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(-) Description

Title :  EVOLUTIONARY OPTIMIZATION OF COMPUTATIONALLY DESIGNED ENZYMES: KEMP ELIMINASES OF THE KE07 SERIES
 
Authors :  O. Khersonsky, O. Dym, D. S. Tawfik
Date :  03 Aug 09  (Deposition) - 02 Mar 10  (Release) - 02 Mar 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  E  (1x)
Biol. Unit 6:  F  (1x)
Keywords :  Beta Barrel, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. Khersonsky, D. Rothlisberger, O. Dym, S. Albeck, C. J. Jackson, D. Baker, D. S. Tawfik
Evolutionary Optimization Of Computationally Designed Enzymes: Kemp Eliminases Of The Ke07 Series.
J. Mol. Biol. V. 396 1025 2010
PubMed-ID: 20036254  |  Reference-DOI: 10.1016/J.JMB.2009.12.031

(-) Compounds

Molecule 1 - KE7 R6 3/7F
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A     
Biological Unit 2 (1x):  B    
Biological Unit 3 (1x):   C   
Biological Unit 4 (1x):    D  
Biological Unit 5 (1x):     E 
Biological Unit 6 (1x):      F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
115P3Ligand/IonPOLYETHYLENE GLYCOL (N=34)
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
115P1Ligand/IonPOLYETHYLENE GLYCOL (N=34)
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
115P1Ligand/IonPOLYETHYLENE GLYCOL (N=34)
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
115P-1Ligand/IonPOLYETHYLENE GLYCOL (N=34)
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
115P-1Ligand/IonPOLYETHYLENE GLYCOL (N=34)
Biological Unit 5 (1, 1)
No.NameCountTypeFull Name
115P1Ligand/IonPOLYETHYLENE GLYCOL (N=34)
Biological Unit 6 (0, 0)
No.NameCountTypeFull Name
115P-1Ligand/IonPOLYETHYLENE GLYCOL (N=34)

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:117 , GLY A:121 , SER A:122 , ALA D:117 , SER D:122BINDING SITE FOR RESIDUE 15P A 256
2AC2SOFTWAREALA B:117 , GLY B:121 , SER B:122 , GLU B:161 , HOH B:269 , SER C:122BINDING SITE FOR RESIDUE 15P B 256
3AC3SOFTWAREALA E:117 , SER E:122 , GLU E:161 , GLY F:121 , SER F:122 , HOH F:275BINDING SITE FOR RESIDUE 15P E 256

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Gly A:80 -Gly A:81
2Gly C:80 -Gly C:81
3Gly D:80 -Gly D:81
4Gly E:80 -Gly E:81
5Gly F:80 -Gly F:81

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3IIP)

(-) 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:249
                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee..ee.............hhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhh...eeeeeeeeee..eeeeee....eeeeeehhhhhhhhhhh...eeeeee.hhh......hhhhhhhhhhhh...eeee.....hhhhhhhhhh...eeeehhhhhh...hhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3iip A   1 ALAKRIDAALIVKDGRVVEGSNFENLRDSGDPVELGKFYSEIGIDELSFWDITAVEKRKTMLELVEKVAEQIDIPFTVGGGIHDFETASELILRGADKVEINTAAVENPSLITQIAQTFGSQAVVVYIAAKRVDGEFMVFTYSGTKNTGILLRDWVVEVEKRGAGEIVLGSIDRLGTKSGYDTEMIRFVRPLTTLPIIAHRGAGKMEHFLEAFLAGADAAKADSVFHFREIDVRELKEYLKKHGVNVRL 250
                                    10        20        30        40        50   ||   61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241         
                                                                                54|                                                                                                                                                                                                  
                                                                                 56                                                                                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:248
                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee..ee.............hhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhh...eeeeeeeeee..eeeeee....eeeeeehhhhhhhhhhh...eeeeee.hhh......hhhhhhhhhhhh...eeee.....hhhhhhhhhhh..eeeehhhhhh...hhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3iip B   1 ALAKRIDAALIVKDGRVVEGSNFENLRDSGDPVELGKFYSEIGIDELSFWDITASKRKTMLELVEKVAEQIDIPFTVGGGIHDFETASELILRGADKVEINTAAVENPSLITQIAQTFGSQAVVVYIAAKRVDGEFMVFTYSGTKNTGILLRDWVVEVEKRGAGEIVLGSIDRLGTKSGYDTEMIRFVRPLTTLPIIAHRGAGKMEHFLEAFLAGADAAKADSVFHFREIDVRELKEYLKKHGVNVRL 250
                                    10        20        30        40        50    ||  62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242        
                                                                                 55|                                                                                                                                                                                                
                                                                                  58                                                                                                                                                                                                


Chain C from PDB  Type:PROTEIN  Length:250
                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee..ee.............hhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhh...eeeeeeeeee..eeeeee....eeeeeehhhhhhhhhhh...eeeeee.hhh......hhhhhhhhhhhh...eeee.....hhhhhhhhhh...eeeehhhhhh...hhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3iip C   1 ALAKRIDAALIVKDGRVVEGSNFENLRDSGDPVELGKFYSEIGIDELSFWDITASVEKRKTMLELVEKVAEQIDIPFTVGGGIHDFETASELILRGADKVEINTAAVENPSLITQIAQTFGSQAVVVYIAAKRVDGEFMVFTYSGTKNTGILLRDWVVEVEKRGAGEIVLGSIDRLGTKSGYDTEMIRFVRPLTTLPIIAHRGAGKMEHFLEAFLAGADAAKADSVFHFREIDVRELKEYLKKHGVNVRL 250
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250


Chain D from PDB  Type:PROTEIN  Length:247
                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee..ee.............hhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhh...eeeeeeeeee..eeeeee....eeeeeehhhhhhhhhhh...eeeeee.hhh......hhhhhhhhhhhh...eeee....hhhhhhhhhhh...eeeehhhhhh...hhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3iip D   1 ALAKRIDAALIVKDGRVVEGSNFENLRDSGDPVELGKFYSEIGIDELSFWDITAKRKTMLELVEKVAEQIDIPFTVGGGIHDFETASELILRGADKVEINTAAVENPSLITQIAQTFGSQAVVVYIAAKRVDGEFMVFTYSGTKNTGILLRDWVVEVEKRGAGEIVLGSIDRLGTKSGYDTEMIRFVRPLTTLPIIAHRGAGKMEHFLEAFLAGADAAKADSVFHFREIDVRELKEYLKKHGVNVRL 250
                                    10        20        30        40        50   ||   63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       
                                                                                54|                                                                                                                                                                                                
                                                                                 58                                                                                                                                                                                                


Chain E from PDB  Type:PROTEIN  Length:247
                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee..ee.............hhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhh...eeeeeeeeee..eeeeee....eeeeeehhhhhhhhhhhh..eeeeee.hhh......hhhhhhhhhhhh...eeee.....hhhhhhhhhh...eeeehhhhhh...hhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3iip E   1 ALAKRIDAALIVKDGRVVEGSNFENLRDSGDPVELGKFYSEIGIDELSFWDITAKRKTMLELVEKVAEQIDIPFTVGGGIHDFETASELILRGADKVEINTAAVENPSLITQIAQTFGSQAVVVYIAAKRVDGEFMVFTYSGTKNTGILLRDWVVEVEKRGAGEIVLGSIDRLGTKSGYDTEMIRFVRPLTTLPIIAHRGAGKMEHFLEAFLAGADAAKADSVFHFREIDVRELKEYLKKHGVNVRL 250
                                    10        20        30        40        50   ||   63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       
                                                                                54|                                                                                                                                                                                                
                                                                                 58                                                                                                                                                                                                


Chain F from PDB  Type:PROTEIN  Length:247
                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee..ee.............hhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhh...eeeeeeeeee..eeeeee....eeeeeehhhhhhhhhhh...eeeeee.hhh......hhhhhhhhhhhh...eeee....hhhhhhhhhhh...eeeehhhhhh...hhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3iip F   1 ALAKRIDAALIVKDGRVVEGSNFENLRDSGDPVELGKFYSEIGIDELSFWDITAKRKTMLELVEKVAEQIDIPFTVGGGIHDFETASELILRGADKVEINTAAVENPSLITQIAQTFGSQAVVVYIAAKRVDGEFMVFTYSGTKNTGILLRDWVVEVEKRGAGEIVLGSIDRLGTKSGYDTEMIRFVRPLTTLPIIAHRGAGKMEHFLEAFLAGADAAKADSVFHFREIDVRELKEYLKKHGVNVRL 250
                                    10        20        30        40        50   ||   63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       
                                                                                54|                                                                                                                                                                                                
                                                                                 58
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  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 3IIP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
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  3iip
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3iio 3iiv