SMTL ID : 7y4q.1

Semaphorin 6D in complex with Plexin A1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 4.70 Å

Oligo State

hetero-2-2-mer

Ligands

5 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 6 residues within 4Å: Chain B: V.551, T.605, R.606, N.636, S.638, V.639 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.606 NAG-NAG.2: 7 residues within 4Å: Chain C: R.3, N.265, S.267, F.273, Y.275, A.384, D.390 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain C: Y.415, N.417, Y.418, F.440, Q.537, E.540 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.418 NAG-NAG.4: 6 residues within 4Å: Chain D: N.265, S.267, F.273, Y.275, A.384, D.390 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:F.273 NAG-NAG.5: 4 residues within 4Å: Chain D: Y.415, N.417, F.440, Q.537 No protein-ligand interaction detected (PLIP)

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

NAG.6: 3 residues within 4Å: Chain A: R.18, N.53, T.55 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.53, A:T.55 NAG.7: 6 residues within 4Å: Chain A: Q.545, P.546, R.547, N.548, S.650, F.651 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.651 Hydrogen bonds: A:Q.545, A:R.547, A:N.548 NAG.8: 3 residues within 4Å: Chain B: R.18, N.53, T.55 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.18, B:T.55 NAG.9: 4 residues within 4Å: Chain B: Q.545, N.548, S.650, F.651 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.651 Hydrogen bonds: B:Q.545, B:N.548

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tanaka, T. et al., Hybrid in vitro/in silico analysis of low-affinity protein-protein interactions that regulate signal transduction by Sema6D. Protein Sci. (2022)

Release Date

2022-10-19

Peptides

Plexin-A1: AB
Semaphorin 6D: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

C
D

D
C

Plexin-A1

Semaphorin 6D

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