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 :  DESIGNED PROTEIN KE59 R8_2/7A
 
Authors :  O. Khersonsky, G. Kiss, D. Roethlisberger, O. Dym, S. Albeck, K. N. Houk D. S. Tawfik, Israel Structural Proteomics Center (Ispc)
Date :  06 Dec 11  (Deposition) - 06 Jun 12  (Release) - 11 Jul 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Structural Genomics, Israel Structural Proteomics Center, Ispc, Beta Barrel, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. Khersonsky, G. Kiss, D. Rothlisberger, O. Dym, S. Albeck, K. N. Houk D. Baker, D. S. Tawfik
Bridging The Gaps In Design Methodologies By Evolutionary Optimization Of The Stability And Proficiency Of Designed Kemp Eliminase Ke59.
Proc. Natl. Acad. Sci. Usa V. 109 10358 2012
PubMed-ID: 22685214  |  Reference-DOI: 10.1073/PNAS.1121063109

(-) Compounds

Molecule 1 - KEMP ELIMINASE KE59 R8_2/7A
    Chains: A, B
    EC Number: 4.-.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 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
1PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:53 , HIS A:182 , SER A:211 , GLY A:212 , GLY A:233 , SER A:234BINDING SITE FOR RESIDUE PO4 A 300
2AC2SOFTWARELYS B:53 , HIS B:182 , SER B:211 , GLY B:233 , SER B:234 , HOH B:276BINDING SITE FOR RESIDUE PO4 B 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3UYC)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3UYC)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3UYC)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3UYC)

(-) Exons   (0, 0)

(no "Exon" information available for 3UYC)

(-) 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:241
                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhh..........hhhhhhhhhhhh....eeeee..........hhhhhhhhhh....eeeee........hhhhhhhhhhhh...eeee.....hhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhh....eeee.hhhhhhhhhhh...eeeee............hhhhhhhh.....eeeee....hhhhhhhhhhh...eeeehhhhhhh..hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3uyc A   2 PRYLKGWLEDVVQLSLRRPSLHARPIISLRERILEFNKRNNTAIIAVYKRKSPLNVERDPIEYAKFMERGVVGLAILTEEKYFNGSYEDLRKIASSVSIPILMWDIIVKESQIDDAYNLGADTVGLIVKILTERELKSLLEYARSYGMEPAIVINDENDLDIALRIGARFIIISSHDLETLEINKENQRKLISMVPSDVVKVVASGISERNEIEELRKLGVNAFEIGSSLMRNPEKIKEFI 247
                                    11        21  ||    34        44        54  ||    66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246 
                                                 24|                           57|                                                                                                                                                                                           
                                                  28                            60                                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:246
                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhh.............hhhhhhhhhhhh....eeeee............hhhhhhhhhh....eeeee........hhhhhhhhhhhh...eeee....hhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhh....eeee.hhhhhhhhhhh...eeeee............hhhhhhhhh....eeeee....hhhhhhhhhhh...eeeehhhhhhh..hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3uyc B   2 PRYLKGWLEDVVQLSLRRPSLHASRQRPIISLRERILEFNKRNNTAIIAVYKRKSPSGLNVERDPIEYAKFMERGVVGLAILTEEKYFNGSYEDLRKIASSVSIPILMWDIIVKESQIDDAYNLGADTVGLIVKILTERELKSLLEYARSYGMEPAIVINDENDLDIALRIGARFIIISSHDLETLEINKENQRKLISMVPSDVVKVVASGISERNEIEELRKLGVNAFEIGSSLMRNPEKIKEFI 247
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241
   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 3UYC)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3UYC)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3UYC)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3UYC)

 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
    PO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3uyc)
 
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
  3uyc
    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
  (no 'UniProt ID/Accession number' available) |
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProt
 
Access by Enzyme Classificator   (EC Number)
  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
  (no 'UniProt ID/Accession number' available) |
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3UYC)

(-) Related Entries Specified in the PDB File

3uxa DESIGNED PROTEIN KE59 R1 7/10H
3uxd DESIGNED PROTEIN KE59 R1 7/10H WITH DICHLOROBENZOTRIAZOLE (DBT)
3uy7 DESIGNED PROTEIN KE59 R1 7/10H WITH G130S MUTATION
3uy8 DESIGNED PROTEIN KE59 R5_11/5F
3uz5 DESIGNED PROTEIN KE59 R13 3/11H
3uzj DESIGNED PROTEIN KE59 R13 3/11H WITH BENZOTRIAZOLE