SMTL ID : 4urt.1

The crystal structure of a fragment of netrin-1 in complex with FN5- FN6 of DCC

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

hetero-2-1-mer

Ligands

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

SO4.1: 2 residues within 4Å: Chain A: R.18, T.63 Ligand excluded by PLIP SO4.8: 3 residues within 4Å: Chain B: G.130, W.133, R.210 Ligand excluded by PLIP SO4.9: 3 residues within 4Å: Chain B: D.186, G.187 Ligands: SO4.22 Ligand excluded by PLIP SO4.10: 4 residues within 4Å: Chain B: R.117, H.169, D.171, P.174 Ligand excluded by PLIP SO4.11: 3 residues within 4Å: Chain B: R.269, H.270, N.271 Ligand excluded by PLIP SO4.12: 3 residues within 4Å: Chain B: R.311, N.332 Chain C: K.68 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain B: G.393, I.394, R.398 Ligand excluded by PLIP SO4.14: 6 residues within 4Å: Chain A: T.91, A.92, H.93 Chain B: C.399, Y.403, Q.404 Ligand excluded by PLIP SO4.15: 5 residues within 4Å: Chain B: R.311, R.313 Chain C: G.66, Y.73 Ligands: SO4.18 Ligand excluded by PLIP SO4.16: 4 residues within 4Å: Chain B: Y.124, W.133, R.210 Ligands: NAG-NAG.5 Ligand excluded by PLIP SO4.17: 4 residues within 4Å: Chain B: G.339, R.340, H.343, Y.344 Ligand excluded by PLIP SO4.18: 4 residues within 4Å: Chain B: R.311, L.331, N.332 Ligands: SO4.15 Ligand excluded by PLIP SO4.19: 4 residues within 4Å: Chain B: T.392, R.398, A.400, K.401 Ligand excluded by PLIP SO4.20: 4 residues within 4Å: Chain B: R.310, R.334, H.335, R.360 Ligand excluded by PLIP SO4.21: 5 residues within 4Å: Chain B: R.144, N.148, R.149, P.150 Ligands: SO4.23 Ligand excluded by PLIP SO4.22: 2 residues within 4Å: Chain B: R.152 Ligands: SO4.9 Ligand excluded by PLIP SO4.23: 1 residues within 4Å: Ligands: SO4.21 Ligand excluded by PLIP SO4.24: 3 residues within 4Å: Chain B: R.279 Chain C: R.18, T.63 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: A.9, A.11, A.94, T.95 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.9, A:A.11, A:T.95, A:T.95, A:T.95 GOL.25: 4 residues within 4Å: Chain C: A.9, A.11, A.94, T.95 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:A.9, C:A.11, C:T.95, C:T.95

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

NAG-NAG.3: 4 residues within 4Å: Chain B: P.36, N.57, S.59, D.60 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain B: K.62, N.78 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.62 NAG-NAG.5: 3 residues within 4Å: Chain B: N.93, Y.124 Ligands: SO4.16 No protein-ligand interaction detected (PLIP)

1 x CA: CALCIUM ION(Non-covalent)

CA.6: 5 residues within 4Å: Chain B: F.69, D.72, N.74, T.80, S.239 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:F.69, B:D.72, B:T.80, B:T.80, B:S.239

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

CL.7: 7 residues within 4Å: Chain B: R.279, C.280, K.281, P.282, Y.285 Chain C: T.13, D.15 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Finci, L.I. et al., The Crystal Structure of Netrin-1 in Complex with Dcc Reveals the Bi-Functionality of Netrin-1 as a Guidance Cue. Neuron (2014)

Release Date

2014-09-10

Peptides

NETRIN RECEPTOR DCC: AC
NETRIN-1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

C
B

B
A

NETRIN RECEPTOR DCC

NETRIN-1