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SMTL ID : 3p70.4 (3 other biounits)

Structural basis of thrombin-mediated factor V activation: essential role of the hirudin-like sequence Glu666-Glu672 for processing at the heavy chain-B domain junction

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

hetero-1-1-1-mer

Ligands

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.1:

3 residues within 4Å:

Chain B: L.46, N.53, T.55

No protein-ligand interaction detected (PLIP)

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

NA.2:	2 residues within 4Å: Chain A: Y.32 Chain B: Y.134 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.134, B:Y.134
NA.4:	4 residues within 4Å: Chain B: Y.190, D.232, R.233, K.236 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.233 Water bridges: B:R.233, B:D.234

1 x BEN: BENZAMIDINE(Non-functional Binders)

BEN.3:

11 residues within 4Å:

Chain B: D.199, A.200, E.202, S.205, V.225, S.226, W.227, G.228, G.230, C.231, G.238

3 PLIP interactions:

3 interactions with chain B

Hydrophobic interactions: B:V.225
Hydrogen bonds: B:D.199, B:A.200

1 x BGC: beta-D-glucopyranose(Non-covalent)

BGC.5:

9 residues within 4Å:

Chain B: L.130, I.167, V.168, E.169, R.170, C.173, F.186, C.187, H.242

3 PLIP interactions:

3 interactions with chain B

Hydrogen bonds: B:R.170, B:R.170, B:C.187

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Corral-Rodriguez, M.A. et al., Structural basis of thrombin-mediated factor V activation: the Glu666-Glu672 sequence is critical for processing at the heavy chain-B domain junction. Blood (2011)

Release Date

2011-09-28

Peptides

HUMAN ALPHA-THROMBIN, LIGHT CHAIN: A
HUMAN ALPHA-THROMBIN, HEAVY CHAIN: B
HUMAN FACTOR V, A2-B DOMAIN LINKER: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
P

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

HUMAN ALPHA-THROMBIN, LIGHT CHAIN

HUMAN ALPHA-THROMBIN, HEAVY CHAIN

HUMAN FACTOR V, A2-B DOMAIN LINKER

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