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SMTL ID : 4ch8.3 (3 other biounits)

High-salt crystal structure of a thrombin-GpIbalpha peptide complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NA.1:

2 residues within 4Å:

Chain B: R.233, K.236

3 PLIP interactions:

3 interactions with chain B

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

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

0G6.2:

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, V.225, S.226, W.227, G.228, G.230, C.231, G.238

18 PLIP interactions:

18 interactions with chain B

Hydrophobic interactions: B:Y.47, B:L.96, B:L.96, B:I.179, B:V.225, B:W.227
Hydrogen bonds: B:A.200, B:G.203, B:D.204, B:S.205, B:S.226, B:G.228, B:G.228, B:G.230
Water bridges: B:W.227, B:D.232, B:Y.240
Salt bridges: B:D.199

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3:

7 residues within 4Å:

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

4 PLIP interactions:

4 interactions with chain B

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

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Lechtenberg, B.C. et al., Gpibalpha Interacts Exclusively with Exosite II of Thrombin. J.Mol.Biol. (2014)

Release Date

2013-12-11

Peptides

THROMBIN, LIGHT CHAIN: A
THROMBIN, HEAVY CHAIN: B
PLATELET GLYCOPROTEIN IB ALPHA CHAIN, RESIDUES 287-300: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
R

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

PLATELET GLYCOPROTEIN IB ALPHA CHAIN, RESIDUES 287-300

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