SMTL ID : 3vyk.1

Crystal structure of C-type lectin domain of murine dendritic cell inhibitory receptor 2 in complex with N-glycan

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

1 x MMA- MAN- NAG- MAN- NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)][2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]methyl alpha-D-mannopyranoside

MMA-MAN-NAG-MAN-NAG-NAG.1: 13 residues within 4Å: Chain A: E.92, N.94, W.97, E.98, N.104, N.113, D.114, I.115, P.116, D.119, H.121 Ligands: CA.2, EDO.5 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.95, A:Q.95, A:Q.95 Hydrogen bonds: A:E.98, A:D.119

1 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: E.92, N.94, E.98, N.113, D.114 Ligands: MMA-MAN-NAG-MAN-NAG-NAG.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.92, A:E.98, A:D.114, A:D.114

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

SO4.3: 2 residues within 4Å: Chain A: R.99, K.118 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.99, A:K.118 SO4.4: 2 residues within 4Å: Chain A: G.109, W.110 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.110, A:W.110 Water bridges: A:T.52

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

EDO.5: 4 residues within 4Å: Ligands: MMA-MAN-NAG-MAN-NAG-NAG.1, MMA-MAN-NAG-MAN-NAG-NAG.1, MMA-MAN-NAG-MAN-NAG-NAG.1, MMA-MAN-NAG-MAN-NAG-NAG.1 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nagae, M. et al., Recognition of Bisecting N-Acetylglucosamine: STRUCTURAL BASIS FOR ASYMMETRIC INTERACTION WITH THE MOUSE LECTIN DENDRITIC CELL INHIBITORY RECEPTOR 2. J.Biol.Chem. (2013)

Release Date

2013-10-02

Peptides

C-type lectin domain family 4, member a4: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C-type lectin domain family 4, member a4

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