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(-) Description

Title :  OPTIMIZATION OF THE IN SILICO DESIGNED KEMP ELIMINASE KE70 BY COMPUTATIONAL DESIGN AND DIRECTED EVOLUTION
 
Authors :  O. Khersonsky, D. Rothlisberge, A. M. Wollacott, P. Murphy, O. Dym, S. A G. Kiss, K. N. Houk, D. Baker, D. S. Tawfik, Israel Structural Proteo Center (Ispc)
Date :  20 Dec 10  (Deposition) - 09 Feb 11  (Release) - 19 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.19
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Structural Genomics, Israel Structural Proteomics Center, Ispc, Tim, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. Khersonsky, D. Rothlisberger, A. M. Wollacott, P. Murphy, O. Dym, S. Albeck, G. Kiss, K. N. Houk, D. Baker, D. S. Tawfik
Optimization Of The In-Silico-Designed Kemp Eliminase Ke70 By Computational Design And Directed Evolution
J. Mol. Biol. V. 407 391 2011
PubMed-ID: 21277311  |  Reference-DOI: 10.1016/J.JMB.2011.01.041

(-) Compounds

Molecule 1 - DEOXYRIBOSE PHOSPHATE ALDOLASE
    Chains: A, B
    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
13NY2Ligand/Ion5-NITRO-1H-BENZOTRIAZOLE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
13NY1Ligand/Ion5-NITRO-1H-BENZOTRIAZOLE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
13NY1Ligand/Ion5-NITRO-1H-BENZOTRIAZOLE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:17 , PHE A:49 , SER A:102 , ALA A:104 , ALA A:139 , ILE A:203 , VAL A:205 , GLY A:238BINDING SITE FOR RESIDUE 3NY A 273
2AC2SOFTWAREPHE B:49 , CYS B:73 , ALA B:104 , ALA B:139 , ILE B:203 , VAL B:205BINDING SITE FOR RESIDUE 3NY B 273

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3Q2D)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Phe A:78 -Pro A:79
2Phe B:78 -Pro B:79

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

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(-) 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:246
                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhh.eeee...hhhhhhhhhhhhee..ee..eee.hhhhhhhhhhhhhhh.....eeeeee.......hhhhhhhhhhhhhhhh..eeeee.hhhhhhh..hhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhhhh...eee..........hhhhhhhhhhhhhhhh.....eee......hhhhhhhhhhhhhhhhh..........eeeehhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3q2d A   3 TDLKASSLRALKLMHLATSDTDENVIALCHQAKTPVGNTDAIFIYPRFIPIARKTLKEQGTPEIRICTSTNFPHGNDDIDIALAETRAAIAYGADSVAVVFPYRALMAGNEQVGFDLVKACKEACAAANVLLAVIIETGELKDEALIRKASEISIKAGADNIVTSTGKVAVGATPESARIMMEVIRDMGVEKTVGFIPVGGVRTAEDAQKYLAIADELFGADWADARHYAFGASASLLASLLKALG 252
                                    12        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246      
                                             21|                                                                                                                                                                                                                                  
                                              26                                                                                                                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:227
                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhee..ee..eee.hhhhhhhhhhhhhhh.....eeeeee.......hhhhhhhhhhhhhhh...eeeee.hhhhhhh.hhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhhhh...eee..........hhhhhhhhhhhhhhhh.....eee......hhhhhhhhhhhhhhhhh.............hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q2d B  27 TDENVIALCHQAKTPVGNTDAIFIYPRFIPIARKTLKEQGTPEIRICTSTNFPHGNDDIDIALAETRAAIAYGADSVAVVFPYRALMAGNEQVGFDLVKACKEACAAANVLLAVIIETGELKDEALIRKASEISIKAGADNIVTSTGKVAVGATPESARIMMEVIRDMGVEKTVGFIPVGGVRTAEDAQKYLAIADELFGADWADARHYAFGASASLLASLLKALGH 253
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246
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  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 3Q2D)

(-) CATH Domains  (0, 0)

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(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
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 Related Entries

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(-) Related Entries Specified in the PDB File

3npu 3npv 3npw 3npx 3nq2 3nq8 3nqv