SMTL ID : 4fom.1

Crystal structure of human nectin-3 full ectodomain (D1-D3)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.93 Å

Oligo State

homo-dimer

Ligands

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.1: 2 residues within 4Å: Chain A: N.16, H.79 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.4: 6 residues within 4Å: Chain A: W.13, F.83, V.111, T.140, F.163, N.165 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.140 NAG-NAG-BMA-MAN-MAN.6: 2 residues within 4Å: Chain B: N.16, H.79 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.9: 6 residues within 4Å: Chain B: W.13, F.83, V.111, T.140, F.163, N.165 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.140

2 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.2: 3 residues within 4Å: Chain A: K.67, N.68, D.73 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 3 residues within 4Å: Chain B: K.67, N.68, D.73 No protein-ligand interaction detected (PLIP)

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.3: 3 residues within 4Å: Chain A: N.129, E.130, V.132 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.132 NAG-NAG-BMA-MAN-MAN-FUC.8: 3 residues within 4Å: Chain B: N.129, E.130, V.132 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.132

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

NAG.5: 2 residues within 4Å: Chain A: Q.253, N.274 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.253, A:N.274 NAG.10: 2 residues within 4Å: Chain B: Q.253, N.274 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.253, B:N.274

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Harrison, O.J. et al., Nectin ectodomain structures reveal a canonical adhesive interface. Nat.Struct.Mol.Biol. (2012)

Release Date

2012-08-22

Peptides

Poliovirus receptor-related protein 3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Poliovirus receptor-related protein 3