SMTL ID : 8edk.1

Structure of C. elegans UNC-6 LamN and EGF domains

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

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

NAG-NAG-BMA-MAN-FUC-FUC.1: 4 residues within 4Å: Chain A: H.79, F.80, S.93, N.96 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.80 Water bridges: A:H.79 Hydrophobic interactions: A:F.80

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 4 residues within 4Å: Chain A: K.336, R.337, N.358, R.360 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.358 Salt bridges: A:R.337, A:R.360 SO4.3: 4 residues within 4Å: Chain A: H.20, K.295, H.296, N.297 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.296, A:N.297, A:N.297, A:N.297 Salt bridges: A:H.20

1 x CA: CALCIUM ION(Non-covalent)

CA.4: 5 residues within 4Å: Chain A: L.87, D.90, N.92, T.98, G.265 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:L.87, A:T.98, A:T.98, A:G.265, H2O.1

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

NAG.5: 1 residues within 4Å: Chain A: N.110 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Priest, J.M. et al., Structural insights into the formation of repulsive netrin guidance complexes. Sci Adv (2024)

Release Date

2023-01-11

Peptides

Netrin unc-6: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Netrin unc-6