Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  ZINC PEPTIDASE FROM GRIFOLA FRONDOSA
 
Authors :  T. Hori, T. Kumasaka, M. Yamamoto, T. Nonaka, N. Tanaka, Y. Hashimoto, T. Ueki, K. Takio
Date :  11 Oct 00  (Deposition) - 14 Mar 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Zinc Coordinate, Metalloprotease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Hori, T. Kumasaka, M. Yamamoto, N. Nonaka, N. Tanaka, Y. Hashimoto, U. Ueki, K. Takio
Structure Of A New 'Aspzincin' Metalloendopeptidase From Grifola Frondosa: Implications For The Catalytic Mechanism And Substrate Specificity Based On Several Different Crystal Forms.
Acta Crystallogr. , Sect. D V. 57 361 2001
PubMed-ID: 11223512  |  Reference-DOI: 10.1107/S0907444900019740
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PEPTIDYL-LYS METALLOENDOPEPTIDASE
    Chains: A
    EC Number: 3.4.24.20
    Organism Scientific: GRIFOLA FRONDOSA
    Organism Taxid: 5627
    Tissue: FRUITING BODY

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1MAN1Ligand/IonALPHA-D-MANNOSE
2ZN1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:39 , THR A:42BINDING SITE FOR RESIDUE MAN A 900
2AC2SOFTWAREHIS A:117 , HIS A:121 , ASP A:130 , HOH A:216 , HOH A:324BINDING SITE FOR RESIDUE ZN A 200

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:5 -A:75
2A:77 -A:97

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asn A:163 -Pro A:164

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1GE5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1GE5)

(-) Exons   (0, 0)

(no "Exon" information available for 1GE5)

(-) 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:167
 aligned with PLMP_GRIFR | P81054 from UniProtKB/Swiss-Prot  Length:348

    Alignment length:167
                                   191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       
           PLMP_GRIFR   182 TYNGCSSSEQSALAAAASAAQSYVAESLSYLQTHTAATPRYTTWFGSYISSRHSTVLQHYTDMNSNDFSSYSFDCTCTAAGTFAYVYPNRFGTVYLCGAFWKAPTTGTDSQAGTLVHESSHFTRNGGTKDYAYGQAAAKSLATMDPDKAVMNADNHEYFSENNPAQS 348
               SCOP domains d1ge5a_ A: Fungal zinc peptidase                                                                                                                                        SCOP domains
               CATH domains 1ge5A00 A:1-167 Collagenase (Catalytic Domain)                                                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhheee.........ee.......eeeehhhhhhh......hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh.hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ge5 A   1 TYNGCSSSEQSALAAAASAAQSYVAESLSYLQTHTAATPRYTTWFGSYISSRHSTVLQHYTDMNSNDFSSYSFDCTCTAAGTFAYVYPNRFGTVYLCGAFWKAPTTGTDSQAGTLVHESSHFTRNGGTKDYAYGQAAAKSLATMDPDKAVMNADNHEYFSENNPAQS 167
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160
   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: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1GE5)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PLMP_GRIFR | P81054)
molecular function
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004222    metalloendopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008237    metallopeptidase activity    Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

 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
    MAN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asn A:163 - Pro A:164   [ 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
  1ge5
    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
  PLMP_GRIFR | P81054
    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)
  3.4.24.20
    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
  PLMP_GRIFR | P81054
    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
        PLMP_GRIFR | P81054: 1g12 1ge6 1ge7

(-) Related Entries Specified in the PDB File

1g12 1G12 CONTAINS THE SAME ENZYME WITH DIFFERENT CRYSTAL FORM.
1ge6 1GE6 CONTAINS THE SAME ENZYME WITH DIFFERENT CRYSTAL FORM.
1ge7 1GE7 CONTAINS THE SAME ENZYME WITH DIFFERENT CRYSTAL FORM.