SMTL ID : 8snp.1 (1 other biounit)

Crystal structure of mouse Netrin-1 in complex with samarium ions

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.40 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.1: 6 residues within 4Å: Chain A: N.131, T.133, M.184, Y.185, R.248, S.252 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.133 Hydrogen bonds: A:N.131 NAG-NAG-FUC.9: 6 residues within 4Å: Chain B: N.131, T.133, M.184, Y.185, R.248, S.252 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:T.133 Hydrogen bonds: B:N.131

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: 10 residues within 4Å: Chain A: C.416, N.417, Q.418 Chain B: N.417, Q.422, C.423, P.424, C.425 Ligands: NAG-NAG.10, NAG-NAG.10 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 10 residues within 4Å: Chain A: N.417, Q.422, C.423, P.424, C.425 Chain B: C.416, N.417, Q.418 Ligands: NAG-NAG.2, NAG-NAG.2 No protein-ligand interaction detected (PLIP)

8 x SM: SAMARIUM (III) ION(Non-covalent)

SM.3: 3 residues within 4Å: Chain A: D.43, E.44, H.47 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.43 SM.4: 2 residues within 4Å: Chain A: E.262, D.263 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.262, A:E.262 SM.5: 1 residues within 4Å: Chain A: D.54 No protein-ligand interaction detected (PLIP) SM.6: 6 residues within 4Å: Chain A: F.107, D.110, L.111, N.112, T.118, S.277 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:F.107, A:D.110, A:T.118, A:S.277 SM.11: 3 residues within 4Å: Chain B: D.43, E.44, H.47 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.43 SM.12: 2 residues within 4Å: Chain B: E.262, D.263 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.262, B:E.262 SM.13: 1 residues within 4Å: Chain B: D.54 No protein-ligand interaction detected (PLIP) SM.14: 6 residues within 4Å: Chain B: F.107, D.110, L.111, N.112, T.118, S.277 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:F.107, B:D.110, B:T.118, B:S.277

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

NAG.7: 6 residues within 4Å: Chain A: P.74, N.95, S.97, D.98, P.99 Ligands: NAG.8 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.74 Hydrogen bonds: A:N.95, A:D.98 NAG.8: 1 residues within 4Å: Ligands: NAG.7 No protein-ligand interaction detected (PLIP) NAG.15: 6 residues within 4Å: Chain B: P.74, N.95, S.97, D.98, P.99 Ligands: NAG.16 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:P.74 Hydrogen bonds: B:N.95, B:D.98 NAG.16: 1 residues within 4Å: Ligands: NAG.15 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Legare, S. et al., Investigating the structural and functional roles of calcium binding in Netrin-1. To Be Published

Release Date

2024-02-07

Peptides

Netrin-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Netrin-1

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