SMTL ID : 4r9w.1

Crystal structure of platelet factor 4 complexed with fondaparinux

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

2 x ZDO- IDS- SUS- BDP- SGN: 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2-deoxy-3,6-di-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-methyl 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranoside(Non-covalent)

ZDO-IDS-SUS-BDP-SGN.1: 12 residues within 4Å: Chain A: K.31, P.34, H.35 Chain B: R.22, H.23, K.46 Chain C: Q.18, V.19, R.20, H.23, L.45, R.49 8 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B, 1 interactions with chain C Salt bridges: A:H.35, B:R.22, B:K.46, C:R.20, A:K.31, A:K.31, C:R.49, B:K.46 Hydrogen bonds: A:K.31, C:Q.18, C:R.20, A:K.31, A:K.31, B:R.22, B:H.23 ZDO-IDS-SUS-BDP-SGN.2: 12 residues within 4Å: Chain A: Q.18, V.19, R.20, H.23, L.45, R.49 Chain C: K.31, P.34, H.35 Chain D: R.22, H.23, K.46 7 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D, 1 interactions with chain A Salt bridges: C:H.35, D:R.22, D:K.46, A:R.20, A:R.49, C:K.31, C:K.31, D:K.46 Hydrogen bonds: C:K.31, A:Q.18, A:R.20, C:K.31, C:K.31, D:R.22

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cai, Z. et al., Atomic description of the immune complex involved in heparin-induced thrombocytopenia. Nat Commun (2015)

Release Date

2015-12-16

Peptides

Platelet factor 4: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Platelet factor 4

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