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 BETA-GLYCOSIDASE FROM ACIDILOBUS SACCHAROVORANS IN COMPLEX WITH GLYCEROL
 
Authors :  A. A. Trofimov, K. M. Polyakov, A. V. Tikhonov, E. Y. Bezsudnova, P. V. Dorovatovskii, V. M. Gumerov, N. V. Ravin, K. G. Skryabin, V. O. Po
Date :  25 Sep 12  (Deposition) - 10 Oct 12  (Release) - 04 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.37
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Tim Barrel, Beta-Glycosidase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. A. Trofimov, K. M. Polyakov, A. V. Tikhonov, E. Y. Bezsudnova, P. V. Dorovatovskii, V. M. Gumerov, N. V. Ravin, K. G. Skryabin, V. O. Popov
Structures Of Beta-Glycosidase From Acidilobus Saccharovorans In Complexes With Tris And Glycerol.
Dokl. Biochem. Biophys. V. 449 99
PubMed-ID: 23657657  |  Reference-DOI: 10.1134/S1607672913020129

(-) Compounds

Molecule 1 - BETA-GALACTOSIDASE
    Chains: A
    EC Number: 3.2.1.23
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE60
    Expression System Strain: DLT1270 (PRARE2)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ASAC1390, ASAC_1390
    Organism Scientific: ACIDILOBUS SACCHAROVORANS
    Organism Taxid: 666510
    Strain: DSM 16705 / VKM B-2471 / 345-15

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 13)

Asymmetric Unit (5, 13)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2NA1Ligand/IonSODIUM ION
3PG47Ligand/IonTETRAETHYLENE GLYCOL
4PG61Ligand/Ion1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE
5SIN1Ligand/IonSUCCINIC ACID
Biological Unit 1 (4, 48)
No.NameCountTypeFull Name
1GOL12Ligand/IonGLYCEROL
2NA-1Ligand/IonSODIUM ION
3PG428Ligand/IonTETRAETHYLENE GLYCOL
4PG64Ligand/Ion1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE
5SIN4Ligand/IonSUCCINIC ACID

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:393 , HOH A:613 , HOH A:652BINDING SITE FOR RESIDUE NA A 501
02AC2SOFTWAREARG A:461 , LYS A:465 , HOH A:858BINDING SITE FOR RESIDUE SIN A 502
03AC3SOFTWARETRP A:153 , LEU A:215 , PHE A:224 , PHE A:357 , GLU A:430 , TRP A:431 , GOL A:505 , HOH A:672 , HOH A:816 , HOH A:1077BINDING SITE FOR RESIDUE GOL A 503
04AC4SOFTWAREGLU A:391 , ARG A:438 , MET A:443 , ARG A:454 , PRO A:481 , HOH A:747 , HOH A:820 , HOH A:1120BINDING SITE FOR RESIDUE GOL A 504
05AC5SOFTWAREGLN A:19 , HIS A:152 , ASN A:207 , GLU A:208 , GLU A:385 , TRP A:423 , GLU A:430 , TRP A:431 , GOL A:503BINDING SITE FOR RESIDUE GOL A 505
06AC6SOFTWAREASN A:210 , GLY A:214 , LEU A:215 , GLN A:323 , PG4 A:507BINDING SITE FOR RESIDUE PG4 A 506
07AC7SOFTWAREALA A:265 , ASN A:266 , SER A:267 , GLN A:323 , HIS A:340 , PG4 A:506 , HOH A:629 , HOH A:693 , HOH A:931 , HOH A:1136BINDING SITE FOR RESIDUE PG4 A 507
08AC8SOFTWARETRP A:374 , HIS A:378 , LEU A:379 , PRO A:380 , ASN A:416 , HOH A:1073BINDING SITE FOR RESIDUE PG4 A 508
09AC9SOFTWAREASN A:63 , LYS A:66 , LYS A:449 , HOH A:647 , HOH A:686 , HOH A:1036BINDING SITE FOR RESIDUE PG4 A 509
10BC1SOFTWARETYR A:201 , MET A:202 , LYS A:253 , LYS A:257 , PRO A:259 , ASP A:313BINDING SITE FOR RESIDUE PG6 A 510
11BC2SOFTWARELYS A:253 , ALA A:254 , ILE A:255 , LYS A:257BINDING SITE FOR RESIDUE PG4 A 511
12BC3SOFTWARETRP A:194 , LYS A:195 , GLU A:232BINDING SITE FOR RESIDUE PG4 A 512
13BC4SOFTWAREVAL A:112 , GLU A:114 , ALA A:254 , HOH A:733 , HOH A:1135BINDING SITE FOR RESIDUE PG4 A 513

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:230 -A:233

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Pro A:225 -Pro A:226
2Trp A:423 -Ser A:424

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4HA4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4HA4)

(-) Exons   (0, 0)

(no "Exon" information available for 4HA4)

(-) 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:489
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains d4ha4a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.....eeeeeehhhhhh..........hhhhhhhhhhhhhhh......hhhhh.hhhhhhhhhhhhhhhh...eeeee.hhhhhh.........eeeee..eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee...........hhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeehhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhee..ee..........eeeeeeeeeeeeee..eeee............................hhhhhhhhhhhhhhhh..eeeee.........hhhhhhhhhhhhhhhhhhh...eeeeee.......hhhhhhhh....eee......eeehhhhhhhhhhhhhhee...hhhhh............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ha4 A   2 AVTFPKDFLFGWSQAGFQSEMGTPGSEDPNSDWYAWVHDRENIAAGLVSGDFPENGPGYWGNYRKFHDAAQAMGLTAARIGVEWSRIFPRPTFDVKVDAEVKGDDVLSVYVSEGALEQLDKMANRDAINHYREMFSDLRSRGITFILNLYHWPLPLWLHDPIAIRRGNLSAPSGWLDVRTVIEFAKFSAYVAWKLDDLVYMYSTMNEPNVVWGLGYAAVKSGFPPGYLCLECAGRAMKNLVQAHARAYDAVKAITKKPVGVIYANSDFTPLTDADREAAERAKFDNRWAFFDAVVRGQLGGSTRDDLKGRLDWIGVNYYTRQVVRARGSGYEIVPGYGHGCEPNGVSPAGRPCSDFGWEFYPEGLYNVLKEYWDRYHLPLLVTENGIADEGDYQRPYYLVSHVYQVHRALQDGVNVIGYLHWSLADNYEWASGFSKRFGLLMVDYSTKRLHWRPSAFIYREIAKSRAITDEIEHLNSVPPLRGLSPGHR 490
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481
   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  (1, 1)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4HA4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4HA4)

(-) Gene Ontology  (6, 6)

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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PG4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PG6  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SIN  [ 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 ]
    BC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Pro A:225 - Pro A:226   [ RasMol ]  
    Trp A:423 - Ser A:424   [ 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
  4ha4
    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
  D9PZ08_ACIS3 | D9PZ08
    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)
  3.2.1.23
    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
  D9PZ08_ACIS3 | D9PZ08
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        D9PZ08_ACIS3 | D9PZ08: 4ha3

(-) Related Entries Specified in the PDB File

4ha3 STRUCTURE OF BETA-GLYCOSIDASE FROM ACIDILOBUS SACCHARAVORANS IN COMPLEX WITH TRIS