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
(-)Biological Unit 2
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)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF TANNASE FROM LACTOBACILLUS PLANTARUM IN THE ORTHORHOMBIC CRYSTAL
 
Authors :  Y. Matoba, N. Tanaka, M. Sugiyama
Date :  27 Apr 13  (Deposition) - 24 Jul 13  (Release) - 06 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Alpha/Beta-Hydrolase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Matoba, N. Tanaka, M. Noda, F. Higashikawa, T. Kumagai, M. Sugiyama
Crystallographic And Mutational Analyses Of Tannase From Lactobacillus Plantarum
Proteins V. 81 2052 2013
PubMed-ID: 23836494  |  Reference-DOI: 10.1002/PROT.24355

(-) Compounds

Molecule 1 - TANNASE
    Chains: A
    EC Number: 3.1.1.20
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-21A(+)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: LACTOBACILLUS PLANTARUM
    Organism Taxid: 1590
    Strain: SN35N

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:289 , ARG A:293 , ARG A:297 , LEU A:330 , ASP A:331 , LEU A:332 , SER A:333 , HOH A:781 , HOH A:920BINDING SITE FOR RESIDUE SO4 A 501
2AC2SOFTWAREGLY A:76 , GLY A:77 , SER A:163 , HIS A:451 , HOH A:701 , HOH A:766 , HOH A:805BINDING SITE FOR RESIDUE SO4 A 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3WA6)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Trp A:91 -Pro A:92
2Ala A:129 -Pro A:130
3Val A:345 -Pro A:346

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3WA6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3WA6)

(-) Exons   (0, 0)

(no "Exon" information available for 3WA6)

(-) 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:466
 aligned with B3Y018_LACPN | B3Y018 from UniProtKB/TrEMBL  Length:469

    Alignment length:466
                                    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       363       373       383       393       403       413       423       433       443       453       463      
         B3Y018_LACPN     4 RLIFDADWLVPEQVQVAGQAIQYYAARNIQYVQHPVAAIQVLNVFVPAAYLHGSSVNGYQRATAPILMPNTVGGYLPGPADDPQRVTWPTNAGTIQQALKRGYVVVAAGIRGRTTVDKSGQRVGQAPAFIVDMKAAIRYVKYNQGRLPGDANRIITNGTSAGGATSALAGASGNSAYFEPALTALGAAPATDDIFAVSAYCPIHNLEHADMAYEWQFNGINDWHRYQPVAGTTKNGRPKFEPVSGQLTVEEQALSLALKAQFSTYLNQLKLTASDGTHLTLNEAGMGSFRDVVRQLLISSAQTAFDQGTDIHKYAGFVVTGNQVTDLDLSAYLKSLTRMKAVPAFDQLDLTSPENNLFGDATAKAKHFTALAQTRSTVTAQLADAELIQAINPLSYLTTTSSQVAKHWRIRHGAADRDTSFAIPIILAIMLENHGYGIDFALPWDIPHSGDYDLGDLFSWIDGLCQ 469
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhheeeeeee..eeeeeeeeeeee..........eeeeeee.hhhh.............eeee.....................hhhhhhhhhhhh.eeeee..................hhhhhhhhhhhhhhhhh..........eeee..hhhhhhhhhhhhh..hhhhhhhhhhhh.........eeeee....hhhhhhhhhhhhhh...eeeeeeeeeee.hhh.eeeeeeeee.hhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhh.........eeee..eeeeehhhhhhhhhh..............hhhhhhh..........hhhhhhh........hhhhhhhhhhhhhh.........eeeee.........hhhhhhhhhhhhhh..eeeee...........hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wa6 A   4 RLIFDADWLVPEQVQVAGQAIQYYAARNIQYVQHPVAAIQVLNVFVPAAYLHGSSVNGYQRATAPILMPNTVGGYLPGPADDPQRVTWPTNAGTIQQALKRGYVVVAAGIRGRTTVDKSGQRVGQAPAFIVDMKAAIRYVKYNQGRLPGDTNRIITNGTSAGGATSALAGASGNSAYFEPALTALGAAPATDDIFAVSAYCPIHNLEHADMAYEWQFNGINDWHRYQPVAGTTKNGRPKFEPVSGQLTVEEQALSLALKAQFSTYLNQLQLTASDGTHLTLNEAGMGSFRDVVRQLLISSAQTAFDQGTDIHKYAGFVVTGNQVTDLDLSAYLKSLTRMKAVPAFDQLDLTSPENNLFGDATAKAKHFTALAQTRSTVTAQLADAELIQAINPLSYLTTTSSQVAKHWRIRHGAADRDTSFAIPIILAIMLENHGYGIDFALPWDIPHSGDYDLGDLFSWIDGLCQ 469
                                    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       363       373       383       393       403       413       423       433       443       453       463
   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 3WA6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3WA6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3WA6)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3WA6)

 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
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala A:129 - Pro A:130   [ RasMol ]  
    Trp A:91 - Pro A:92   [ RasMol ]  
    Val A:345 - Pro A:346   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ 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 | Biol. Unit 2 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
  3wa6
    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
  B3Y018_LACPN | B3Y018
    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)
  3.1.1.20
    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
  B3Y018_LACPN | B3Y018
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        B3Y018_LACPN | B3Y018: 3wa7 4j0c 4j0d 4j0g 4j0h 4j0i 4j0j 4j0k 4jui

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3WA6)