SMTL ID : 4pln.1

Crystal Structure of Chicken Netrin-1 (LN-LE3) complexed with mouse Neogenin (FN4-5)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

hetero-2-2-mer

Ligands

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

NAG.1: 6 residues within 4Å: Chain A: P.51, L.70, N.72, S.74, D.75, R.78 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.70 Hydrogen bonds: A:N.72 NAG.2: 4 residues within 4Å: Chain A: P.76, N.93, L.94, T.95 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.76, A:N.93 NAG.3: 6 residues within 4Å: Chain A: P.106, H.107, N.108, Y.139, T.227, S.229 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.227 Hydrogen bonds: A:H.107, A:N.108 NAG.5: 5 residues within 4Å: Chain B: P.51, L.70, N.72, S.74, D.75 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.70 NAG.6: 4 residues within 4Å: Chain B: P.76, F.84, N.93, L.94 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.93 NAG.7: 6 residues within 4Å: Chain B: P.106, H.107, N.108, Y.139, T.227, S.229 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:T.227 Hydrogen bonds: B:H.107, B:N.108

2 x CA: CALCIUM ION(Non-covalent)

CA.4: 4 residues within 4Å: Chain A: F.84, D.87, T.95, S.254 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:F.84, A:D.87, A:T.95, A:T.95, A:S.254 CA.8: 4 residues within 4Å: Chain B: F.84, D.87, T.95, S.254 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:F.84, B:D.87, B:T.95, B:T.95, B:S.254

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, K. et al., Neural migration. Structures of netrin-1 bound to two receptors provide insight into its axon guidance mechanism. Science (2014)

Release Date

2014-06-18

Peptides

Netrin-1: AB
Neogenin: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Netrin-1

Neogenin

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