SMTL ID : 8bb7.2 (1 other biounit)

Crystal structure of Mouse Plexin-B1 (20-535) in complex with VHH15

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.95 Å

Oligo State

hetero-1-1-mer

Ligands

5 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)(Post Translational Modification)

NAG.1: 7 residues within 4Å: Chain A: A.7, A.8, F.9, L.39, L.43, Q.44, L.45 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.7, A:L.45, A:L.45 Water bridges: A:T.10 NAG.2: 5 residues within 4Å: Chain A: A.11, N.12, F.35, F.37 Chain B: R.105 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.35 Water bridges: A:T.10, A:N.12 Hydrogen bonds: B:R.105, B:R.105 NAG.3: 7 residues within 4Å: Chain A: N.55, P.66, C.69, P.70, A.72 Chain B: E.44, Y.109 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.109, A:P.66 NAG.4: 6 residues within 4Å: Chain A: D.308, D.311, Q.312, N.315, R.318, P.357 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:D.311, A:Q.312 Hydrogen bonds: A:N.315, A:R.318, A:R.318 NAG.5: 3 residues within 4Å: Chain A: Y.316, A.328, N.330 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.316

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cowan, R. et al., Nanobody inhibitors of Plexin-B1 identify allostery in plexin-semaphorin interactions and signaling. J.Biol.Chem. (2023)

Release Date

2023-05-03

Peptides

Plexin-B1: A
VHH15 Nanobody: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Plexin-B1

VHH15 Nanobody

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