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 :  THE STRUCTURE OF A GLYCOSIDE HYDROLASE FAMILY 81 ENDO-[BETA]-1,3-GLUCANASE
 
Authors :  Z. Q. Jiang, P. Zhou, Z. Z. Chen, Q. J. Yan, S. Q. Yang, R. Hilgenfeld
Date :  10 Apr 13  (Deposition) - 02 Oct 13  (Release) - 02 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Glucoside Hydrolases Family 81, Endo-Beta-1, 3-Glucanase, Rhzmucor Miehei, (Alpha/Alpha)6-Barrel, Supersandwich, Beta-1, 3-Glucanase, Extracellular, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Zhou, Z. Z. Chen, Q. J. Yan, S. Q. Yang, R. Hilgenfeld, Z. Q. Jiang
The Structure Of A Glycoside Hydrolase Family 81 Endo-[Beta]-1, 3-Glucanase
Acta Crystallogr. , Sect. D V. 69 2027 2013
PubMed-ID: 18802694  |  Reference-DOI: 10.1107/S090744491301799X

(-) Compounds

Molecule 1 - GLYCOSIDE HYDROLASE FAMILY 81 ENDO-BETA-1,3-GLUCANASE
    Chains: A, B
    EC Number: 3.2.1.39
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RMLAM81A
    Organism Scientific: RHIZOMUCOR MIEHEI
    Organism Taxid: 4839
    Strain: RHIZOMUCOR MIEHEI CAU432

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

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, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:73 , TYR A:74 , GLY A:75 , GLY A:76 , ASN A:77 , ARG A:116 , HOH A:985 , HOH A:1169 , HOH A:1184BINDING SITE FOR RESIDUE SO4 A 801
2AC2SOFTWAREGLY B:73 , TYR B:74 , GLY B:75 , GLY B:76 , ASN B:77 , ARG B:116 , HOH B:1078 , HOH B:1129BINDING SITE FOR RESIDUE SO4 B 801

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4K3A)

(-) Cis Peptide Bonds  (7, 7)

Asymmetric Unit
No.Residues
1Asp A:64 -Pro A:65
2Asp A:210 -Pro A:211
3Leu A:642 -Pro A:643
4Asp B:64 -Pro B:65
5Asp B:193 -Asn B:194
6Asp B:210 -Pro B:211
7Leu B:642 -Pro B:643

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4K3A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4K3A)

(-) Exons   (0, 0)

(no "Exon" information available for 4K3A)

(-) 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:720
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........hhhhh..ee......................hhhhhh.hhhhh........eeee.........eeee.....eee..............eee......eeeee.hhh....eeeeeeee..eeeeeeee..eeeeeeeeeee.....eeeeeeee.eeee....eeeeee..........eeee.eeeeee......eeeeee.....eeeeeee..eeee...eeeeeeeee..hhhhhhhhhhh....eeeeeeeeee.....eeeeeeeee.......eeeehhhhhhhhhhhhheeeeeeee.....eeeeee..eeeeee...............hhhhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh......eeee....eeee....hhhhh.....hhhhhhhhh.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.............ee....ee..............ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhh.....eee..eee.......hhhhhhhhhhh..hhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh..hhhhhhhhhh........hhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4k3a A   5 GDDLFVPVSNFDPKSIFPEIKHPFEPMYANTENGKIVPTNSWISNLFYPSADNLAPTTPDPYTLRLLDGYGGNPGLTIRQPSAKVLGSYPPTNDVPYTDAGYMINSVVVDLRLTSSEWSDVVPDRQVTDWDHLSANLRLSTPQDSNSYIDFPIVRGMAYITANYNNLTPQFLSQHAIISVEADEKKSDDNTSTFSGRKFKITMNDDPTSTFIIYSLGDKPLELRKQDNSNLVASKPYTGVIRVAKLPAPEFETLLDASRAVWPTGGDISARSDDNNGASYTIKWKTNSNEAPLLTYAYAHHLTSIDDSNVKRTDMTLQSATKGPMTALVGNEWTLRETELSPVEWLPLQAAPNPTTINEIMTEINKDIASNYTQETAKEDNYFSGKGLQKFAMLALILNKSDQTQLRNPELAQIALDKLKAAFLPYLQNEQADPFRYDTLYKGIVAKAGLPTSMGGTDDLSAEFGHSYYSDHHYHQGYFVVTAAIIHHLDPTWNADRLKAWTEALIRDVNNANDGDEYFAAFRNWDWFAGHSWAGGIKPDGALDGRDQESVPESVNFYWGAKLWGLATGNTPLTKLASLQLAVTKRTTYEYFWMLDGNKNRPENIVRNKVIGIYFEQKTDYTTYFGRFLEYIHGIQQLPMTPELMEYIRTPEFVSQEWDEKLGAIAPTVQSPWAGVLYLNYAIINPAEAYPALRKVQMDDGQTRSYSLYLTATRPHFFRR 724
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724


Chain B from PDB  Type:PROTEIN  Length:717
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhh..ee......................hhhhhh.hhhhh........eeee.........eeee.....eee...........eee......eeeee.hhh....eeeeeeee..eeeeeeee..eeeeeeeeeee.....eeeeeeee.eeee....eeeeee..........eeee.eeeeee......eeeeee.....eeeeeee..eeee...eeeeeeeee..hhhhhhhhhhh....eeeeeeeeee.....eeeeeeeee.......eeeehhhhhhhh.....eeeeeeee.....eeeeee..eeeeee...............hhhhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh......eeee....eeee....hhhhh.....hhhhhhhhh.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.............ee....ee..............ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhh.....eee..eee.......hhhhhhhhhhh..hhhhhhh..hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh..hhhhhhhhhh........hhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k3a B   5 GDDLFVPVSNFDPKSIFPEIKHPFEPMYANTENGKIVPTNSWISNLFYPSADNLAPTTPDPYTLRLLDGYGGNPGLTIRQPSAKVLGSYPPTPYTDAGYMINSVVVDLRLTSSEWSDVVPDRQVTDWDHLSANLRLSTPQDSNSYIDFPIVRGMAYITANYNNLTPQFLSQHAIISVEADEKKSDDNTSTFSGRKFKITMNDDPTSTFIIYSLGDKPLELRKQDNSNLVASKPYTGVIRVAKLPAPEFETLLDASRAVWPTGGDISARSDDNNGASYTIKWKTNSNEAPLLTYAYAHHLTSIDDSNVKRTDMTLQSATKGPMTALVGNEWTLRETELSPVEWLPLQAAPNPTTINEIMTEINKDIASNYTQETAKEDNYFSGKGLQKFAMLALILNKSDQTQLRNPELAQIALDKLKAAFLPYLQNEQADPFRYDTLYKGIVAKAGLPTSMGGTDDLSAEFGHSYYSDHHYHQGYFVVTAAIIHHLDPTWNADRLKAWTEALIRDVNNANDGDEYFAAFRNWDWFAGHSWAGGIKPDGALDGRDQESVPESVNFYWGAKLWGLATGNTPLTKLASLQLAVTKRTTYEYFWMLDGNKNRPENIVRNKVIGIYFEQKTDYTTYFGRFLEYIHGIQQLPMTPELMEYIRTPEFVSQEWDEKLGAIAPTVQSPWAGVLYLNYAIINPAEAYPALRKVQMDDGQTRSYSLYLTATRPHFFRR 724
                                    14        24        34        44        54        64        74        84        94 ||    107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       
                                                                                                                      96|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
                                                                                                                      100
   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 4K3A)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4K3A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4K3A)

(-) Gene Ontology  (2, 2)

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
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asp A:210 - Pro A:211   [ RasMol ]  
    Asp A:64 - Pro A:65   [ RasMol ]  
    Asp B:193 - Asn B:194   [ RasMol ]  
    Asp B:210 - Pro B:211   [ RasMol ]  
    Asp B:64 - Pro B:65   [ RasMol ]  
    Leu A:642 - Pro A:643   [ RasMol ]  
    Leu B:642 - Pro B:643   [ 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
  4k3a
    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
  U5HK45_RHIMI | U5HK45
    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)
  3.2.1.39
    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
  U5HK45_RHIMI | U5HK45
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        U5HK45_RHIMI | U5HK45: 4k35

(-) Related Entries Specified in the PDB File

4k35