2B5T

2.1 Angstrom structure of a nonproductive complex between antithrombin, synthetic heparin mimetic SR123781 and two S195A thrombin molecules


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of monomeric native antithrombin reveals a novel reactive center loop conformation.

Johnson, D.J.Langdown, J.Li, W.Luis, S.A.Baglin, T.P.Huntington, J.A.

(2006) J.Biol.Chem. 281: 35478-35486

  • DOI: 10.1074/jbc.M607204200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The poor inhibitory activity of circulating antithrombin (AT) is critical to the formation of blood clots at sites of vascular damage. AT becomes an efficient inhibitor of the coagulation proteases only after binding to a specific heparin pentasaccha ...

    The poor inhibitory activity of circulating antithrombin (AT) is critical to the formation of blood clots at sites of vascular damage. AT becomes an efficient inhibitor of the coagulation proteases only after binding to a specific heparin pentasaccharide, which alters the conformation of the reactive center loop (RCL). The molecular basis of this activation event lies at the heart of the regulation of hemostasis and accounts for the anticoagulant properties of the low molecular weight heparins. Although several structures of AT have been solved, the conformation of the RCL in native AT remains unknown because of the obligate crystal contact between the RCL of native AT and its latent counterpart. Here we report the crystallographic structure of a variant of AT in its monomeric native state. The RCL shifted approximately 20 A, and a salt bridge was observed between the P1 residue (Arg-393) and Glu-237. This contact explains the effect of mutations at the P1 position on the affinity of AT for heparin and also the properties of AT-Truro (E237K). The relevance of the observed conformation was verified through mutagenesis studies and by solving structures of the same variant in different crystal forms. We conclude that the poor inhibitory activity of the circulating form of AT is partially conferred by intramolecular contacts that restrain the RCL, orient the P1 residue away from attacking proteases, and additionally block the exosite utilized in protease recognition.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thrombin
A, C
49Homo sapiensMutation(s): 0 
Gene 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
B, D
259Homo sapiensMutation(s): 1 
Gene 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 sapiensMutation(s): 3 
Gene Names: SERPINC1 (AT3)
Find proteins for P01008 (Homo sapiens)
Go to Gene View: SERPINC1
Go to UniProtKB:  P01008
Small Molecules
Ligands 16 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GU6
Query on GU6

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Download CCD File 
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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Download CCD File 
I
2,3,6-TRI-O-SULFONATO-ALPHA-L-GALACTOPYRANOSE
C6 H9 O15 S3
GRHWGVDHRAZFMQ-VFUOTHLCSA-K
 Ligand Interaction
SO4
Query on SO4

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B, D, I
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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A, B, D, I
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 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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B, D, I
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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D, 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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B, I
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
GU9
Query on GU9

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Download CCD File 
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: 2.1 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.209 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 59.280α = 77.55
b = 59.530β = 78.94
c = 108.410γ = 68.08
Software Package:
Software NamePurpose
MOSFLMdata reduction
CNSrefinement
CCP4data scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-09-19
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance