SMTL ID : 3pmh.1

Mechanism of Sulfotyrosine-Mediated Glycoprotein Ib Interaction with Two Distinct alpha-Thrombin Sites

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- NAG- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG-MAN-MAN-MAN.1: 2 residues within 4Å: Chain B: N.53, T.55 No protein-ligand interaction detected (PLIP)

1 x 0G7: D-phenylalanyl-N-[(3S)-6-carbamimidamido-1-chloro-2-oxohexan-3-yl]-L-prolinamide(Non-covalent)

0G7.2: 20 residues within 4Å: Chain B: H.43, Y.47, 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, E.229, G.230, C.231, G.238 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:Y.47, B:L.96, B:L.96, B:I.179, B:W.227 Hydrogen bonds: B:A.200, B:S.205, B:S.226, B:G.228, B:G.228, B:G.230 Salt bridges: B:D.199

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

NAG.3: 3 residues within 4Å: Chain C: E.135, K.137, N.159 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.135, C:K.137

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zarpellon, A. et al., Binding of alpha-thrombin to surface-anchored platelet glycoprotein Ib(alpha) sulfotyrosines through a two-site mechanism involving exosite I. Proc.Natl.Acad.Sci.USA (2011)

Release Date

2011-06-01

Peptides

THROMBIN ALPHA-CHAIN: A
THROMBIN BETA-CHAIN: B
Platelet glycoprotein Ib alpha chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
G

THROMBIN ALPHA-CHAIN

THROMBIN BETA-CHAIN

Platelet glycoprotein Ib alpha chain

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