SMTL ID : 4fmk.1

Crystal structure of mouse nectin-2 extracellular fragment D1-D2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.56 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: 9 residues within 4Å: Chain A: T.30, E.31, P.106, N.107 Chain B: T.44, P.58, N.59, S.60, Q.61 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.60, B:S.60, B:S.60 NAG-NAG-BMA-MAN-MAN-FUC.7: 9 residues within 4Å: Chain A: T.44, P.58, N.59, S.60, Q.61 Chain B: T.30, E.31, P.106, N.107 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.60, A:S.60, A:S.60

2 x NAG- NAG- BMA- MAN- FUC: alpha-D-mannopyranose-(1-3)-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-FUC.2: 4 residues within 4Å: Chain A: E.95, G.96, N.97, W.115 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-FUC.8: 4 residues within 4Å: Chain B: E.95, G.96, N.97, W.115 No protein-ligand interaction detected (PLIP)

8 x CD: CADMIUM ION(Non-covalent)

CD.3: 3 residues within 4Å: Chain A: H.125, E.127, R.142 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.125, A:E.127, A:E.127 CD.4: 2 residues within 4Å: Chain A: D.192, H.221 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.192, A:D.192, A:H.221, H2O.1, H2O.1 CD.5: 2 residues within 4Å: Chain A: H.24, D.82 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.82 CD.6: 1 residues within 4Å: Chain A: H.220 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.220, H2O.2 CD.9: 3 residues within 4Å: Chain B: H.125, E.127, R.142 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.125, B:E.127, B:E.127 CD.10: 2 residues within 4Å: Chain B: D.192, H.221 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.192, B:D.192, B:H.221, H2O.3, H2O.3 CD.11: 2 residues within 4Å: Chain B: H.24, D.82 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.82 CD.12: 1 residues within 4Å: Chain B: H.220 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.220, H2O.3

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 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Poliovirus receptor-related protein 2

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