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T0521

© 2010 Grishin lab/HHMI/UTSW

updated on 2010-12-20

Targets
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643

T0521

pf110239_CAD from Plasmodium Falciparum

Target sequence:

>T0521 pf110239_CAD, Plasmodium Falciparum, 179 residues
ISPNVLNNMKSYMKHSNIRNIIINIMAHELSVINNHIKYINELFYKLDTNHNGSLSHREIYTVLASVGIKKWDINRILQALDINDRGNITYTEFMAGCYRWKNIESTFLKAAFNKIDKDEDGYISKSDIVSLVHDKVLDNNDIDNFFLSVHSIKKGIPREHIINKISFQEFKDYMLSTF

HHsearch_pdb70_15May10,  HHsearch_scop70_1.75,  HHsearch_pfamA.24.0, HorAServer, HorAServer (T0521d1s), HorAServer (T0521d2), Dali Result

Structure:

Method: X-ray, res= Å, R/Rfree=

Determined by: SGC

PDB ID: 3mse

Domains:   PyMOL of domains

Two domains.

To compute the weighted sum, GDT-TS for each domain was multiplied by the domain length, and this sum was divided by the sum of domain lengths. Each point represents first server model. Green, gray and black points are top 10, bottom 25% and the rest of prediction models. Blue line is the best-fit slope line (intersection 0) to the top 10 server models. Red line is the diagonal. Slope and root mean square y-x distance for the top 10 models (average difference between the weighted sum of domain GDT-TS scores and the whole chain GDT-TS score) are shown above the plot.

Structure classification:

The description below was written months before target structure release, thus it only presents shuoyong's personal thoughts simply based on sequence. Please be aware that it may contain laughable errors. It is certainly not our final assessment on this target. We will revise this section (and the sequence classification too) in a short time

This is a homologue of T0519 Duplication. EF-hand fold, and onsists of two EF-hand units: each is made of two helices connected with calcium-binding loop.

CASP category:

T0521 needs domain-based evaluation

1st domain: TBM  alignment. 2nd domain: TBM  alignment.

Closest templates:

Template manually selected by shuoyong:

3k21_A | PyMOL of 3k21 A

  

Template selected by HHpred server group:

• 3k21_A | PyMOL

• 3khe_A | PyMOL

• 2ggm_A | PyMOL | this pdbchain contains scop domain: d2ggma1 A:24-166

• 3lij_A | PyMOL

• 2aao_A | PyMOL

• 2mys_C | PyMOL | this pdbchain contains scop domain: d2mysc_ C:

• 1exr_A | PyMOL | this pdbchain contains scop domain: d1exra_ A:

• 2ehb_A | PyMOL

• 3fwb_A | PyMOL

Target sequence - PDB file inconsistencies:

Sequence classification:

This is a calcium-dependent protein kinase (Calmodulin-like domain). The top two Pfam hits belong to SPARC_Ca_bdg (PF10591), which is Secreted protein acidic and rich in cysteine Ca binding region, and this family is a member of clan EF_hand (CL0220. The third Pfam hit is EF hand (PF00036). Note in pfam: Many calcium-binding proteins belong to the same evolutionary family and share a type of calcium-binding domain known as the EF-hand. This type of domain consists of a twelve residue loop flanked on both side by a twelve residue alpha-helical domain. In an EF-hand loop the calcium ion is coordinated in a pentagonal bipyramidal configuration.

All predictions:

TS (GDT_TS score), TR (GDT_TS with penalty [reference]

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