SMTL ID : 6fkk.1

Drosophila Semaphorin 1b, extracellular domains 1-2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.78 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.1: 10 residues within 4Å: Chain A: R.254, N.256, S.258, P.260, G.261, E.262, F.263, P.264, Y.266, A.367 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.261

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.2: 5 residues within 4Å: Chain A: F.37, L.39, N.48, I.57, Y.89 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.37

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

NAG.3: 1 residues within 4Å: Chain A: N.23 No protein-ligand interaction detected (PLIP) NAG.4: 8 residues within 4Å: Chain A: A.150, N.152, V.167, G.172, P.175, Q.194, P.195, D.196 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.150 Hydrogen bonds: A:G.172

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rozbesky, D. et al., Diversity of oligomerization in Drosophila semaphorins suggests a mechanism of functional fine-tuning. Nat Commun (2019)

Release Date

2019-02-06

Peptides

MIP07328p: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

MIP07328p

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