SMTL ID : 6lfj.1

Crystal structure of mouse DCAR2 CRD domain complex with IPM2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

homo-dimer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: E.95, S.97, E.101, N.117, D.118 Ligands: MAN.5 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.95, A:S.97, A:E.101, A:D.118, A:D.118 CA.6: 6 residues within 4Å: Chain B: E.95, S.97, E.101, N.117, D.118 Ligands: MAN.8 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.95, B:S.97, B:E.101, B:D.118, B:D.118

1 x B3P: 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

B3P.2: 6 residues within 4Å: Chain A: W.28, N.29, E.32, W.69, K.102, C.121 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.69 Hydrogen bonds: A:N.29, A:N.29, A:E.32, A:E.32 Water bridges: A:N.29, A:H.41, A:D.70, A:C.121

3 x MAN: alpha-D-mannopyranose(Non-covalent)

MAN.3: 3 residues within 4Å: Chain A: E.101, S.120 Ligands: IPD.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.101 MAN.5: 8 residues within 4Å: Chain A: E.95, S.97, E.101, N.117, D.118, I.119 Ligands: CA.1, IPD.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.101, A:N.117, A:N.117 MAN.8: 8 residues within 4Å: Chain B: E.95, S.97, E.101, N.117, D.118, I.119 Ligands: CA.6, IPD.7 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.97, B:N.117, B:N.117

2 x IPD: D-MYO-INOSITOL-1-PHOSPHATE(Non-functional Binders)

IPD.4: 2 residues within 4Å: Ligands: MAN.3, MAN.5 No protein-ligand interaction detected (PLIP) IPD.7: 1 residues within 4Å: Ligands: MAN.8 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Omahdi, Z. et al., Structural insight into the recognition of pathogen-derived phosphoglycolipids by C-type lectin receptor DCAR. J.Biol.Chem. (2020)

Release Date

2020-03-25

Peptides

C-type lectin domain family 4, member b1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C-type lectin domain family 4, member b1

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