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SMTL ID : 3p70.1 (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: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1:

2 residues within 4Å:

Chain B: L.46, N.53

No protein-ligand interaction detected (PLIP)

1 x BEN: BENZAMIDINE(Non-functional Binders)

BEN.2:

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:G.230

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

NA.3:	4 residues within 4Å: Chain B: Y.190, D.232, R.233, K.236 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.232
NA.4:	7 residues within 4Å: Chain B: A.30, S.31, L.39, G.206, G.207, P.208, Q.221 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.31, B:Q.221

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

BGC.5:

2 residues within 4Å:

Chain B: K.145, E.146

1 PLIP interactions:

1 interactions with chain B

Hydrogen bonds: B:E.146

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
A

B
B

C
M

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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