SMTL ID : 7vf3.2 (1 other biounit)

Plexin B1 extracellular fragment in complex with lasso-grafted PB1m7 peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.29 Å

Oligo State

hetero-1-1-mer

Ligands

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

NAG.1: 5 residues within 4Å: Chain A: D.309, D.312, R.313, N.316, R.319 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:D.312 Hydrogen bonds: A:N.316, A:R.319, A:R.319

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.2: 5 residues within 4Å: Chain A: R.325, R.328, A.329, E.330, G.332 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.328

4 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.3: 8 residues within 4Å: Chain A: D.23, P.24, T.25, V.85, S.86, P.87, G.88, L.106 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.88, A:G.88 PG4.4: 7 residues within 4Å: Chain A: A.264, T.265, V.392, T.393, M.394, T.399, F.445 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.265, A:T.393, A:T.399 PG4.5: 6 residues within 4Å: Chain A: N.343, S.344, D.345, D.362, H.363, T.364 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.343, A:N.343, A:S.344, A:D.345 Water bridges: A:S.366 PG4.6: 4 residues within 4Å: Chain A: F.38, T.49, V.50, S.51 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.49, A:S.51

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sugano-Nakamura, N. et al., De novo Fc-based receptor dimerizers differentially modulate PlexinB1 function. Structure (2022)

Release Date

2022-08-17

Peptides

Plexin-B1: A
Uteroglobin,PB1m7 peptide,Uteroglobin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Plexin-B1

Uteroglobin,PB1m7 peptide,Uteroglobin

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