SMTL ID : 8b3k.1

Crystal structure of human Plexin-B1 (20-535) in the unbound state

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.68 Å

Oligo State

homo-dimer

Ligands

14 x CD: CADMIUM ION(Non-covalent)

CD.1: 3 residues within 4Å: Chain A: E.250, R.253, E.380 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.250, A:E.250, A:E.380, A:E.380, H2O.1 CD.2: 1 residues within 4Å: Chain A: H.446 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.446, H2O.3, H2O.3 CD.3: 1 residues within 4Å: Chain A: H.198 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.198, H2O.4, H2O.4 CD.4: 1 residues within 4Å: Chain A: H.397 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.397 CD.5: 1 residues within 4Å: Chain A: H.421 No protein-ligand interaction detected (PLIP) CD.6: 2 residues within 4Å: Chain A: H.466, H.475 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.466, A:H.475, H2O.4 CD.7: 2 residues within 4Å: Chain A: H.18, D.437 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.18, A:D.437, A:D.437 CD.9: 2 residues within 4Å: Chain B: H.198, P.290 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.198 CD.10: 1 residues within 4Å: Chain B: H.446 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.446, H2O.7, H2O.8 CD.11: 1 residues within 4Å: Chain B: H.397 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.397, H2O.8 CD.12: 3 residues within 4Å: Chain B: E.250, R.253, E.380 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.250, B:E.250, B:E.380, B:E.380 CD.13: 1 residues within 4Å: Chain B: H.362 No protein-ligand interaction detected (PLIP) CD.14: 1 residues within 4Å: Chain B: H.421 No protein-ligand interaction detected (PLIP) CD.15: 2 residues within 4Å: Chain B: H.466, H.475 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.466, B:H.475

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

NAG.8: 5 residues within 4Å: Chain A: D.311, R.312, N.315, R.318, P.357 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.318, A:R.318 Water bridges: A:D.311 NAG.16: 5 residues within 4Å: Chain B: D.308, R.312, N.315, R.318, P.357 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:R.312 Hydrogen bonds: B:R.318, B:R.318

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Plexin-B1