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 :  CRYSTAL STRUCTURE OF LIGL IN COMPLEX WITH NADH AND GGE FROM SPHINGOBIUM SP. STRAIN SYK-6
 
Authors :  J. H. Pereira, R. P. Mcandrew, R. A. Heins, K. L. Sale, B. A. Simmons, P. D.
Date :  17 Feb 15  (Deposition) - 09 Mar 16  (Release) - 01 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Short Chain Dehydrogenase/Reductase Sdr Family, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. H. Pereira, R. A. Heins, D. L. Gall, R. P. Mcandrew, K. Deng, K. C. Holland, T. J. Donohue, D. R. Noguera, B. A. Simmons, K. L. Sale, J. Ralph, P. D. Adams
Structural And Biochemical Characterization Of The Early An Late Enzymes In The Lignin Beta-Aryl Ether Cleavage Pathway From Sphingobium Sp. Syk-6.
J. Biol. Chem. V. 291 10228 2016
PubMed-ID: 26940872  |  Reference-DOI: 10.1074/JBC.M115.700427

(-) Compounds

Molecule 1 - C ALPHA-DEHYDROGENASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: LIGL, SLG_33660
    Organism Scientific: SPHINGOBIUM SP. SYK-6
    Organism Taxid: 627192
    Synonym: CALPHA-DEHYDROGENASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1GGE1Ligand/Ion(1S,2R)-1-(4-HYDROXY-3-METHOXYPHENYL)-2-(2-METHOXYPHENOXY)PROPANE-1,3-DIOL
2MG1Ligand/IonMAGNESIUM ION
3NAI2Ligand/Ion1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:12 , SER A:15 , GLY A:16 , ILE A:17 , ASP A:36 , ILE A:37 , ARG A:38 , HIS A:41 , LEU A:63 , ASP A:64 , VAL A:65 , ASN A:91 , ALA A:92 , GLY A:93 , ILE A:114 , THR A:142 , ALA A:143 , SER A:144 , TYR A:158 , LYS A:162 , PRO A:188 , GLY A:189 , PRO A:190 , ILE A:191 , SER A:193 , ARG A:194 , ILE A:195 , ASN A:201 , HOH A:694 , HOH A:695 , HOH A:699 , HOH A:701 , HOH A:863 , HOH A:874binding site for residue NAD A 500
2AC2SOFTWAREHOH A:603 , HOH A:620 , HOH A:626 , HOH A:669 , HOH A:674 , HOH A:777binding site for residue MG A 501
3AC3SOFTWAREGLY B:12 , SER B:15 , GLY B:16 , ILE B:17 , ASP B:36 , ILE B:37 , ARG B:38 , HIS B:41 , LEU B:63 , ASP B:64 , VAL B:65 , ASN B:91 , ALA B:92 , GLY B:93 , ILE B:114 , THR B:142 , ALA B:143 , SER B:144 , TYR B:158 , LYS B:162 , PRO B:188 , GLY B:189 , PRO B:190 , ILE B:191 , SER B:193 , ARG B:194 , ILE B:195 , GGE B:501 , HOH B:685 , HOH B:695 , HOH B:713 , HOH B:811binding site for residue NAD B 500
4AC4SOFTWAREASP B:95 , SER B:144 , MET B:155 , TYR B:158 , PRO B:188 , GLY B:189 , ILE B:195 , ARG B:222 , TRP B:255binding site for residue GGE B 501

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:84 -Pro A:85
2Gly B:84 -Pro B:85

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YAI)

(-) 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:273
                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh.hhh.eeeee....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee......hhhhhhhhhhhhhh....hhhhhhhhh.........hhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yai A   1 MDIAGTTAFITGGASGIGFGIAQRLLANGARLVLADIRQDHLDEARQFFEERQQGRNVHTIRLDVSDRAQMAEAARECEAVMGGPDILINNAGIDPSGPFKDATYQDWDYGLAINLMGPINGIMAFTPGMRARGRGGHIVNTASLAGLTPMPSFMAIYATAKAAVITLTETIRDSMAEDNIGVTVLMPGPIKSRIHESGQNRPERFRAGSGLAETEQQLAKRVVADNWMEPTEVGDMIVDAIVHNKLYVSTHGNWRETCEARFQALLDSMPEA 273
                                    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   


Chain B from PDB  Type:PROTEIN  Length:273
                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhh..hhh.eeeee....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee......hhhhhhhhhhhhhh....hhhhhhhhh.........hhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yai B   1 MDIAGTTAFITGGASGIGFGIAQRLLANGARLVLADIRQDHLDEARQFFEERQQGRNVHTIRLDVSDRAQMAEAARECEAVMGGPDILINNAGIDPSGPFKDATYQDWDYGLAINLMGPINGIMAFTPGMRARGRGGHIVNTASLAGLTPMPSFMAIYATAKAAVITLTETIRDSMAEDNIGVTVLMPGPIKSRIHESGQNRPERFRAGSGLAETEQQLAKRVVADNWMEPTEVGDMIVDAIVHNKLYVSTHGNWRETCEARFQALLDSMPEA 273
                                    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
   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 4YAI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

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
    GGE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAI  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:84 - Pro A:85   [ RasMol ]  
    Gly B:84 - Pro B:85   [ 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
  4yai
    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
  C0SUJ9_9SPHN | C0SUJ9
    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)
  (no 'Enzyme Classificator' available)
    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
  C0SUJ9_9SPHN | C0SUJ9
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        C0SUJ9_9SPHN | C0SUJ9: 4yae 4yag

(-) Related Entries Specified in the PDB File

4y98 4y9d 4ya6 4yac 4yae 4yag 4yai 4yan 4yap 4yav