SMTL ID : 4c9f.1 (1 other biounit)

Structure of SIGN-R1 in complex with Sulfodextran

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

2 x GQ1- GLC: alpha-D-glucopyranose-(1-6)-4-O-sulfo-alpha-D-glucopyranose(Non-covalent)

GQ1-GLC.1: 11 residues within 4Å: Chain A: E.96, N.98, N.99, E.103, E.107, N.114, D.115, S.116, L.120, K.122 Ligands: CA.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.107, A:N.114, A:D.115, A:K.122, A:N.98, A:N.99, A:N.114 GQ1-GLC.2: 12 residues within 4Å: Chain B: P.62, E.96, N.98, N.99, E.103, E.107, N.114, D.115, S.116, L.120, K.122 Ligands: CA.5 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.107, B:N.114, B:S.116, B:K.122, B:N.98, B:N.98, B:N.99

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain A: E.96, N.98, E.103, D.115 Ligands: GQ1-GLC.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.96, A:E.103, A:D.115, A:D.115 CA.5: 5 residues within 4Å: Chain B: E.96, N.98, E.103, D.115 Ligands: GQ1-GLC.2 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.96, B:E.103, B:D.115, B:D.115

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

SO4.4: 7 residues within 4Å: Chain A: R.4, L.5, C.6, F.12 Chain B: F.20, K.22, K.60 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:F.20, A:L.5, A:C.6 Salt bridges: B:K.22, B:K.60 Water bridges: A:F.12 SO4.6: 7 residues within 4Å: Chain A: K.22, K.60 Chain B: C.3, R.4, L.5, C.6, F.12 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Salt bridges: A:K.22, A:K.60 Hydrogen bonds: B:L.5, B:C.6 Water bridges: B:F.12 SO4.7: 7 residues within 4Å: Chain B: L.14, N.16, Y.18, N.45, S.46, E.49, K.127 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.14, B:N.16, B:Y.18 Salt bridges: B:K.127 SO4.8: 4 residues within 4Å: Chain B: S.46, D.47, E.48 Ligands: SO4.9 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.48, B:E.48 SO4.9: 6 residues within 4Å: Chain B: N.45, S.46, D.47, R.87, F.88 Ligands: SO4.8 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.47 Water bridges: B:R.87 Salt bridges: B:R.87 SO4.10: 5 residues within 4Å: Chain B: F.19, S.21, K.22, S.23, W.124 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.22, B:S.23

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Silva-Martin, N. et al., Structural Basis for Selective Recognition of Endogenous and Microbial Polysaccharides by Macrophage Receptor Sign-R1. Structure (2014)

Release Date

2014-10-15

Peptides

CD209 ANTIGEN-LIKE PROTEIN B: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

CD209 ANTIGEN-LIKE PROTEIN B

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