SMTL ID : 6hhd.1

Mouse Prion Protein in complex with Nanobody 484

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.3: 1 residues within 4Å: Chain B: Q.116 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain D: D.112, H.113, W.114 Ligands: SO4.8 Ligand excluded by PLIP

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 4 residues within 4Å: Chain B: Q.39, G.44, R.45, R.108 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Q.39, B:R.45 Water bridges: B:R.45, B:R.45, B:R.108 Salt bridges: B:R.45, B:R.108 SO4.5: 3 residues within 4Å: Chain C: M.20, H.22, R.33 3 PLIP interactions: 3 interactions with chain C Water bridges: C:H.22 Salt bridges: C:H.22, C:R.33 SO4.7: 4 residues within 4Å: Chain D: Q.1, V.2, R.98, H.113 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:V.2 Water bridges: D:R.98, D:R.98 Salt bridges: D:R.98, D:H.113 SO4.8: 2 residues within 4Å: Chain D: D.112 Ligands: CL.9 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain C: S.104, Q.105, A.106, Y.107 No protein-ligand interaction detected (PLIP)

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

NA.6: 3 residues within 4Å: Chain C: R.46, Q.50 Chain D: G.109 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.46, C:Q.50, C:Q.50

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abskharon, R. et al., Structural evidence for the critical role of the prion protein hydrophobic region in forming an infectious prion. Plos Pathog. (2019)

Release Date

2019-12-11

Peptides

Major prion protein: A
Nanobody 484: B
Major prion protein: C
Nanobody 484: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Major prion protein

Nanobody 484

Major prion protein

Nanobody 484

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