Sandbox Reserved 350

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'''The Three Loops'''
'''The Three Loops'''
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<br />
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(1)-Ser21-Trp31
+
(1)-Ser21-Trp31; Apex containing Indole moieties able to form hydrogen bonds (Two consecutive Trp's 26 & 27).
<br />
<br />
-
(2)-Asn39-Asn45
+
(2)-Asn39-Asn45; Apex capped with a basic residue able to form hydrogen bonds (Arg 43.
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-
(3)-Gly75-Tyr84
+
(3)-Gly75-Tyr84; Apex Hydrophobic (Leu 79).
All are described by ''Authors of the paper'' to protrude like spikes from the bottom of the barrel in monomeric FVa-C2. It is also worth noting that spike (1) & spike (3) are separated by β-hairpin structures and spike (2) is described as a wider irregularly loop comparatively. These three loops extending from the C2 domain, are all linked to each other, and to '''three shorter loops''' by an intricate '''H-bonding network''' which extends to residues at the bottom of the β-barrel.
All are described by ''Authors of the paper'' to protrude like spikes from the bottom of the barrel in monomeric FVa-C2. It is also worth noting that spike (1) & spike (3) are separated by β-hairpin structures and spike (2) is described as a wider irregularly loop comparatively. These three loops extending from the C2 domain, are all linked to each other, and to '''three shorter loops''' by an intricate '''H-bonding network''' which extends to residues at the bottom of the β-barrel.
The overall Barrel structure is closed at the top and bottom by '''three''' and '''two''' straight segments, giving it an '''overall spherical shape''' with a flattened upper surface.
The overall Barrel structure is closed at the top and bottom by '''three''' and '''two''' straight segments, giving it an '''overall spherical shape''' with a flattened upper surface.

Revision as of 15:10, 16 March 2011

This Sandbox is Reserved from January 10, 2010, through April 10, 2011 for use in BCMB 307-Proteins course taught by Andrea Gorrell at the University of Northern British Columbia, Prince George, BC, Canada.
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Introduction

Protein: cHuman Coagulation factor V, 1czv [1]

PDB ID 1czv

Drag the structure with the mouse to rotate
1czv, resolution 2.40Å ()
Related: 1czs, 1czt
Resources: FirstGlance, OCA, RCSB, PDBsum
Coordinates: save as pdb, mmCIF, xml



Contents

Structure

The structure of Human Coagulation Factor V (FV) is sculpted from, originates from, precursors from a polypeptide to a A1-A2-B-A3-C1-C2 layout which results in the activated (FVa) protein.
-Heavy A1-A2 Chain
-Light A3-C1-C2 Chain
FVa consists of a conserved β-Barrel framework acting as a scaffold for three loops and a C2 domain (FVa-C2).
The FVa-C2, which is classified as a distorted jelly-roll β-barrel motif, is compossed of eight major antiparallel strands arranged into two β-sheets of five and three strands packed against one another.
Salt bridges located within the "upper" segment (Asp61-Arg134)--Fig2.-- and the "lower" segment considered basic, due to the XXX basic residues present in number and alkalinity?. Both together..
The Three Loops
(1)-Ser21-Trp31; Apex containing Indole moieties able to form hydrogen bonds (Two consecutive Trp's 26 & 27).
(2)-Asn39-Asn45; Apex capped with a basic residue able to form hydrogen bonds (Arg 43.
(3)-Gly75-Tyr84; Apex Hydrophobic (Leu 79). All are described by Authors of the paper to protrude like spikes from the bottom of the barrel in monomeric FVa-C2. It is also worth noting that spike (1) & spike (3) are separated by β-hairpin structures and spike (2) is described as a wider irregularly loop comparatively. These three loops extending from the C2 domain, are all linked to each other, and to three shorter loops by an intricate H-bonding network which extends to residues at the bottom of the β-barrel. The overall Barrel structure is closed at the top and bottom by three and two straight segments, giving it an overall spherical shape with a flattened upper surface.


Which once activated, enhances the ability of factor Xa to generate α-thrombin from prothrombin (5-Fold).




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References

  1. ↑ 10586886
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