SMTL ID : 5g6u.1

Crystal structure of langerin carbohydrate recognition domain with GlcNS6S

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

homo-tetramer

Ligands

3 x TRP: TRYPTOPHAN(Non-covalent)

TRP.1: 11 residues within 4Å: Chain A: K.190, A.191, G.192, M.193, E.194, G.195, N.221, H.227 Chain C: Q.154, V.157, S.158 10 PLIP interactions: 3 Ligand-Ligand interactions, 1 interactions with chain C, 6 interactions with chain A Hydrogen bonds: W.1, W.1, W.1, A:M.193, A:N.221 Hydrophobic interactions: C:Q.154, A:K.190, A:K.190 Salt bridges: A:K.190 pi-Stacking: A:H.227 TRP.7: 11 residues within 4Å: Chain B: K.190, A.191, G.192, M.193, E.194, G.195, N.221, H.227 Chain D: Q.154, V.157, S.158 7 PLIP interactions: 1 interactions with chain D, 6 interactions with chain B Hydrophobic interactions: D:V.157, B:K.190, B:K.190 Hydrogen bonds: B:G.192, B:N.221 Salt bridges: B:K.190 pi-Stacking: B:H.227 TRP.24: 11 residues within 4Å: Chain B: Q.154, V.157, S.158 Chain D: K.190, A.191, G.192, M.193, E.194, G.195, N.221, H.227 11 PLIP interactions: 9 interactions with chain D, 1 Ligand-Ligand interactions, 1 interactions with chain B Hydrophobic interactions: D:K.190, D:H.227, B:Q.154 Hydrogen bonds: D:G.192, D:E.194, D:N.221, D:N.221, W.24 Salt bridges: D:K.190, D:H.227 pi-Stacking: D:H.227

4 x SGN: 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose(Non-covalent)

SGN.2: 12 residues within 4Å: Chain A: E.218, N.220, E.226, K.232, N.240, D.241, A.242, P.243, K.246, F.248 Ligands: EU.3, CA.4 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.220, A:K.232, A:N.240, A:N.240 Water bridges: A:E.218 Salt bridges: A:K.232, A:K.232, A:K.246 SGN.8: 13 residues within 4Å: Chain B: E.218, N.220, E.226, K.232, N.240, D.241, A.242, P.243, K.246, F.248 Ligands: EU.6, EU.9, CA.10 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:N.220, B:N.240 Water bridges: B:E.218, B:K.232, B:K.232, B:K.232, B:K.232, B:K.232, B:K.232, B:K.232 Salt bridges: B:K.232, B:K.246 SGN.17: 14 residues within 4Å: Chain C: E.218, N.220, A.222, E.226, K.232, N.240, D.241, A.242, P.243, K.246, F.248 Ligands: CA.18, EU.19, EU.20 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:N.220, C:N.240 Water bridges: C:E.218, C:K.232, C:K.232, C:K.232, C:K.232 Salt bridges: C:K.232, C:K.246 SGN.25: 12 residues within 4Å: Chain D: E.218, N.220, A.222, E.226, K.232, N.240, D.241, A.242, P.243, K.246, F.248 Ligands: CA.26 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:E.218, D:N.220, D:N.240, D:D.241 Water bridges: D:E.226, D:N.230, D:K.232, D:K.232 Salt bridges: D:K.232, D:K.246

6 x EU: EUROPIUM ION(Non-covalent)(Non-functional Binders)

EU.3: 7 residues within 4Å: Chain A: E.218, N.220, E.226, N.240, D.241 Ligands: SGN.2, CA.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.218, A:E.226, A:D.241, A:D.241 EU.6: 1 residues within 4Å: Ligands: SGN.8 No protein-ligand interaction detected (PLIP) EU.9: 7 residues within 4Å: Chain B: E.218, N.220, E.226, N.240, D.241 Ligands: SGN.8, CA.10 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.218, B:E.226, B:D.241, B:D.241 EU.16: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EU.19: 7 residues within 4Å: Chain C: E.218, N.220, E.226, N.240, D.241 Ligands: SGN.17, CA.18 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.218, C:E.226, C:D.241, C:D.241 EU.20: 1 residues within 4Å: Ligands: SGN.17 No protein-ligand interaction detected (PLIP)

4 x CA: CALCIUM ION(Non-covalent)

CA.4: 7 residues within 4Å: Chain A: E.218, N.220, E.226, N.240, D.241 Ligands: SGN.2, EU.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.218, A:E.226, A:D.241, A:D.241 CA.10: 7 residues within 4Å: Chain B: E.218, N.220, E.226, N.240, D.241 Ligands: SGN.8, EU.9 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.218, B:E.226, B:D.241, B:D.241 CA.18: 8 residues within 4Å: Chain C: E.218, N.220, A.222, E.226, N.240, D.241 Ligands: SGN.17, EU.19 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.218, C:E.226, C:D.241, C:D.241 CA.26: 7 residues within 4Å: Chain D: E.218, N.220, A.222, E.226, N.240, D.241 Ligands: SGN.25 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.218, D:E.226, D:D.241, D:D.241

12 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 4 residues within 4Å: Chain A: Y.141, S.143, L.144, I.145 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain B: Y.141, S.143, L.144, I.145 Ligand excluded by PLIP CL.12: 6 residues within 4Å: Chain B: V.208, Q.209, V.211, R.212 Ligands: CL.14, CL.15 Ligand excluded by PLIP CL.13: 5 residues within 4Å: Chain B: W.214, I.215, P.216, G.217, E.218 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain B: Q.209, R.212 Ligands: CL.12 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain B: V.211, R.212 Ligands: CL.12 Ligand excluded by PLIP CL.21: 2 residues within 4Å: Chain C: F.135, K.136 Ligand excluded by PLIP CL.22: 4 residues within 4Å: Chain C: Y.141, S.143, L.144, I.145 Ligand excluded by PLIP CL.23: 3 residues within 4Å: Chain C: S.168, E.169, S.170 Ligand excluded by PLIP CL.27: 3 residues within 4Å: Chain D: V.211, R.212 Ligands: CL.28 Ligand excluded by PLIP CL.28: 6 residues within 4Å: Chain D: V.208, Q.209, V.211, R.212 Ligands: CL.27, CL.29 Ligand excluded by PLIP CL.29: 3 residues within 4Å: Chain D: Q.209, R.212 Ligands: CL.28 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Porkolab, V. et al., Rational-Differential Design of Highly Specific Glycomimetic Ligands: Targeting DC-SIGN and Excluding Langerin Recognition. ACS Chem. Biol. (2018)

Release Date

2018-02-21

Peptides

LANGERIN: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

LANGERIN