SMTL ID : 3laf.1

Structure of DCC, a netrin-1 receptor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

2 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: S.29, L.40, N.42 Ligands: NAG-NAG-BMA.2, NAG-NAG-BMA.2, SO4.14 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 9 residues within 4Å: Chain A: L.40, N.42, L.74, N.76, S.78, L.80 Ligands: NAG-NAG-BMA.1, NAG-NAG-BMA.1, SO4.12 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.40

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

NAG.3: 2 residues within 4Å: Chain A: K.267, N.281 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.281 NAG.4: 3 residues within 4Å: Chain A: V.293, T.295, N.300 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.293, A:T.295 Hydrogen bonds: A:N.300

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

SO4.5: 2 residues within 4Å: Chain A: E.235, W.314 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.235 SO4.6: 2 residues within 4Å: Chain A: Q.226, R.227 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.227, A:R.227 SO4.7: 3 residues within 4Å: Chain A: S.302, A.303, S.304 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.304 Water bridges: A:S.304 SO4.8: 3 residues within 4Å: Chain A: R.123, F.124, R.203 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.124 Salt bridges: A:R.203 SO4.9: 4 residues within 4Å: Chain A: H.89, H.90, K.91, P.92 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.91 Salt bridges: A:H.90 SO4.10: 2 residues within 4Å: Chain A: K.348, N.349 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.349 Water bridges: A:K.348, A:K.348 Salt bridges: A:K.348 SO4.11: 1 residues within 4Å: Chain A: R.112 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.112, A:R.112 Salt bridges: A:R.112 SO4.12: 2 residues within 4Å: Ligands: NAG-NAG-BMA.2, NAG-NAG-BMA.2 No protein-ligand interaction detected (PLIP) SO4.13: 2 residues within 4Å: Chain A: V.362, G.363 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.363, A:G.364 SO4.14: 2 residues within 4Å: Ligands: NAG-NAG-BMA.1, NAG-NAG-BMA.1 No protein-ligand interaction detected (PLIP) SO4.15: 3 residues within 4Å: Chain A: W.314, F.315, H.318 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.315 Salt bridges: A:H.318 SO4.16: 2 residues within 4Å: Chain A: G.288, T.289 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.289, A:T.289, A:T.289

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, Q. et al., N-terminal horseshoe conformation of DCC is functionally required for axon guidance and might be shared by other neural receptors. J.Cell.Sci. (2013)

Release Date

2011-03-02

Peptides

Deleted in Colorectal Cancer: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Deleted in Colorectal Cancer