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SMTL ID : 4ch2.1 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

hetero-1-1-1-mer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1:	7 residues within 4Å: Chain A: S.4, G.5, E.6, A.7, C.9 Chain B: R.218, Y.220 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.4, A:A.7, B:Y.220, B:Y.220 Water bridges: A:G.5
GOL.3:	11 residues within 4Å: Chain B: E.8, I.9, G.10, M.11, S.12, P.13, G.64, K.65, H.66, Y.114, L.160 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.10, B:S.12, B:S.12, B:H.66

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

0G6.2:

17 residues within 4Å:

Chain B: H.43, Y.47, E.94, L.96, I.179, D.199, A.200, C.201, G.203, D.204, S.205, S.226, W.227, G.228, G.230, C.231, G.238

14 PLIP interactions:

14 interactions with chain B

Hydrophobic interactions: B:L.96, 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:W.227, 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

5 PLIP interactions:

5 interactions with chain B

Hydrogen bonds: B:K.236, B:K.236
Water bridges: B:R.197, B:G.235, B:G.238

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
A

B
B

C
P

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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