SMTL ID : 6r0x.1

The extracellular domain of G6b-B in complex with Fab fragment and DP12 heparin oligosaccharide.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.13 Å

Oligo State

hetero-2-2-2-mer

Ligands

2 x A2G- GAL- SIA: beta-D-galactopyranose-(1-3)-[N-acetyl-alpha-neuraminic acid-(2-6)]2-acetamido-2-deoxy-alpha-D-galactopyranose

A2G-GAL-SIA.1: 2 residues within 4Å: Chain E: A.54, T.56 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:T.56 A2G-GAL-SIA.3: 5 residues within 4Å: Chain F: A.50, P.55, T.56, R.66, I.74 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:R.66

1 x SGN- IDS- SGN- IDS- SGN- IDS- SGN- IDS: 2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose

SGN-IDS-SGN-IDS-SGN-IDS-SGN-IDS.2: 19 residues within 4Å: Chain E: V.28, P.34, G.42, R.43, K.92, G.93, R.94, H.95, E.96 Chain F: V.28, A.30, A.35, K.41, G.42, R.43, P.45, W.48, K.92, R.94 3 PLIP interactions: 1 interactions with chain F, 2 interactions with chain E Hydrophobic interactions: F:A.35 Hydrogen bonds: F:S.32, E:H.95, F:K.41 Salt bridges: E:H.95

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vogtle, T. et al., Heparan sulfates are critical regulators of the inhibitory megakaryocyte-platelet receptor G6b-B. Elife (2019)

Release Date

2019-09-04

Peptides

antibody fab fragment heavy chain: AC
antibody fab fragment light chain: BD
Megakaryocyte and platelet inhibitory receptor G6b: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

E
E

F
F

antibody fab fragment heavy chain

antibody fab fragment light chain

Megakaryocyte and platelet inhibitory receptor G6b