SMTL ID : 6sny.1 (1 other biounit)

Synthetic mimic of an EPCR-binding PfEMP1 bound to EPCR

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.11 Å

Oligo State

hetero-1-1-mer

Ligands

2 x NAG- NAG- MAN: alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN.1: 3 residues within 4Å: Chain B: L.14, N.30, R.96 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.96 NAG-NAG-MAN.3: 3 residues within 4Å: Chain B: A.90, P.92, N.119 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.92

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 3 residues within 4Å: Chain B: E.42, P.44, N.47 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.42, B:E.42

1 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.4: 32 residues within 4Å: Chain A: F.80 Chain B: L.11, M.13, L.14, Q.15, N.30, A.31, H.39, I.50, T.65, L.69, Y.72, Q.75, F.76, V.80, L.89, I.95, L.99, V.116, F.123, W.133, T.147, L.151, R.156, T.157, E.160, L.161, E.163, F.164, T.168, C.169, Y.172 37 PLIP interactions: 36 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.11, B:M.13, B:Q.15, B:A.31, B:H.39, B:I.50, B:T.65, B:L.69, B:L.69, B:Y.72, B:Y.72, B:Y.72, B:Q.75, B:F.76, B:F.76, B:V.80, B:L.89, B:I.95, B:L.99, B:L.99, B:V.116, B:V.116, B:F.123, B:F.123, B:W.133, B:L.151, B:F.164, B:F.164, B:T.168, B:Y.172, B:Y.172, A:F.80 Hydrogen bonds: B:E.163, B:E.163 Salt bridges: B:R.156, B:R.156, B:R.156

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Barber, N.M. et al., Structure-Guided Design of a Synthetic Mimic of an Endothelial Protein C Receptor-Binding PfEMP1 Protein. Msphere (2021)

Release Date

2019-09-04

Peptides

Synthetic EPCR binding protein: A
Endothelial protein C receptor: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Synthetic EPCR binding protein

Endothelial protein C receptor

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