Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym.Unit - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asym.Unit - manually
Asym.Unit - manually  (Jmol Viewer)
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 :  A NOVEL CUTINASE-LIKE PROTEIN FROM CRYPTOCOCCUS SP.
 
Authors :  K. Masaki, N. R. Kamini, H. Ikeda, H. Iefuji, H. Kondo, M. Suzuki, S. Tsud
Date :  14 Jul 05  (Deposition) - 14 Jul 06  (Release) - 13 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.05
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Alpha/Beta Hydrolase Fold, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kodama, K. Masaki, H. Kondo, M. Suzuki, S. Tsuda, T. Nagura, N. Shimba, E. Suzuki, H. Iefuji
Crystal Structure And Enhanced Activity Of A Cutinase-Like Enzyme From Cryptococcus Sp. Strain S-2
Proteins V. 77 710 2009
PubMed-ID: 19544571  |  Reference-DOI: 10.1002/PROT.22484
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CUTINASE-LIKE PROTEIN
    Chains: A, B
    EC Number: 3.1.1.-
    Organism Scientific: CRYPTOCOCCUS SP.
    Organism Taxid: 87049
    Strain: S-2

 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  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1CIT2Ligand/IonCITRIC ACID
2EDO2Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2EDO1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2EDO1Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:42 , ILE A:43 , TYR A:44 , ARG A:66 , ASN A:137 , ALA A:171 , HIS A:172 , HOH A:609 , HOH A:667 , HOH A:717 , HOH A:731BINDING SITE FOR RESIDUE CIT A 501
2AC2SOFTWAREASN B:55 , ARG B:65 , ARG B:66 , SER B:69 , GLY B:70 , HOH B:635 , HOH B:646 , HOH B:732 , HOH B:784BINDING SITE FOR RESIDUE CIT B 502
3AC3SOFTWAREHOH A:818 , GLY B:16 , THR B:17 , TYR B:84 , LEU B:181 , HOH B:698BINDING SITE FOR RESIDUE EDO B 601
4AC4SOFTWAREGLY A:16 , THR A:17 , TYR A:84 , HOH A:612 , HOH A:681 , HOH A:820BINDING SITE FOR RESIDUE EDO A 602

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:6 -A:78
2A:161 -A:168
3B:6 -B:78
4B:161 -B:168

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2CZQ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2CZQ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2CZQ)

(-) Exons   (0, 0)

(no "Exon" information available for 2CZQ)

(-) 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:205
 aligned with Q874E9_9TREE | Q874E9 from UniProtKB/TrEMBL  Length:239

    Alignment length:205
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234     
         Q874E9_9TREE    35 ATSSACPQYVLINTRGTGEPQGQSAGFRTMNSQITAALSGGTIYNTVYTADFSQNSAAGTADIIRRINSGLAANPNVCYILQGYSQGAAATVVALQQLGTSGAAFNAVKGVFLIGNPDHKSGLTCNVDSNGGTTTRNVNGLSVAYQGSVPSGWVSKTLDVCAYGDGVCDTAHGFGINAQHLSYPSDQGVQTMGYKFAVNKLGGSA 239
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeee............hhhhhhhhhhhh..eeeee..........hhhhhhhhhhhhhhhhhhh...eeeeeeehhhhhhhhhhhhhhh..hhhhhheeeeeee...........ee..............hhhhhh..hhhhhh.eeee................hhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2czq A   1 ATSSACPQYVLINTRGTGEPQGQSAGFRTMNSQITAALSGGTIYNTVYTADFSQNSAAGTADIIRRINSGLAANPNVCYILQGYSQGAAATVVALQQLGTSGAAFNAVKGVFLIGNPDHKSGLTCNVDSNGGTTTRNVNGLSVAYQGSVPSGWVSKTLDVCAYGDGVCDTAHGFGINAQHLSYPSDQGVQTMGYKFAVNKLGGSA 205
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200     


Chain B from PDB  Type:PROTEIN  Length:205
 aligned with Q874E9_9TREE | Q874E9 from UniProtKB/TrEMBL  Length:239

    Alignment length:205
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234     
         Q874E9_9TREE    35 ATSSACPQYVLINTRGTGEPQGQSAGFRTMNSQITAALSGGTIYNTVYTADFSQNSAAGTADIIRRINSGLAANPNVCYILQGYSQGAAATVVALQQLGTSGAAFNAVKGVFLIGNPDHKSGLTCNVDSNGGTTTRNVNGLSVAYQGSVPSGWVSKTLDVCAYGDGVCDTAHGFGINAQHLSYPSDQGVQTMGYKFAVNKLGGSA 239
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeee.........hhhhhhhhhhhhhhh..eeeee..........hhhhhhhhhhhhhhhhhhh...eeeeeeehhhhhhhhhhhhhhh..hhhhhheeeeeee...........ee..............hhhhhh..hhhhhh.eeee................hhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2czq B   1 ATSSACPQYVLINTRGTGEPQGQSAGFRTMNSQITAALSGGTIYNTVYTADFSQNSAAGTADIIRRINSGLAANPNVCYILQGYSQGAAATVVALQQLGTSGAAFNAVKGVFLIGNPDHKSGLTCNVDSNGGTTTRNVNGLSVAYQGSVPSGWVSKTLDVCAYGDGVCDTAHGFGINAQHLSYPSDQGVQTMGYKFAVNKLGGSA 205
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200
   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 2CZQ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2CZQ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2CZQ)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q874E9_9TREE | Q874E9)
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.
biological process
    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.

 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
    CIT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2czq)
 
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
  2czq
    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
  Q874E9_9TREE | Q874E9
    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)
  3.1.1.-
    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
  Q874E9_9TREE | Q874E9
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 2CZQ)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2CZQ)