SMTL ID : 7ne0.1

Structure of the ternary complex between Netrin-1, Repulsive-Guidance Molecule-B (RGMB) and Neogenin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.25 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

4 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: 2 residues within 4Å: Chain A: H.71, K.80 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.71, A:H.71, A:K.80, A:K.80 GU4-YYJ.2: 3 residues within 4Å: Chain A: R.312 Chain B: R.17, R.97 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Salt bridges: B:R.97, B:R.97, A:R.312, B:R.17, B:R.97 GU4-YYJ.3: 3 residues within 4Å: Chain A: R.161, K.162, P.167 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.161, A:K.162 GU4-YYJ.4: 4 residues within 4Å: Chain A: K.337, R.341 Chain D: Q.116, G.118 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain D Salt bridges: A:K.337, A:K.337, A:R.341, A:R.341 Hydrogen bonds: D:G.118, D:G.118

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

NAG.5: 4 residues within 4Å: Chain A: P.78, K.79, N.95, T.97 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.95 NAG.6: 3 residues within 4Å: Chain A: N.110, Y.141, A.229 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.141, A:A.229 NAG.7: 4 residues within 4Å: Chain A: P.53, N.74, S.76, D.77 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:D.77 NAG.10: 4 residues within 4Å: Chain B: Y.143, N.160, A.161, N.162 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.162

1 x CA: CALCIUM ION(Non-covalent)

CA.8: 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

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

SO4.9: 2 residues within 4Å: Chain A: R.134, H.186 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.186 Salt bridges: A:R.134, A:H.186

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
Repulsive Guidance Molecule B: C
Repulsive Guidance Molecule B C-terminal region (chain D): D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Netrin-1

Neogenin

Repulsive Guidance Molecule B

Repulsive Guidance Molecule B C-terminal region (chain D)

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