SMTL ID : 4ove.1

X-ray Crystal Structure of Mouse Netrin-1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.64 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.1: 3 residues within 4Å: Chain A: L.71, N.73, D.76 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.6: 3 residues within 4Å: Chain B: L.71, N.73, D.76 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 3 residues within 4Å: Chain A: N.109, Y.140, A.228 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: N.109, Y.140, A.228 No protein-ligand interaction detected (PLIP)

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

NAG.3: 1 residues within 4Å: Chain A: N.94 No protein-ligand interaction detected (PLIP) NAG.8: 1 residues within 4Å: Chain B: N.94 No protein-ligand interaction detected (PLIP)

2 x CA: CALCIUM ION(Non-covalent)

CA.4: 5 residues within 4Å: Chain A: F.85, D.88, N.90, T.96, S.255 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:F.85, A:T.96, A:T.96, A:S.255, H2O.1 CA.9: 5 residues within 4Å: Chain B: F.85, D.88, N.90, T.96, S.255 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:F.85, B:T.96, B:T.96, B:S.255, H2O.4

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

CL.5: 4 residues within 4Å: Chain A: F.299, Y.301, R.327, C.328 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain B: F.299, Y.301, R.327, C.328 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Grandin, M. et al., Structural Decoding of the Netrin-1/UNC5 Interaction and its Therapeutical Implications in Cancers. Cancer Cell (2016)

Release Date

2015-02-25

Peptides

Netrin-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Netrin-1