolignol Oxidoreductase Zinc-Dependent, Plant- Defense, Biosynthesis, Medium-Chain Dehydrogenase/Reductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. K. Bomati, J. P. Noel
Structural And Kinetic Basis For Substrate Selectivity In Populus Tremuloides Sinapyl Alcohol Dehydrogenase.
Plant Cell V. 17 1598 2005
PubMed-ID: 15829607  |  Reference-DOI: 10.1105/TPC.104.029983
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SINAPYL ALCOHOL DEHYDROGENASE
    Chains: A, B
    EC Number: 1.1.1.195
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PHIS8
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Common: QUAKING ASPEN
    Organism Scientific: POPULUS TREMULOIDES
    Organism Taxid: 3693

 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
1NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2ZN4Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:50 , HIS A:72 , CYS A:166 , NAP A:500 , HOH A:2001BINDING SITE FOR RESIDUE ZN A 1000
2AC2SOFTWARECYS A:103 , HIS A:104 , CYS A:106 , CYS A:109 , CYS A:117BINDING SITE FOR RESIDUE ZN A 2000
3AC3SOFTWARECYS B:103 , CYS B:106 , CYS B:109 , CYS B:117BINDING SITE FOR RESIDUE ZN B 3000
4AC4SOFTWARECYS B:50 , HIS B:72 , CYS B:166 , NAP B:600 , HOH B:4001BINDING SITE FOR RESIDUE ZN B 4000
5AC5SOFTWAREHIS A:51 , SER A:52 , HIS A:55 , TRP A:61 , CYS A:166 , THR A:170 , GLY A:191 , LEU A:192 , GLY A:193 , GLY A:194 , LEU A:195 , SER A:214 , THR A:215 , SER A:216 , LYS A:219 , THR A:254 , VAL A:255 , SER A:256 , ALA A:257 , VAL A:277 , GLY A:278 , ALA A:279 , SER A:301 , GLY A:302 , ILE A:303 , ASN A:343 , ARG A:348 , ZN A:1000 , HOH A:2003 , ILE B:292BINDING SITE FOR RESIDUE NAP A 500
6AC6SOFTWAREILE A:292 , CYS B:50 , HIS B:51 , SER B:52 , HIS B:55 , CYS B:166 , THR B:170 , GLY B:191 , LEU B:192 , GLY B:193 , GLY B:194 , LEU B:195 , SER B:214 , THR B:215 , SER B:216 , LYS B:219 , THR B:254 , VAL B:255 , SER B:256 , VAL B:277 , GLY B:278 , ALA B:279 , SER B:301 , GLY B:302 , ILE B:303 , ASN B:343 , ARG B:348 , ZN B:4000 , HOH B:4014BINDING SITE FOR RESIDUE NAP B 600

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:66 -Pro A:67
2Tyr B:66 -Pro B:67

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1YQX)

(-) 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:359
 aligned with Q94G59_POPTM | Q94G59 from UniProtKB/TrEMBL  Length:362

    Alignment length:359
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353         
         Q94G59_POPTM     4 SPEEEHPVKAFGWAARDQSGHLSPFNFSRRATGEEDVRFKVLYCGVCHSDLHSIKNDWGFSMYPLVPGHEIVGEVTEVGSKVKKVNVGDKVGVGCLVGACHSCESCANDLENYCPKMILTYASIYHDGTITYGGYSDHMVANERYIIRFPDNMPLDGGAPLLCAGITVYSPLKYFGLDEPGKHIGIVGLGGLGHVAVKFAKAFGSKVTVISTSPSKKEEALKNFGADSFLVSRDQEQMQAAAGTLDGIIDTVSAVHPLLPLFGLLKSHGKLILVGAPEKPLELPAFSLIAGRKIVAGSGIGGMKETQEMIDFAAKHNITADIEVISTDYLNTAMERLAKNDVRYRFVIDVGNTLAATKP 362
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1yqxA01 A:4-166,A:324-362 Medium-chain alcohol dehydrogenases, catalytic domain                                                                                    1yqxA02 A:167-323 NAD(P)-binding Rossmann-like Domain                                                                                                        1yqxA01 A:4-166,A:324-362               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeee......eeeeeeee......eeeeeeeeee.hhhhhhhhh...............eeeeeeee...........eeee..eee....hhhhhh.hhhhh...ee..................eeeee.hhhee.........hhhhhhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhhh....eeee..hhhhhhhh...eeeeee.......hhhhhh.eeeeeeeee.......eeehhhhhhh...eeee....hhhhhhhhhhhhhhh.....eeeehhhhhhhhhhhhhh.....eeeeehhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yqx A   4 SPEEEHPVKAFGWAARDQSGHLSPFNFSRRATGEEDVRFKVLYCGVCHSDLHSIKNDWGFSMYPLVPGHEIVGEVTEVGSKVKKVNVGDKVGVGCLVGACHSCESCANDLENYCPKMILTYASIYHDGTITYGGYSNHMVANERYIIRFPDNMPLDGGAPLLCAGITVYSPLKYFGLDEPGKHIGIVGLGGLGHVAVKFAKAFGSKVTVISTSPSKKEEALKNFGADSFLVSRDQEQMQAAAGTLDGIIDTVSAVHPLLPLFGLLKSHGKLILVGAPEKPLELPAFSLIAGRKIVAGSGIGGMKETQEMIDFAAKHNITADIEVISTDYLNTAMERLAKNDVRYRFVIDVGNTLAATKP 362
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353         


Chain B from PDB  Type:PROTEIN  Length:359
 aligned with Q94G59_POPTM | Q94G59 from UniProtKB/TrEMBL  Length:362

    Alignment length:359
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353         
         Q94G59_POPTM     4 SPEEEHPVKAFGWAARDQSGHLSPFNFSRRATGEEDVRFKVLYCGVCHSDLHSIKNDWGFSMYPLVPGHEIVGEVTEVGSKVKKVNVGDKVGVGCLVGACHSCESCANDLENYCPKMILTYASIYHDGTITYGGYSDHMVANERYIIRFPDNMPLDGGAPLLCAGITVYSPLKYFGLDEPGKHIGIVGLGGLGHVAVKFAKAFGSKVTVISTSPSKKEEALKNFGADSFLVSRDQEQMQAAAGTLDGIIDTVSAVHPLLPLFGLLKSHGKLILVGAPEKPLELPAFSLIAGRKIVAGSGIGGMKETQEMIDFAAKHNITADIEVISTDYLNTAMERLAKNDVRYRFVIDVGNTLAATKP 362
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1yqxB01 B:4-166,B:324-362 Medium-chain alcohol dehydrogenases, catalytic domain                                                                                    1yqxB02 B:167-323 NAD(P)-binding Rossmann-like Domain                                                                                                        1yqxB01 B:4-166,B:324-362               CATH domains
           Pfam domains (1) ---------------------------------ADH_N-1yqxB01 B:37-152                                                                                              -----------------------------------------ADH_zinc_N-1yqxB03 B:194-318                                                                                                 -------------------------------------------- Pfam domains (1)
           Pfam domains (2) ---------------------------------ADH_N-1yqxB02 B:37-152                                                                                              -----------------------------------------ADH_zinc_N-1yqxB04 B:194-318                                                                                                 -------------------------------------------- Pfam domains (2)
         Sec.struct. author .......eeeeeeee......eeeeeeee......eeeeeeeeee.hhhhhhhhh...............eeeeeeee...........eeee..eee....hhhhhh.hhhhh...ee..................eeeee.hhhee.....hhhhhhhhhhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhh....eeee..hhhhhhhh...eeeeee.......hhhhhhheeeeeeeee.......eeehhhhhhh...eeee....hhhhhhhhhhhhhhh.....eeeehhhhhhhhhhhhhh.....eeeehhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yqx B   4 SPEEEHPVKAFGWAARDQSGHLSPFNFSRRATGEEDVRFKVLYCGVCHSDLHSIKNDWGFSMYPLVPGHEIVGEVTEVGSKVKKVNVGDKVGVGCLVGACHSCESCANDLENYCPKMILTYASIYHDGTITYGGYSNHMVANERYIIRFPDNMPLDGGAPLLCAGITVYSPLKYFGLDEPGKHIGIVGLGGLGHVAVKFAKAFGSKVTVISTSPSKKEEALKNFGADSFLVSRDQEQMQAAAGTLDGIIDTVSAVHPLLPLFGLLKSHGKLILVGAPEKPLELPAFSLIAGRKIVAGSGIGGMKETQEMIDFAAKHNITADIEVISTDYLNTAMERLAKNDVRYRFVIDVGNTLAATKP 362
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353
   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  (0, 0)

(no "SCOP Domain" information available for 1YQX)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: GroES (70)
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q94G59_POPTM | Q94G59)
molecular function
    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/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
    NAP  [ 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 ]
 
  Cis Peptide Bonds
    Tyr A:66 - Pro A:67   [ RasMol ]  
    Tyr B:66 - Pro B:67   [ 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
  1yqx
    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
  Q94G59_POPTM | Q94G59
    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)
  1.1.1.195
    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
  Q94G59_POPTM | Q94G59
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q94G59_POPTM | Q94G59: 1yqd

(-) Related Entries Specified in the PDB File

1yqd SINAPYL ALCOHOL DEHYDROGENASE COMPLEXED WITH NADP+ AT 1.65 ANGSTROM RESOLUTION