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(-) Description

Title :  CRYSTAL STRUCTURE OF DE NOVO DESIGN OF CYSTEIN ESTERASE ECH13 AT THE RESOLUTION 1.6A, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET OR51
 
Authors :  A. Kuzin, M. Su, J. Seetharaman, S. Sahdev, R. Xiao, E. Kohan, F. Richter J. K. Everett, T. B. Acton, D. Baker, G. T. Montelione, J. F. Hunt, L. Ton Northeast Structural Genomics Consortium (Nesg)
Date :  29 Sep 11  (Deposition) - 23 Nov 11  (Release) - 11 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Structural Genomics, Psi-Biology, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Ech13, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Richter, R. Blomberg, S. D. Khare, G. Kiss, A. P. Kuzin, A. J. Smith, J. Gallaher, Z. Pianowski, R. C. Helgeson, A. Grjasnow, R. Xiao, J. Seetharaman, M. Su, S. Vorobiev, S. Lew, F. Forouhar, G. J. Kornhaber, J. F. Hunt, G. T. Montelione, L. Tong, K. N. Houk, D. Hilvert, D. Baker
Computational Design Of Catalytic Dyads And Oxyanion Holes For Ester Hydrolysis.
J. Am. Chem. Soc. V. 134 16197 2012
PubMed-ID: 22871159  |  Reference-DOI: 10.1021/JA3037367

(-) Compounds

Molecule 1 - ARTIFICIAL PROTEIN OR51
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cell Line: BL21(DE3)
    Expression System Plasmid: PET29B+
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synonym: 5',3'-NUCLEOTIDASE, MITOCHONDRIAL, DEOXY-5'-NUCLEOTIDASE 2, DNT-2

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 8)

Asymmetric Unit (5, 8)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2MSE3Mod. Amino AcidSELENOMETHIONINE
3NA1Ligand/IonSODIUM ION
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
5PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (3, 12)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2MSE6Mod. Amino AcidSELENOMETHIONINE
3NA-1Ligand/IonSODIUM ION
4PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
5PO44Ligand/IonPHOSPHATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:11 , ASP A:13 , TYR A:45 , ASP A:146 , PO4 A:209 , HOH A:271 , HOH A:377BINDING SITE FOR RESIDUE MG A 1003
2AC2SOFTWAREASP A:11 , MSE A:12 , ASP A:13 , TYR A:45 , THR A:100 , SER A:101 , HIS A:103 , LYS A:113 , LYS A:135 , HOH A:388 , MG A:1003BINDING SITE FOR RESIDUE PO4 A 209
3AC3SOFTWAREGLU A:67 , MSE A:105 , TYR A:108 , HIS A:182 , SER A:183 , ASP A:186 , PEG A:211 , NA A:212BINDING SITE FOR RESIDUE PO4 A 210
4AC4SOFTWARELYS A:104 , MSE A:105 , PHE A:106 , GLU A:118 , PRO A:123 , LEU A:126 , HIS A:182 , PO4 A:210 , HOH A:321BINDING SITE FOR RESIDUE PEG A 211
5AC5SOFTWAREMSE A:105 , LYS A:107 , TYR A:108 , CYS A:109 , PO4 A:210BINDING SITE FOR RESIDUE NA A 212

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3U13)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:3 -Arg A:4
2Pro A:176 -Pro A:177

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3U13)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3U13)

(-) Exons   (0, 0)

(no "Exon" information available for 3U13)

(-) 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:195
                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.......hhhhhhhhhhhhhh......hhhhh...hhhhhhhhhh.hhhhhhhhhhh............hhhhhhhhhhhh..eeeeeee.......hhhhhhhhhhhhhhhhhhhh.eee..........eeee..............eeeee..............eee.....hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3u13 A   3 GRALRVLVDmDGVLADVEGGLLRKFRARFPDQPFIALEDRRGYKACEQYGRLRPGLSEKARSIAESKNFFFELEPLPGAVEAVKEmASLQNTDVFICTSPHKmFKYCPYEKYAWVEKYFGPDFLEQIVLTRDKTVVSADLLIDDRPDITGAEPTPSWEHVLFTACHNQHLQLQPPRRRLHSWADDWKAILDSKRP 197
                                    12        22        32        42        52        62        72        82     |  92       102  |    112       122       132       142       152       162       172       182       192     
                                    12-MSE                                                                      88-MSE          105-MSE
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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 3U13)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3U13)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3U13)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3U13)

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 Related Entries

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(-) Related Entries Specified in the PDB File

1q92 95% HOMOLOGY
or51