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PDBsum entry 2i17

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protein ligands links
Oxidoreductase PDB id
2i17
Jmol
Contents
Protein chain
313 a.a. *
Ligands
NDP
LDT
CIT ×2
Waters ×661
* Residue conservation analysis
PDB id:
2i17
Name: Oxidoreductase
Title: Human aldose reductase in complex with NADP+ and the inhibitor idd594 at temperature of 60k
Structure: Aldose reductase. Chain: a. Synonym: ar, aldehyde reductase. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
0.81Å     R-factor:   0.081     R-free:   0.091
Authors: T.Petrova,S.Ginell,A.Mitshler,I.Hasemann,T.Schneider, A.Cousido,V.Y.Lunin,A.Joachimiak,A.Podjarny
Key ref:
T.Petrova et al. (2006). Ultrahigh-resolution study of protein atomic displacement parameters at cryotemperatures obtained with a helium cryostat. Acta Crystallogr D Biol Crystallogr, 62, 1535-1544. PubMed id: 17139089 DOI: 10.1107/S0907444906041035
Date:
13-Aug-06     Release date:   29-Aug-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P15121  (ALDR_HUMAN) -  Aldose reductase
Seq:
Struc:
316 a.a.
313 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.1.1.1.21  - Aldehyde reductase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Alditol + NAD(P)(+) = aldose + NAD(P)H
Alditol
+
NAD(P)(+)
Bound ligand (Het Group name = NDP)
corresponds exactly
= aldose
+ NAD(P)H
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular space   4 terms 
  Biological process     small molecule metabolic process   8 terms 
  Biochemical function     electron carrier activity     5 terms  

 

 
    reference    
 
 
DOI no: 10.1107/S0907444906041035 Acta Crystallogr D Biol Crystallogr 62:1535-1544 (2006)
PubMed id: 17139089  
 
 
Ultrahigh-resolution study of protein atomic displacement parameters at cryotemperatures obtained with a helium cryostat.
T.Petrova, S.Ginell, A.Mitschler, I.Hazemann, T.Schneider, A.Cousido, V.Y.Lunin, A.Joachimiak, A.Podjarny.
 
  ABSTRACT  
 
Two X-ray data sets for a complex of human aldose reductase (h-AR) with the inhibitor IDD 594 and the cofactor NADP(+) were collected from two different parts of the same crystal to a resolution of 0.81 A at 15 and 60 K using cold helium gas as cryogen. The contribution of temperature to the atomic B values was estimated by comparison of the independently refined models. It was found that although being slightly different for different kinds of atoms, the differences (deltaB) in the isotropic equivalents B of atomic displacement parameters (ADPs) were approximately constant (about 1.7 A(2)) for well ordered atoms as the temperature was increased from 15 to 60 K. The mean value of this difference varied according to the number of non-H atoms covalently bound to the parent atom. Atoms having a B value of higher than 8 A(2) at 15 K showed much larger deviations of deltaB from the average value, which might reflect partial occupancy of atomic sites. An analysis of the anisotropy of ADPs for individual atoms revealed an increase in the isotropy of ADPs with the increase of the temperature from 15 to 60 K. In a separate experiment, a 0.93 A resolution data set was collected from a different crystal of the same complex at 100 K using cold nitrogen as a cryogen. The effects of various errors on the atomic B values were estimated by comparison of the refined models and the temperature-dependent component was inferred. It was found that both decreasing the data redundancy and increasing the resolution cutoff led to an approximately constant increase in atomic B values for well ordered atoms.
 
  Selected figure(s)  
 
Figure 1.
Figure 1 The distribution of the atoms according to their B values. Only atoms of residues in a single conformation are shown.
Figure 2.
Figure 2 F[obs] - F[calc] H-omit maps in the vicinity of His110 at 2.5 . Protein models obtained at (a) 15 K, (b) 60 K and (c) 100 K. An electron-density peak corresponding to the H atom near CE1 is observed in the 15 and 60 K maps but is not present in the 100 K map.
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2006, 62, 1535-1544) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20944241 T.Petrova, S.Ginell, A.Mitschler, Y.Kim, V.Y.Lunin, G.Joachimiak, A.Cousido-Siah, I.Hazemann, A.Podjarny, K.Lazarski, and A.Joachimiak (2010).
X-ray-induced deterioration of disulfide bridges at atomic resolution.
  Acta Crystallogr D Biol Crystallogr, 66, 1075-1091.
PDB codes: 3mnb 3mnc 3mns 3mnx 3mo3 3mo6 3mo9 3moc 3mty 3mu0 3mu1 3mu4 3mu5 3mu8 3odd 3odf
19275144 C.Mulakala, and Y.N.Kaznessis (2009).
Path-integral method for predicting relative binding affinities of protein-ligand complexes.
  J Am Chem Soc, 131, 4521-4528.  
19271215 M.Schmidt, K.Achterhold, V.Prusakov, and F.G.Parak (2009).
Protein dynamics of a beta-sheet protein.
  Eur Biophys J, 38, 687-700.  
18007035 P.V.Afonine, R.W.Grosse-Kunstleve, P.D.Adams, V.Y.Lunin, and A.Urzhumtsev (2007).
On macromolecular refinement at subatomic resolution with interatomic scatterers.
  Acta Crystallogr D Biol Crystallogr, 63, 1194-1197.  
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 codes are shown on the right.