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 :  CRYSTAL STRUCTURE OF A CELL WALL INVERTASE INHIBITOR FROM TOBACCO (PH 9.5)
 
Authors :  M. Hothorn, K. Scheffzek
Date :  29 Mar 06  (Deposition) - 03 Apr 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.38
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Inhibitor, Protein Binding, Four-Helix Bundle, Helical Hairpin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Hothorn, K. Scheffzek
Multiple Crystal Forms Of The Cell-Wall Invertase Inhibitor From Tobacco Support High Conformational Rigidity Over A Broad Ph-Range
Acta Crystallogr. , Sect. D V. 62 665 2006
PubMed-ID: 16699194  |  Reference-DOI: 10.1107/S0907444906011693

(-) Compounds

Molecule 1 - INVERTASE INHIBITOR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETM20
    Expression System Strain: ORIGAMI DE3
    Expression System Taxid: 562
    Organism Common: COMMON TOBACCO
    Organism Scientific: NICOTIANA TABACUM
    Organism Taxid: 4097
    Tissue: CELL WALL

 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, 18)

Asymmetric Unit (1, 18)
No.NameCountTypeFull Name
1IOD18Ligand/IonIODIDE ION
Biological Unit 1 (1, 9)
No.NameCountTypeFull Name
1IOD9Ligand/IonIODIDE ION
Biological Unit 2 (1, 9)
No.NameCountTypeFull Name
1IOD9Ligand/IonIODIDE ION

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:79 , GLU A:116 , TYR A:120BINDING SITE FOR RESIDUE IOD A1151
02AC2SOFTWARETYR A:120 , LYS B:70BINDING SITE FOR RESIDUE IOD A1152
03AC3SOFTWAREARG A:61BINDING SITE FOR RESIDUE IOD A1153
04AC4SOFTWAREPRO A:72BINDING SITE FOR RESIDUE IOD A1154
05AC5SOFTWAREGLN A:115BINDING SITE FOR RESIDUE IOD A1155
06AC6SOFTWAREHOH A:2003BINDING SITE FOR RESIDUE IOD A1156
07AC7SOFTWARETYR A:17 , GLU B:8 , LEU B:21BINDING SITE FOR RESIDUE IOD A1157
08AC8SOFTWAREGLU A:137 , HOH A:2020BINDING SITE FOR RESIDUE IOD A1158
09AC9SOFTWARELEU A:19BINDING SITE FOR RESIDUE IOD A1159
10BC1SOFTWARELYS A:125 , TYR B:120BINDING SITE FOR RESIDUE IOD B1150
11BC2SOFTWARESER B:58 , ARG B:61BINDING SITE FOR RESIDUE IOD B1151
12BC3SOFTWAREGLU B:137 , HOH B:2024BINDING SITE FOR RESIDUE IOD B1152
13BC4SOFTWAREPRO B:127BINDING SITE FOR RESIDUE IOD B1153
14BC5SOFTWARETYR B:120BINDING SITE FOR RESIDUE IOD B1154
15BC6SOFTWAREILE B:133BINDING SITE FOR RESIDUE IOD B1156
16BC7SOFTWAREGLU A:8 , TYR B:17 , GLN B:18BINDING SITE FOR RESIDUE IOD B1157
17BC8SOFTWARELYS B:81BINDING SITE FOR RESIDUE IOD B1158

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:11 -A:20
2A:76 -A:117
3B:11 -B:20
4B:76 -B:117

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2CJ8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2CJ8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2CJ8)

(-) Exons   (0, 0)

(no "Exon" information available for 2CJ8)

(-) 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:147
 aligned with O49908_TOBAC | O49908 from UniProtKB/TrEMBL  Length:166

    Alignment length:147
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       
         O49908_TOBAC    20 NNLVETTCKNTPNYQLCLKTLLSDKRSATGDITTLALIMVDAIKAKANQAAVTISKLRHSNPPAAWKGPLKNCAFSYKVILTASLPEAIEALTKGDPKFAEDGMVGSSGDAQECEEYFKGSKSPFSALNIAVHELSDVGRAIVRNLL 166
               SCOP domains d2cj8a_ A: automated matches                                                                                                                        SCOP domains
               CATH domains 2cj8A00 A:4-150 Invertase/pectin methylesterase inhibitor family protein                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cj8 A   4 NNLVETTCKNTPNYQLCLKTLLSDKRSATGDITTLALIMVDAIKAKANQAAVTISKLRHSNPPAAWKGPLKNCAFSYKVILTASLPEAIEALTKGDPKFAEDGMVGSSGDAQECEEYFKGSKSPFSALNIAVHELSDVGRAIVRNLL 150
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       


Chain B from PDB  Type:PROTEIN  Length:145
 aligned with O49908_TOBAC | O49908 from UniProtKB/TrEMBL  Length:166

    Alignment length:145
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160     
         O49908_TOBAC    21 NLVETTCKNTPNYQLCLKTLLSDKRSATGDITTLALIMVDAIKAKANQAAVTISKLRHSNPPAAWKGPLKNCAFSYKVILTASLPEAIEALTKGDPKFAEDGMVGSSGDAQECEEYFKGSKSPFSALNIAVHELSDVGRAIVRNL 165
               SCOP domains d2cj8b_ B: automated matches                                                                                                                      SCOP domains
               CATH domains 2cj8B00 B:5-149 Invertase/pectin methylesterase inhibitor family protein                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh..hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cj8 B   5 NLVETTCKNTPNYQLCLKTLLSDKRSATGDITTLALIMVDAIKAKANQAAVTISKLRHSNPPAAWKGPLKNCAFSYKVILTASLPEAIEALTKGDPKFAEDGMVGSSGDAQECEEYFKGSKSPFSALNIAVHELSDVGRAIVRNL 149
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144
   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, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2CJ8)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (O49908_TOBAC | O49908)
molecular function
    GO:0004857    enzyme inhibitor activity    Binds to and stops, prevents or reduces the activity of an enzyme.
biological process
    GO:0043086    negative regulation of catalytic activity    Any process that stops or reduces the activity of an enzyme.

 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
    IOD  [ 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 ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
    BC8  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2cj8)
 
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
  2cj8
    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
  O49908_TOBAC | O49908
    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)
  (no 'Enzyme Classificator' available)
    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
  O49908_TOBAC | O49908
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        O49908_TOBAC | O49908: 1rj1 1rj4 2cj4 2cj5 2cj6 2cj7 2xqr

(-) Related Entries Specified in the PDB File

1rj1 CRYSTAL STRUCTURE OF A CELL WALL INVERTASE INHIBITOR FROMTOBACCO
1rj4 STRUCTURE OF A CELL WALL INVERTASE INHIBITOR FROM TOBACCOIN COMPLEX WITH CD2+
2cj4 CRYSTAL STRUCTURE OF A CELL WALL INVERTASE INHIBITOR FROM TOBACCO AT PH 4.6
2cj5 CRYSTAL STRUCTURE OF A CELL WALL INVERTASE INHIBITOR FROM TOBACCO (PH 5.0)
2cj6 CRYSTAL STRUCTURE OF A CELL WALL INVERTASE INHIBITOR FROM TOBACCO (PH 7.5)
2cj7 CRYSTAL STRUCTURE OF A CELL WALL INVERTASE INHIBITOR FROM TOBACCO (PH 9.0)