SMTL ID : 7lrf.1

Netrin-1 in complex with SOS

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.21 Å

Oligo State

homo-dimer

Ligands

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

NAG-NAG-BMA.1: 4 residues within 4Å: Chain A: S.48, N.112, T.114, T.231 No protein-ligand interaction detected (PLIP)

7 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: 2 residues within 4Å: Chain A: N.76, D.79 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain A: N.398, T.401 Chain B: N.398 Ligands: NAG-NAG.8, NAG-NAG.8, PEG.14 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain A: N.97 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain B: P.55, N.76, S.78 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 1 residues within 4Å: Chain B: N.97 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: P.110, H.111, N.112 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain A: N.398, Q.403 Chain B: N.398, T.401 Ligands: NAG-NAG.3 No protein-ligand interaction detected (PLIP)

2 x GU4- YYJ: 1,3,4,6-tetra-O-sulfo-beta-D-fructofuranose-(2-1)-2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose(Non-covalent)

GU4-YYJ.9: 7 residues within 4Å: Chain A: R.332, F.333, N.334 Chain B: R.426, S.427, P.428, I.429 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.426, B:R.426, A:N.334, A:R.332 Salt bridges: B:R.426, A:R.332, A:R.332, A:R.332 GU4-YYJ.10: 3 residues within 4Å: Chain B: R.329, R.353, R.379 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.379, B:R.329 Water bridges: B:R.330 Salt bridges: B:R.329, B:R.329, B:R.353, B:R.353, B:R.379, B:R.329

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.11: 6 residues within 4Å: Chain A: R.298, C.299, Y.304, R.306, P.307, W.308 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.306, A:W.308 EDO.12: 7 residues within 4Å: Chain A: H.388, N.416, R.417, C.418, Q.424, P.431, C.432 No protein-ligand interaction detected (PLIP) EDO.13: 4 residues within 4Å: Chain A: P.34, C.266, R.274, C.275 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.35 EDO.17: 7 residues within 4Å: Chain B: C.299, H.303, Y.304, R.306, P.307, W.308, F.333 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:C.299, B:W.308

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.14: 10 residues within 4Å: Chain A: Y.363, N.398, Q.399, T.400 Chain B: A.393, P.405, C.406, K.407, D.408 Ligands: NAG-NAG.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.400 PEG.19: 8 residues within 4Å: Chain B: P.34, D.35, V.37, F.123, C.266, R.274, C.275, L.283 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:C.275

2 x CA: CALCIUM ION(Non-covalent)

CA.15: 6 residues within 4Å: Chain A: F.88, D.91, N.93, T.99, S.258, D.259 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:F.88, A:D.91, A:T.99, A:S.258 CA.20: 5 residues within 4Å: Chain B: F.88, D.91, N.93, T.99, S.258 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:F.88, B:D.91, B:T.99, B:T.99, B:S.258

1 x NA: SODIUM ION(Non-functional Binders)

NA.16: 4 residues within 4Å: Chain A: D.240, S.246, E.247, D.251 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.247

1 x NHE: 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID(Non-covalent)

NHE.18: 8 residues within 4Å: Chain B: H.388, G.391, N.416, R.417, C.418, Q.424, P.431, C.432 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.431

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

CL.21: 2 residues within 4Å: Chain B: N.178, Q.180 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Meier, M. et al., The dynamic nature of netrin-1 and the structural basis for glycosaminoglycan fragment-induced filament formation. Nat Commun (2023)

Release Date

2022-02-23

Peptides

Netrin-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Netrin-1

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