3U13 - JenaLib

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

Ligands, Modified Residues, Ions (5, 8)

Asymmetric Unit (5, 8)

No.	Name	Count	Type	Full Name
1	MG	1	Ligand/Ion	MAGNESIUM ION
2	MSE	3	Mod. Amino Acid	SELENOMETHIONINE
3	NA	1	Ligand/Ion	SODIUM ION
4	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
5	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (3, 12)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	MSE	6	Mod. Amino Acid	SELENOMETHIONINE
3	NA	-1	Ligand/Ion	SODIUM ION
4	PEG	2	Ligand/Ion	DI(HYDROXYETHYL)ETHER
5	PO4	4	Ligand/Ion	PHOSPHATE ION

Sites (5, 5)

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:11 , ASP A:13 , TYR A:45 , ASP A:146 , PO4 A:209 , HOH A:271 , HOH A:377	BINDING SITE FOR RESIDUE MG A 1003
2	AC2	SOFTWARE	ASP 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:1003	BINDING SITE FOR RESIDUE PO4 A 209
3	AC3	SOFTWARE	GLU A:67 , MSE A:105 , TYR A:108 , HIS A:182 , SER A:183 , ASP A:186 , PEG A:211 , NA A:212	BINDING SITE FOR RESIDUE PO4 A 210
4	AC4	SOFTWARE	LYS 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:321	BINDING SITE FOR RESIDUE PEG A 211
5	AC5	SOFTWARE	MSE A:105 , LYS A:107 , TYR A:108 , CYS A:109 , PO4 A:210	BINDING SITE FOR RESIDUE NA A 212

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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

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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)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (0, 0)

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