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T0604

© 2010 Grishin lab/HHMI/UTSW

updated on 2010-12-20

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643

T0604

3NLC from Vibrio parahaemolyticus

Target sequence:

>T0604 3NLC, Vibrio parahaemolyticus, 549 residues
MGHHHHHHSHMIRINEIKLPLDHEEGALLDAITKKLGIPAEKVISFNVFRRGYDARKKTNIHLIYTLDIIVEGDETALLAKFANDPHVRQTPDMEYKFVAKAPENLTERPIVIGFGPCGLFAGLVLAQMGFNPIIVERGKEVRERTKDTFGFWRKRTLNPESNVQFGEGGAGTFSDGKLYSQVKDPNFYGRKVITEFVEAGAPEEILYVSKPHIGTFKLVTMIEKMRATIIELGGEIRFSTRVDDLHMEDGQITGVTLSNGEEIKSRHVVLAVGHSARDTFEMLHERGVYMEAKPFSVGFRIEHKQSMIDEARFGPNAGHPILGAADYKLVHHCKNGRTVYSFCMCPGGTVVAATSEEGRVVTNGMSQYSRAERNANSAIVVGISPEVDYPGDPLAGIRFQRELESNAYKLGGENYDAPAQKIGDFLKGRDPSQLGDVEPSFTPGIKLTDLSKALPPFAVEAIREAIPAFDRKIKGFASEDGLLTGVETRTSSPVCIKRGKDFQSVNLKGFYPAGEGAGYAGGILSAGIDGIKVAEAVARDIVAAMENA

HHsearch_pdb70_15May10,  HHsearch_scop70_1.75,  HHsearch_pfamA.24.0,  HorAServer,  HorAServer (T0604d1),  HorAServer (T0604d2),  HorAServer (T0604d3),  Dali Result

Structure:

Method: X-ray, res= Å, R/Rfree=

Determined by: NESG

PDB ID: 3nlc

Domains:   PyMOL of domains

Three 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

five domain protein. 1-192,362-420 of template pdb 2i0z is FAD/NAD(P)-binding domain, and 193-361 is HI0933 insert domain-like, which could be furthur cut into two domains: greek key containing barrel and four helical bundel. The template covers the target seq from 103 to end. The N-terminal part contains mainly alpha helices with a flexible? linker to the C-terminal part

CASP category:

T0604 needs domain-based evaluation

1st domain: FM  alignment. 2nd domain: TBM  alignment. 3rd domain: FM  alignment.

Closest templates:

Template manually selected by shuoyong:

2i0z_A | PyMOL of 2i0z A, The alignment covers target seq from 103 to the end. As to the N-terminal, it has similariy with pdb 1o94302-385.

  

Template selected by HHpred server group:

• 1y0p_A | PyMOL | this pdbchain contains scop domain: d1y0pa1 A:1-102, d1y0pa2 A:111-361,A:512-568, d1y0pa3 A:362-504

• 3k30_A | PyMOL

• 2gmh_A | PyMOL | this pdbchain contains scop domain: d2gmha1 A:4-236,A:336-482, d2gmha2 A:237-335, d2gmha3 A:483-584

• 2bs2_A | PyMOL | this pdbchain contains scop domain: d2bs2a1 A:458-655, d2bs2a2 A:1-250,A:372-457, d2bs2a3 A:251-371

Target sequence - PDB file inconsistencies:

Sequence classification:

C-terminal matches (start around 109) HI0933-like protein (PF03486); N-terminal not finds good matches

All predictions:

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

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