PDBsum entry 1azx

Serine protease inhibitor

PDB id: 1azx

Contents

Protein chain

417 a.a. *

Ligands

Z9L-Z9K-GU6-GU1-Z9H ×2

NAG ×3

* Residue conservation analysis

PDB id:

1azx

Name:

Serine protease inhibitor

Title:

Antithrombin/pentasaccharide complex

Structure:

Antithrombin. Chain: i, l

Source:

Homo sapiens. Human. Organism_taxid: 9606. Organ: plasma. Tissue: plasma. Other_details: pentasaccharide was chemically synthesized

Resolution:

2.90Å R-factor: 0.203 R-free: 0.280

Authors:

L.Jin,J.P.Abrahams,R.Skinner,M.Petitou,R.N.Pike,R.W.Carrell

Key ref:

L.Jin et al. (1997). The anticoagulant activation of antithrombin by heparin. Proc Natl Acad Sci U S A, 94, 14683-14688. PubMed id: 9405673 DOI: 10.1073/pnas.94.26.14683

Date:

23-Nov-97 Release date: 13-Jan-99

Protein chains

P01008  (ANT3_HUMAN) -  Antithrombin-III from Homo sapiens

Seq: 464 a.a.

Struc: 417 a.a.

DOI no: 10.1073/pnas.94.26.14683

Proc Natl Acad Sci U S A 94:14683-14688 (1997)

PubMed id: 9405673

The anticoagulant activation of antithrombin by heparin.

L.Jin, J.P.Abrahams, R.Skinner, M.Petitou, R.N.Pike, R.W.Carrell.

ABSTRACT

Antithrombin, a plasma serpin, is relatively inactive as an inhibitor of the coagulation proteases until it binds to the heparan side chains that line the microvasculature. The binding specifically occurs to a core pentasaccharide present both in the heparans and in their therapeutic derivative heparin. The accompanying conformational change of antithrombin is revealed in a 2.9-A structure of a dimer of latent and active antithrombins, each in complex with the high-affinity pentasaccharide. Inhibitory activation results from a shift in the main sheet of the molecule from a partially six-stranded to a five-stranded form, with extrusion of the reactive center loop to give a more exposed orientation. There is a tilting and elongation of helix D with the formation of a 2-turn helix P between the C and D helices. Concomitant conformational changes at the heparin binding site explain both the initial tight binding of antithrombin to the heparans and the subsequent release of the antithrombin-protease complex into the circulation. The pentasaccharide binds by hydrogen bonding of its sulfates and carboxylates to Arg-129 and Lys-125 in the D-helix, to Arg-46 and Arg-47 in the A-helix, to Lys-114 and Glu-113 in the P-helix, and to Lys-11 and Arg-13 in a cleft formed by the amino terminus. This clear definition of the binding site will provide a structural basis for developing heparin analogues that are more specific toward their intended target antithrombin and therefore less likely to exhibit side effects.

Selected figure(s)

Figure 1.
Fig. 1. Schematic: i, circulating antithrombin; ii, contacts endothelial heparans with induction of high-affinity binding and reactive^ site loop exposure; iii-iv, complexes with factor Xa followed^ by loop cleavage and insertion with diminished heparin affinity; and v, the complex is released into the circulation for catabolism by the liver.

Figure 3.
Fig. 3. Ribbon diagrams of (from left) I-antithrombin (15), pentasaccharide-complexed I-antithrombin, and [1]-antitrypsin (32). The pentasaccharide activation of I-antithrombin is seen to involve^ a closing of the A-sheet (magenta), an extension (blue) of helix D (yellow), and an expulsion of residues P[14] (green sphere) and^ P[15] (black sphere) of the reactive site loop (red). The reactive^ loop of both antithrombin molecules is constrained by the dimer contact (see Fig. 2a) of the -pleated P[3]-P[8] (ribboned arrow). An indication of the likely free conformation, with exposure of^ the P[1] reactive center (shown as a ball-stick model), is provided^ by the optimal inhibitory conformation of the reactive loop present in [1]-antitrypsin (32).

Figures were selected by an automated process.