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SMTL ID : 1xmn.2 (4 other biounits)

Crystal structure of thrombin bound to heparin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

hetero-1-1-mer

Ligands

1 x IDS- SGN- IDS- SGN- IDS- SGN: 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid(Covalent)

IDS-SGN-IDS-SGN-IDS-SGN.1:

10 residues within 4Å:

Chain B: H.87, R.89, R.98, R.123, R.170, F.244, R.245, K.248, W.249
Ligands: GOL.6

3 PLIP interactions:

3 interactions with chain B

Hydrogen bonds: B:R.245, B:R.245
Salt bridges: B:R.123, B:R.170
Water bridges: B:R.170, B:R.170

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2:

3 residues within 4Å:

Chain B: L.46, P.48, N.53

No protein-ligand interaction detected (PLIP)

1 x 0G6: D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide(Covalent)

0G6.3:

19 residues within 4Å:

Chain B: H.43, Y.47, W.50, E.94, N.95, L.96, I.179, D.199, A.200, C.201, E.202, G.203, D.204, S.205, S.226, W.227, G.228, G.230, G.238

20 PLIP interactions:

20 interactions with chain B

Hydrophobic interactions: B:Y.47, B:W.50, B:L.96, B:I.179, B:W.227
Hydrogen bonds: B:A.200, B:G.203, B:S.205, B:S.226, B:G.228, B:G.228, B:G.230
Water bridges: B:E.202, B:E.202, B:W.227, B:E.229, B:G.230, B:D.232, B:Y.240
Salt bridges: B:D.199

1 x NA: SODIUM ION(Non-functional Binders)

NA.4:

2 residues within 4Å:

Chain B: R.233, K.236

4 PLIP interactions:

4 interactions with chain B

Hydrogen bonds: B:Y.190, B:K.236
Water bridges: B:R.197, B:R.233

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5:	5 residues within 4Å: Chain A: E.16, S.19, E.21 Chain B: K.212, N.217 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:S.19, B:K.212, B:K.212, B:N.217 Water bridges: B:N.217
GOL.6:	6 residues within 4Å: Chain B: L.130, I.167, V.168, R.170, F.186 Ligands: IDS-SGN-IDS-SGN-IDS-SGN.1 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.130, B:R.170, B:R.170

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Carter, W.J. et al., Crystal structure of thrombin bound to heparin. J.Biol.Chem. (2005)

Release Date

2004-11-23

Peptides

Thrombin light chain: A
Thrombin heavy chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Thrombin light chain

Thrombin heavy chain

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