1TB6

2.5A Crystal Structure of the Antithrombin-Thrombin-Heparin Ternary Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the antithrombin-thrombin-heparin ternary complex reveals the antithrombotic mechanism of heparin.

Li, W.Johnson, D.J.Esmon, C.T.Huntington, J.A.

(2004) Nat.Struct.Mol.Biol. 11: 857-862

  • DOI: 10.1038/nsmb811

  • PubMed Abstract: 
  • The maintenance of normal blood flow depends completely on the inhibition of thrombin by antithrombin, a member of the serpin family. Antithrombin circulates at a high concentration, but only becomes capable of efficient thrombin inhibition on intera ...

    The maintenance of normal blood flow depends completely on the inhibition of thrombin by antithrombin, a member of the serpin family. Antithrombin circulates at a high concentration, but only becomes capable of efficient thrombin inhibition on interaction with heparin or related glycosaminoglycans. The anticoagulant properties of therapeutic heparin are mediated by its interaction with antithrombin, although the structural basis for this interaction is unclear. Here we present the crystal structure at a resolution of 2.5 A of the ternary complex between antithrombin, thrombin and a heparin mimetic (SR123781). The structure reveals a template mechanism with antithrombin and thrombin bound to the same heparin chain. A notably close contact interface, comprised of extensive active site and exosite interactions, explains, in molecular detail, the basis of the antithrombotic properties of therapeutic heparin.


    Organizational Affiliation

    University of Cambridge, Department of Haematology, Division of Structural Medicine, Thrombosis Research Unit, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 2XY, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
thrombin
L
49Homo sapiensGene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Go to Gene View: F2
Go to UniProtKB:  P00734
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
thrombin
H
259Homo sapiensGene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Go to Gene View: F2
Go to UniProtKB:  P00734
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Antithrombin-III
I
432Homo sapiensGene Names: SERPINC1 (AT3)
Find proteins for P01008 (Homo sapiens)
Go to Gene View: SERPINC1
Go to UniProtKB:  P01008
Small Molecules
Ligands 15 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GU6
Query on GU6

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I
2,3,6-TRI-O-SULFONATO-ALPHA-D-GLUCOPYRANOSE
C6 H12 O15 S3
GRHWGVDHRAZFMQ-DVKNGEFBSA-N
 Ligand Interaction
GU0
Query on GU0

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I
2,3,6-TRI-O-SULFONATO-ALPHA-L-GALACTOPYRANOSE
C6 H9 O15 S3
GRHWGVDHRAZFMQ-VFUOTHLCSA-K
 Ligand Interaction
MAN
Query on MAN

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I
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
FUC
Query on FUC

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H
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
GU5
Query on GU5

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I
2,3-DI-O-METHYL-6-O-SULFONATO-ALPHA-D-GLUCOPYRANOSE
C8 H15 O9 S
SYRNRUURZIIPLL-IINKRSELSA-M
 Ligand Interaction
BMA
Query on BMA

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I
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
GU3
Query on GU3

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I
methyl 3-O-methyl-2,6-di-O-sulfo-alpha-D-glucopyranoside
C8 H16 O12 S2
GFHCIIGKYHICQU-CBQIKETKSA-N
 Ligand Interaction
GU8
Query on GU8

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I
2,3,6-TRI-O-METHYL-BETA-D-GLUCOPYRANOSE
C9 H18 O6
LXJBARMBDDODTG-SRBFPGQKSA-N
 Ligand Interaction
GU1
Query on GU1

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I
2,3-DI-O-METHYL-BETA-D-GLUCOPYRANURONIC ACID
C8 H14 O7
YEGNNGDFCAGXPA-GRJZWZNASA-N
 Ligand Interaction
GU4
Query on GU4

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I
2,3,4,6-TETRA-O-SULFONATO-ALPHA-D-GLUCOPYRANOSE
C6 H8 O18 S4
SPIXVQOXHJQNTH-DVKNGEFBSA-J
 Ligand Interaction
NDG
Query on NDG

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H, I
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
 Ligand Interaction
NAG
Query on NAG

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H, I
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
MPD
Query on MPD

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H, I
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
GU9
Query on GU9

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I
2,3,6-TRI-O-METHYL-ALPHA-D-GLUCOPYRANOSE
C9 H18 O6
LXJBARMBDDODTG-MSMGWUHYSA-N
 Ligand Interaction
GU2
Query on GU2

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Download CCD File 
I
2,3-DI-O-METHYL-ALPHA-L-IDOPYRANURONIC ACID
C8 H14 O7
YEGNNGDFCAGXPA-OHZVEFKRSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 88.409α = 90.00
b = 88.404β = 90.00
c = 117.218γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-08-17
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance