SMTL ID : 9d77.1

Crystal form of Netrin-1 mimics nanotubes

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.40 Å

Oligo State

homo-dimer

Ligands

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

NAG-NAG-BMA-MAN-MAN-FUC.1: 2 residues within 4Å: Chain A: P.110, N.112 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-FUC.9: 2 residues within 4Å: Chain B: P.110, N.112 No protein-ligand interaction detected (PLIP)

4 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.2: 7 residues within 4Å: Chain A: N.398, Q.399, T.400 Chain B: N.398, T.401 Ligands: NAG-NAG-BMA-MAN-MAN.10, MPD.16 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.401 NAG-NAG-BMA-MAN-MAN.3: 4 residues within 4Å: Chain A: P.55, N.76, S.78, D.79 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.10: 7 residues within 4Å: Chain A: N.398, T.401 Chain B: N.398, Q.399, T.400 Ligands: NAG-NAG-BMA-MAN-MAN.2, MPD.8 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.401 NAG-NAG-BMA-MAN-MAN.11: 4 residues within 4Å: Chain B: P.55, N.76, S.78, D.79 No protein-ligand interaction detected (PLIP)

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

NAG.4: 3 residues within 4Å: Chain A: H.96, N.97, L.98 No protein-ligand interaction detected (PLIP) NAG.12: 3 residues within 4Å: Chain B: H.96, N.97, L.98 No protein-ligand interaction detected (PLIP)

2 x CA: CALCIUM ION(Non-covalent)

CA.5: 5 residues within 4Å: Chain A: F.88, D.91, T.99, S.258, D.259 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:F.88, A:D.91, A:T.99, A:T.99, A:D.259 CA.13: 5 residues within 4Å: Chain B: F.88, D.91, T.99, S.258, D.259 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:F.88, B:D.91, B:T.99, B:T.99, B:D.259

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

CL.6: 2 residues within 4Å: Chain A: H.354, R.379 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain B: H.354, R.379 Ligand excluded by PLIP

4 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.7: 5 residues within 4Å: Chain A: N.334, M.335, E.336, K.339 Chain B: R.426 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.336, A:E.336 Hydrogen bonds: A:N.334 MPD.8: 6 residues within 4Å: Chain A: P.405, C.406, K.407, D.408 Chain B: Y.363 Ligands: NAG-NAG-BMA-MAN-MAN.10 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:P.405, B:Y.363 Hydrogen bonds: A:D.408 MPD.15: 5 residues within 4Å: Chain A: R.426 Chain B: N.334, M.335, E.336, K.339 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:E.336, B:E.336 Hydrogen bonds: B:N.334 MPD.16: 6 residues within 4Å: Chain A: Y.363 Chain B: P.405, C.406, K.407, D.408 Ligands: NAG-NAG-BMA-MAN-MAN.2 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.363, B:P.405 Hydrogen bonds: B:D.408

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rafiei, F. et al., Mechanistic insights in the higher-order protein assemblies of netrin-1. To Be Published

Release Date

2024-10-09

Peptides

Netrin-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Netrin-1

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