SMTL ID : 3ol2.1

Receptor-ligand structure of Human Semaphorin 4D with Plexin B1.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.99 Å

Oligo State

hetero-2-2-mer

Ligands

6 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 6 residues within 4Å: Chain A: Y.27, N.28, Y.90, P.139, Q.453, N.471 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 2 residues within 4Å: Chain A: N.308, S.310 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 6 residues within 4Å: Chain B: D.311, D.314, R.315, N.318, R.321, P.360 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.360 NAG-NAG-BMA.8: 6 residues within 4Å: Chain C: Y.27, N.28, Y.90, P.139, Q.453, N.471 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 2 residues within 4Å: Chain C: N.308, S.310 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 6 residues within 4Å: Chain D: D.311, D.314, R.315, N.318, R.321, P.360 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:P.360

6 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: 4 residues within 4Å: Chain A: N.118, T.120, S.121, L.125 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 8 residues within 4Å: Chain A: N.298, V.299, G.300, D.396, V.397, N.398 Chain C: F.3, S.265 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 6 residues within 4Å: Chain A: Y.103, G.150, E.151, L.152, N.170, S.172 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain C: N.118, T.120, S.121, L.125 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 8 residues within 4Å: Chain A: F.3, S.265 Chain C: N.298, V.299, G.300, D.396, V.397, N.398 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 6 residues within 4Å: Chain C: Y.103, G.150, E.151, L.152, N.170, S.172 No protein-ligand interaction detected (PLIP)

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

NAG.7: 3 residues within 4Å: Chain A: N.56, S.58, E.59 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:E.59 NAG.14: 3 residues within 4Å: Chain C: N.56, S.58, E.59 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:E.59

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Janssen, B.J. et al., Structural basis of semaphorin-plexin signalling. Nature (2010)

Release Date

2010-10-13

Peptides

Semaphorin-4D: AC
Plexin-B1: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

Semaphorin-4D

Plexin-B1

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