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 :  X-RAY CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMICOLA GRISEA CEL12A IN COMPLEX WITH A SOAKED THIO CELLOTETRAOSE
 
Authors :  G. I. Berglund, A. Shaw, J. Stahlberg, L. Kenne, T. H. Driguez, C. Mitchinson, M. Sandgren
Date :  08 Jul 04  (Deposition) - 16 Sep 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.52
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Cellulase, Cellulose Degradation, Endoglucanase, Glycosyl Hydrolase, Gh Family 12, Humicola Grisea Cel12A, Ligand Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Sandgren, G. I. Berglund, A. Shaw, J. Stahlberg, L. Kenne, T. Desmet, C. Mitchinson
Crystal Complex Structures Reveal How Substrate Is Bound In The -4 To The +2 Binding Sites Of Humicola Grisea Cel12A
J. Mol. Biol. V. 342 1505 2004
PubMed-ID: 15364577  |  Reference-DOI: 10.1016/J.JMB.2004.07.098

(-) Compounds

Molecule 1 - ENDOGLUCANASE
    Chains: A
    EC Number: 3.2.1.4
    Engineered: YES
    Expression System: ASPERGILLUS NIGER
    Expression System Taxid: 5061
    Fragment: CATALYTIC DOMAIN RESIDUES 31-254
    Organism Scientific: HUMICOLA GRISEA
    Organism Taxid: 5527
    Other Details: THE CRYSTAL STRUCTURE IS A COMPLEX WITH A SOAKED CELLOPENTAOSE. THE FIFTH GLUCOSE UNIT IS, HOWEVER, NOT VISIBLE IN THE ELECTRON DENSITY

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
1BGC4Ligand/IonBETA-D-GLUCOSE
2PCA1Mod. Amino AcidPYROGLUTAMIC ACID
3PG41Ligand/IonTETRAETHYLENE GLYCOL
4SO41Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:59 , ILE A:131 , TYR A:132 , PHE A:207 , BGC A:302 , HOH A:2067 , HOH A:2251BINDING SITE FOR RESIDUE BGC A 301
2AC2SOFTWAREMET A:122 , TRP A:124 , TYR A:132 , PRO A:133 , ILE A:134 , GLU A:205 , PHE A:207 , BGC A:301 , BGC A:303 , HOH A:2252 , HOH A:2253BINDING SITE FOR RESIDUE BGC A 302
3AC3SOFTWARETRP A:24 , TYR A:64 , ASP A:103 , PHE A:105 , GLU A:120 , MET A:122 , ASN A:155 , GLU A:205 , BGC A:302 , BGC A:304 , HOH A:2254BINDING SITE FOR RESIDUE BGC A 303
4AC4SOFTWAREASN A:22 , TRP A:24 , TRP A:115 , BGC A:303 , HOH A:2235 , HOH A:2255BINDING SITE FOR RESIDUE BGC A 304
5AC5SOFTWAREILE A:2 , ARG A:3 , SER A:4 , ASN A:157 , HOH A:2002 , HOH A:2256 , HOH A:2257BINDING SITE FOR RESIDUE SO4 A 401
6AC6SOFTWARETRP A:54 , GLN A:55 , SER A:88 , GLY A:209 , GLY A:210 , ARG A:217 , HOH A:2156 , HOH A:2200BINDING SITE FOR RESIDUE PG4 A 501

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:6 -A:35

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:210 -Pro A:211

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1W2U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1W2U)

(-) Exons   (0, 0)

(no "Exon" information available for 1W2U)

(-) 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:224
 aligned with Q8NJY3_9PEZI | Q8NJY3 from UniProtKB/TrEMBL  Length:254

    Alignment length:224
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250    
         Q8NJY3_9PEZI    31 QIRSLCELYGYWSGNGYELLNNLWGKDTATSGWQCTYLDGTNNGGIQWSTAWEWQGAPDNVKSYPYVGKQIQRGRKISDINSMRTSVSWTYDRTDIRANVAYDVFTARDPDHPNWGGDYELMIWLARYGGIYPIGTFHSQVNLAGRTWDLWTGYNGNMRVYSFLPPSGDIRDFSCDIKDFFNYLERNHGYPAREQNLIVYQVGTECFTGGPARFTCRDFRADLW 254
               SCOP domains d1w2ua_ A: Family 12 endo-1,4-beta-glucanase (cellulase) catalytic domain                                                                                                                                                        SCOP domains
               CATH domains -1w2uA00 A:2-224  [code=2.60.120.180, no name defined]                                                                                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...................hhhhh.eeeeeeeeee.....eeeeeeeeee.....................hhhh...eeeeeeee.....eeeeeeeeeee................................................................eeeeehhhhhhhhhhhh.................eeeeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w2u A   1 xIRSLCELYGYWSGNGYELLNNLWGKDTATSGWQCTYLDGTNNGGIQWSTAWEWQGAPDNVKSYPYVGKQIQRGRKISDINSMRTSVSWTYDRTDIRANVAYDVFTARDPDHPNWGGDYELMIWLARYGGIYPIGTFHSQVNLAGRTWDLWTGYNGNMRVYSFLPPSGDIRDFSCDIKDFFNYLERNHGYPAREQNLIVYQVGTECFTGGPARFTCRDFRADLW 224
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220    
                            |                                                                                                                                                                                                                               
                            1-PCA
   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/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1W2U)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q8NJY3_9PEZI | Q8NJY3)
molecular function
    GO:0008810    cellulase activity    Catalysis of the endohydrolysis of (1->4)-beta-D-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
    GO:0004553    hydrolase activity, hydrolyzing O-glycosyl compounds    Catalysis of the hydrolysis of any O-glycosyl bond.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0000272    polysaccharide catabolic process    The chemical reactions and pathways resulting in the breakdown of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.

 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
    BGC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PCA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PG4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ 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 ]
 
  Cis Peptide Bonds
    Gly A:210 - Pro A:211   [ 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
  1w2u
    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
  Q8NJY3_9PEZI | Q8NJY3
    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)
  3.2.1.4
    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
  Q8NJY3_9PEZI | Q8NJY3
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q8NJY3_9PEZI | Q8NJY3: 1olr 1uu4 1uu5 1uu6

(-) Related Entries Specified in the PDB File

1olr THE HUMICOLA GRISEA CEL12A ENZYME STRUCTURE AT 1.2 ANGSTROMS RESOLUTION AND THE IMPACT OF ITS FREE CYSTEINE RESIDUES ON THERMAL STABILITY
1uu5 X-RAY CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMICOLA GRISEA CEL12A SOAKED WITH CELLOTETRAOSE
1uu6 X-RAY CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMICOLA GRISEA CEL12A IN COMPLEX WITH A SOAKED CELLOPENTAOSE