SMTL ID : 4plo.1

Crystal Structure of chicken Netrin-1 (LN-LE3) in complex with mouse DCC (FN4-5)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

hetero-2-2-mer

Ligands

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

NAG.1: 4 residues within 4Å: Chain B: P.51, N.72, S.74, D.75 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:P.51 Hydrogen bonds: B:N.72, B:D.75 NAG.2: 4 residues within 4Å: Chain B: P.76, N.93, L.94, T.95 No protein-ligand interaction detected (PLIP) NAG.3: 3 residues within 4Å: Chain B: N.108, Y.139, T.227 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.139, B:T.227, B:T.227 Water bridges: B:N.108 NAG.10: 4 residues within 4Å: Chain D: P.51, N.72, S.74, D.75 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:P.51 Hydrogen bonds: D:N.72, D:D.75 NAG.11: 4 residues within 4Å: Chain D: P.76, N.93, L.94, T.95 No protein-ligand interaction detected (PLIP) NAG.12: 3 residues within 4Å: Chain D: N.108, Y.139, T.227 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Y.139, D:T.227, D:T.227 Water bridges: D:N.108

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

SO4.4: 4 residues within 4Å: Chain B: C.68, H.69, L.70, R.78 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.70 Salt bridges: B:H.69, B:R.78 SO4.5: 3 residues within 4Å: Chain B: R.132, H.184, D.186 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.184, B:D.186 Water bridges: B:H.184 Salt bridges: B:R.132, B:H.184 SO4.6: 5 residues within 4Å: Chain B: T.156, Q.157, C.158, R.159, S.166 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.156, B:C.158, B:R.159, B:S.166, B:S.166 SO4.7: 3 residues within 4Å: Chain B: R.325, R.326, N.347 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.347 Salt bridges: B:R.325, B:R.326 SO4.8: 4 residues within 4Å: Chain B: G.354, R.355, H.358, Y.359 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.355, B:Y.359 Salt bridges: B:R.355, B:H.358 SO4.13: 4 residues within 4Å: Chain D: C.68, H.69, L.70, R.78 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:L.70 Salt bridges: D:H.69, D:R.78 SO4.14: 3 residues within 4Å: Chain D: R.132, H.184, D.186 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:H.184, D:D.186 Water bridges: D:H.184 Salt bridges: D:R.132, D:H.184 SO4.15: 5 residues within 4Å: Chain D: T.156, Q.157, C.158, R.159, S.166 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:T.156, D:C.158, D:R.159, D:S.166, D:S.166 SO4.16: 3 residues within 4Å: Chain D: R.325, R.326, N.347 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.347 Salt bridges: D:R.325, D:R.326 SO4.17: 4 residues within 4Å: Chain D: G.354, R.355, H.358, Y.359 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.355, D:Y.359 Salt bridges: D:R.355, D:H.358

2 x CA: CALCIUM ION(Non-covalent)

CA.9: 4 residues within 4Å: Chain B: F.84, D.87, T.95, S.254 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:F.84, B:T.95, B:T.95, H2O.1, H2O.2 CA.18: 4 residues within 4Å: Chain D: F.84, D.87, T.95, S.254 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:F.84, D:T.95, D:T.95, H2O.4, H2O.5

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 receptor DCC: AC
Netrin-1: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

C
B

B
A

D
A

Netrin receptor DCC

Netrin-1

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