SMTL ID : 6fkq.1

THE CRYSTAL STRUCTURE OF A FRAGMENT OF NETRIN-1 IN COMPLEX WITH A FRAGMENT OF DRAXIN

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.07 Å

Oligo State

hetero-1-1-mer

Ligands

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.1: 5 residues within 4Å: Chain A: P.36, L.55, N.57, S.59, D.60 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: P.91, N.93 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-NAG.2: 3 residues within 4Å: Chain A: N.78 Ligands: SO4.11, SO4.12 No protein-ligand interaction detected (PLIP)

1 x CA: CALCIUM ION(Non-covalent)

CA.4: 5 residues within 4Å: Chain A: F.69, D.72, N.74, T.80, S.239 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:F.69, A:D.72, A:T.80, A:T.80, A:S.239

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

SO4.5: 3 residues within 4Å: Chain A: R.117, H.169, D.171 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.169 Salt bridges: A:R.117, A:H.169 SO4.6: 3 residues within 4Å: Chain A: R.173, F.219, G.220 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.220 Salt bridges: A:R.173 SO4.7: 2 residues within 4Å: Chain A: R.27, R.210 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.27, A:R.210 SO4.8: 3 residues within 4Å: Chain A: N.271, H.284, A.302 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.271 Salt bridges: A:H.284 SO4.9: 3 residues within 4Å: Chain A: G.393, I.394, R.398 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.394 SO4.10: 5 residues within 4Å: Chain A: T.392, R.398, C.399, A.400, K.401 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:C.399, A:K.401 Salt bridges: A:R.398 SO4.11: 2 residues within 4Å: Chain A: N.78 Ligands: NAG-NAG-NAG.2 No protein-ligand interaction detected (PLIP) SO4.12: 1 residues within 4Å: Ligands: NAG-NAG-NAG.2 No protein-ligand interaction detected (PLIP) SO4.13: 2 residues within 4Å: Chain A: K.24, D.25 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.25 Salt bridges: A:K.24 SO4.14: 4 residues within 4Å: Chain A: C.53, H.54, L.55, K.63 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.55, A:L.55 Salt bridges: A:H.54, A:K.63

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.15: 3 residues within 4Å: Chain A: R.269, H.270, N.271 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.270, A:N.271

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, Y. et al., Structural Basis for Draxin-Modulated Axon Guidance and Fasciculation by Netrin-1 through DCC. Neuron (2018)

Release Date

2018-03-21

Peptides

Netrin-1: A
Draxin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Netrin-1

Draxin