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 :  STRUCTURE OF AXE2-W215I, AN ACETYL XYLAN ESTERASE FROM GEOBACILLUS STEAROTHERMOPHILUS
 
Authors :  S. Lansky, O. Alalouf, Y. Shoham, G. Shoham
Date :  25 May 15  (Deposition) - 29 Jun 16  (Release) - 29 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (4x)
Keywords :  Hydrolase, Acetyl Xylan Esterase, Octamer, Mutant, Sgnh (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Lansky, O. Alalouf, H. V. Solomon, A. Alhassid, L. Govada, N. E. Chayen, H. Belrahli, Y. Shoham, G. Shoham
A Unique Octameric Structure Of Axe2, An Intracellular Acetyl-Xylooligosaccharide Esterase From Geobacillus Stearothermophilus
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ACETYL XYLAN ESTERASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: AXE2
    Mutation: YES
    Organism Scientific: GEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid: 1422

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (4x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 9)

Asymmetric Unit (4, 9)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2GOL2Ligand/IonGLYCEROL
3IMD4Ligand/IonIMIDAZOLE
4TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 1 (3, 28)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL8Ligand/IonGLYCEROL
3IMD16Ligand/IonIMIDAZOLE
4TRS4Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:109 , ASP A:111 , HOH A:411 , HOH A:504 , HOH A:512 , HOH A:570binding site for residue GOL A 301
2AC2SOFTWARESER A:15 , GLY A:63 , ASN A:92 , HOH A:596binding site for residue CL A 302
3AC3SOFTWAREARG A:205 , ARG A:209 , GLU A:214 , ILE A:215 , HOH A:417binding site for residue IMD A 303
4AC4SOFTWAREGLU A:114 , ARG A:156 , GLN A:160 , GLU A:164 , HOH A:552 , HOH A:605binding site for residue IMD A 304
5AC5SOFTWARESER B:15 , GLY B:63 , ASN B:92binding site for residue CL B 301
6AC6SOFTWAREARG B:67 , GLU B:74 , GLU B:123 , HOH B:619binding site for residue IMD B 302
7AC7SOFTWAREARG B:205 , ARG B:209 , GLU B:214 , ILE B:215 , HOH B:540binding site for residue IMD B 303
8AC8SOFTWAREPRO A:146 , GLU B:140 , GLY B:141 , ASN B:142 , PRO B:185 , HOH B:418 , HOH B:436 , HOH B:441 , HOH B:494 , HOH B:549binding site for residue TRS B 304
9AC9SOFTWAREGLU A:140 , GLY A:141 , PRO A:185 , HOH A:439 , HOH A:443 , PRO B:146 , HOH B:582binding site for residue GOL B 305

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5BN1)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Arg A:23 -Pro A:24
2Arg B:23 -Pro B:24

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5BN1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5BN1)

(-) Exons   (0, 0)

(no "Exon" information available for 5BN1)

(-) 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:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeehhhhhh..........hhhhh.hhhhhhhhhhhhhh.....eeee......hhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhh.eeeee..........hhhhhhhhhhhhhhhhhhhhhh.eeehhhhhhhhhhh..hhhhh.......hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bn1 A   1 MKIGSGEKLLFIGDSITDCGRARPEGEGSFGALGTGYVAYVVGLLQAVYPELGIRVVNKGISGNTVRDLKARWEEDVIAQKPDWVSIMIGINDVWRQYDLPFMKEKHVYLDEYEATLRSLVLETKPLVKGIILMTPFYIEGNEQDPMRRTMDQYGRVVKQIAEETNSLFVDTQAAFNEVLKTLYPAALAWDRVHPSVAGHMILARAFLREIGFEIVRS 218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210        


Chain B from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeehhhhhh.........hhhhhh.hhhhhhhhhhhhhh.....eeee......hhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhh.eeeee..........hhhhhhhhhhhhhhhhhhhhhh.eeehhhhhhhhhhh..hhhhh.......hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bn1 B   1 MKIGSGEKLLFIGDSITDCGRARPEGEGSFGALGTGYVAYVVGLLQAVYPELGIRVVNKGISGNTVRDLKARWEEDVIAQKPDWVSIMIGINDVWRQYDLPFMKEKHVYLDEYEATLRSLVLETKPLVKGIILMTPFYIEGNEQDPMRRTMDQYGRVVKQIAEETNSLFVDTQAAFNEVLKTLYPAALAWDRVHPSVAGHMILARAFLREIGFEIVRS 218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   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 5BN1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5BN1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5BN1)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)

 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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    IMD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    TRS  [ 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
    Arg A:23 - Pro A:24   [ RasMol ]  
    Arg B:23 - Pro B:24   [ 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
  5bn1
    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
  AXE2_GEOSE | Q09LX1
    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)
  (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
  AXE2_GEOSE | Q09LX1
    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
        AXE2_GEOSE | Q09LX1: 3w7v 4jhl 4jj4 4jj6 4jko 4oao 4oap

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5BN1)