spacer
spacer

PDBsum entry 1vkh

Go to PDB code: 
protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
1vkh
Jmol
Contents
Protein chains
261 a.a. *
Ligands
GOL ×2
Metals
_CL
Waters ×458
* Residue conservation analysis
PDB id:
1vkh
Name: Hydrolase
Title: Crystal structure of a putative serine hydrolase (ydr428c) f saccharomyces cerevisiae at 1.85 a resolution
Structure: Putative serine hydrolase. Chain: a, b. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: ydr428c. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.85Å     R-factor:   0.145     R-free:   0.189
Authors: Joint Center For Structural Genomics (Jcsg)
Key ref:
J.W.Arndt et al. (2005). Crystal structure of an alpha/beta serine hydrolase (YDR428C) from Saccharomyces cerevisiae at 1.85 A resolution. Proteins, 58, 755-758. PubMed id: 15624212 DOI: 10.1002/prot.20336
Date:
20-May-04     Release date:   08-Jun-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q04066  (BNA7_YEAST) -  Kynurenine formamidase
Seq:
Struc:
261 a.a.
261 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cellular_component   1 term 
  Biological process     metabolic process   5 terms 
  Biochemical function     hydrolase activity     2 terms  

 

 
DOI no: 10.1002/prot.20336 Proteins 58:755-758 (2005)
PubMed id: 15624212  
 
 
Crystal structure of an alpha/beta serine hydrolase (YDR428C) from Saccharomyces cerevisiae at 1.85 A resolution.
J.W.Arndt, R.Schwarzenbacher, R.Page, P.Abdubek, E.Ambing, T.Biorac, J.M.Canaves, H.J.Chiu, X.Dai, A.M.Deacon, M.DiDonato, M.A.Elsliger, A.Godzik, C.Grittini, S.K.Grzechnik, J.Hale, E.Hampton, G.W.Han, J.Haugen, M.Hornsby, H.E.Klock, E.Koesema, A.Kreusch, P.Kuhn, L.Jaroszewski, S.A.Lesley, I.Levin, D.McMullan, T.M.McPhillips, M.D.Miller, A.Morse, K.Moy, E.Nigoghossian, J.Ouyang, W.S.Peti, K.Quijano, R.Reyes, E.Sims, G.Spraggon, R.C.Stevens, H.van den Bedem, J.Velasquez, J.Vincent, F.von Delft, X.Wang, B.West, A.White, G.Wolf, Q.Xu, O.Zagnitko, K.O.Hodgson, J.Wooley, I.A.Wilson.
 
  ABSTRACT  
 
No abstract given.

 
  Selected figure(s)  
 
Figure 1.
Figure 1. Crystal structure of YDR428C. A: Stereoview of ribbon diagram of Saccharomyces cerevisiae YDR428C color coded from N-terminus (blue) to C-terminus (red) showing the domain organization. -Helices H1-H12, and -strands ( 1- 7) are indicated. B: Diagram showing the secondary structure elements in YDR428C superimposed on its primary sequence. The -helices, 3[10]-helices, -sheet strands (red A), -bulges, and -turns are indicated. The disordered regions are depicted by a dashed line with the corresponding sequence in brackets.
Figure 2.
Figure 2. A: Ribbon diagram of a superposition of YDR428C (blue) and P. fluorescens carboxylesterase (grey). Residues of the catalytic triad, shown in ball and stick, indicate the active site location. B: Same as A, but a close up view of the catalytic triad. Active site residues as observed in P. fluorescens carboxylesterase (PDB 1auo; grey; P. fluorescens residues shown in parenthesis) and their counterparts in YDR428C (blue) are shown in ball and stick. Hydrogen bond interactions and distances are indicated. C: Ribbon diagram of the YDR428C dimer. 7 strands and helices H10 and H12 forming part of the dimer interface and locations of active sites (arrow) are indicated.
 
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2005, 58, 755-758) copyright 2005.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  16754966 C.Y.Yang, K.H.Chin, C.C.Chou, A.H.Wang, and S.H.Chou (2006).
Structure of XC6422 from Xanthomonas campestris at 1.6 A resolution: a small serine alpha/beta-hydrolase.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 498-503.
PDB code: 2fuk
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.