SMTL ID : 7ne1.1

Structure of the complex between Netrin-1 and its receptor Neogenin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.15 Å

Oligo State

hetero-1-1-mer

Ligands

1 x GU4- YYJ: 1,3,4,6-tetra-O-sulfo-beta-D-fructofuranose-(2-1)-2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose(Non-covalent)

GU4-YYJ.1: 7 residues within 4Å: Chain A: R.55, R.68, S.69, C.70, H.71, L.72, K.80 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.72, A:C.70, A:C.70, A:H.71 Salt bridges: A:H.71, A:K.80, A:K.80

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

NAG.2: 5 residues within 4Å: Chain A: P.78, F.86, N.95, L.96, T.97 No protein-ligand interaction detected (PLIP) NAG.3: 2 residues within 4Å: Chain A: H.109, N.110 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.110 NAG.4: 4 residues within 4Å: Chain A: L.72, N.74, S.76, D.77 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.72 Hydrogen bonds: A:N.74 NAG.9: 2 residues within 4Å: Chain B: Y.143, N.162 No protein-ligand interaction detected (PLIP)

1 x CA: CALCIUM ION(Non-covalent)

CA.5: 4 residues within 4Å: Chain A: F.86, D.89, T.97, S.256 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:F.86, A:D.89, A:T.97, A:T.97, A:S.256

3 x NO3: NITRATE ION(Non-functional Binders)

NO3.6: 5 residues within 4Å: Chain A: V.35, F.121, C.264, C.273, L.281 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.273 NO3.7: 3 residues within 4Å: Chain A: R.296, C.297, W.306 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.297 NO3.8: 3 residues within 4Å: Chain A: R.134, S.185, H.186 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.134, A:R.134, A:D.188

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Robinson, R.A. et al., Simultaneous binding of Guidance Cues NET1 and RGM blocks extracellular NEO1 signaling. Cell (2021)

Release Date

2021-03-31

Peptides

Netrin-1: A
Neogenin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Netrin-1

Neogenin

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