SMTL ID : 4plm.2 (1 other biounit)

Crystal Structure of Chicken Netrin-1 (LN-LE3)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: P.51, N.72, S.74, D.75 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.51 NAG.2: 1 residues within 4Å: Chain A: N.93 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.93 NAG.3: 2 residues within 4Å: Chain A: N.108, S.229 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.229 NAG.8: 4 residues within 4Å: Chain B: P.51, N.72, S.74, D.75 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.51 NAG.9: 1 residues within 4Å: Chain B: N.93 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.93 NAG.10: 2 residues within 4Å: Chain B: N.108, S.229 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.229

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: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:F.84, A:D.87, A:T.95, A:T.95, H2O.3 CA.11: 4 residues within 4Å: Chain B: F.84, D.87, T.95, S.254 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:F.84, B:D.87, B:T.95, B:T.95, H2O.6

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 2 residues within 4Å: Chain A: R.132, H.184 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: H.80, C.96 Ligands: MG.7 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain B: R.132, H.184 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain B: H.80, C.96 Ligands: MG.14 Ligand excluded by PLIP

2 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 2 residues within 4Å: Chain A: Q.98 Ligands: CL.6 No protein-ligand interaction detected (PLIP) MG.14: 2 residues within 4Å: Chain B: Q.98 Ligands: CL.13 No protein-ligand interaction detected (PLIP)

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Netrin-1

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