SMTL ID : 1k9i.1

Complex of DC-SIGN and GlcNAc2Man3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-10-mer

Ligands

5 x MAN- MAN- NAG- MAN- 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)]alpha-D-mannopyranose

MAN-MAN-NAG-MAN-NAG.1: 24 residues within 4Å: Chain A: S.59, S.60, N.63, R.64, F.65, N.96, E.99, N.101, V.103, E.106, S.112, G.113, N.117, D.118, D.119 Chain J: F.65, E.99, N.101, E.106, N.117, D.118, D.119 Ligands: CA.7, CA.34 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.96, A:S.112, A:S.60, A:R.64, A:G.113 MAN-MAN-NAG-MAN-NAG.2: 22 residues within 4Å: Chain C: S.60, N.63, F.65, N.96, E.99, N.101, V.103, E.106, S.112, G.113, N.117, D.118 Chain I: F.65, E.99, N.101, E.106, N.117, D.118, D.119, K.120 Ligands: CA.13, CA.31 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.96, C:S.112, C:N.63, C:G.113 Water bridges: C:N.96, C:S.112, C:S.59, C:F.111 MAN-MAN-NAG-MAN-NAG.3: 25 residues within 4Å: Chain D: S.60, N.63, R.64, F.65, N.96, R.97, E.99, N.101, V.103, E.106, S.112, G.113, N.117, D.118, D.119, K.120 Chain F: F.65, E.99, N.101, E.106, N.117, D.118, D.119 Ligands: CA.16, CA.22 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.96, D:S.112, D:N.63, D:F.111, D:G.113 Water bridges: D:S.112, D:G.115 MAN-MAN-NAG-MAN-NAG.4: 21 residues within 4Å: Chain B: E.99, N.101, E.106, N.117, D.118 Chain E: S.60, N.63, R.64, F.65, N.96, E.99, N.101, V.103, E.106, S.112, G.113, N.117, D.118, D.119 Ligands: CA.10, CA.19 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:N.96, E:S.112, E:N.63, E:R.64, E:G.113 Water bridges: E:N.96, E:N.114 MAN-MAN-NAG-MAN-NAG.5: 24 residues within 4Å: Chain G: F.65, E.99, N.101, V.103, E.106, N.117, D.118, D.119 Chain H: S.60, N.63, R.64, F.65, N.96, E.99, N.101, V.103, E.106, S.112, G.113, N.117, D.118, D.119 Ligands: CA.25, CA.28 3 PLIP interactions: 3 interactions with chain H Hydrogen bonds: H:N.96, H:S.112, H:N.63, H:R.64, H:G.113 Water bridges: H:N.96, H:N.114

30 x CA: CALCIUM ION(Non-covalent)

CA.6: 6 residues within 4Å: Chain A: D.72, E.76, N.102, E.106, D.107 Ligands: CA.8 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.72, A:E.76, A:E.106, A:D.107, H2O.1 CA.7: 6 residues within 4Å: Chain A: E.99, N.101, E.106, N.117, D.118 Ligands: MAN-MAN-NAG-MAN-NAG.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.99, A:E.106, A:D.118, A:D.118 CA.8: 4 residues within 4Å: Chain A: E.76, E.105, D.107 Ligands: CA.6 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.76, A:E.105, A:D.107, A:D.107, H2O.1 CA.9: 6 residues within 4Å: Chain B: D.72, E.76, N.102, E.106, D.107 Ligands: CA.11 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.72, B:D.72, B:E.106, B:D.107, H2O.1 CA.10: 6 residues within 4Å: Chain B: E.99, N.101, E.106, N.117, D.118 Ligands: MAN-MAN-NAG-MAN-NAG.4 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.99, B:E.106, B:D.118, B:D.118 CA.11: 4 residues within 4Å: Chain B: E.76, E.105, D.107 Ligands: CA.9 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.76, B:D.107, B:D.107, H2O.1, H2O.1 CA.12: 6 residues within 4Å: Chain C: D.72, E.76, N.102, E.105, E.106, D.107 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.72, C:D.72, C:E.76, C:D.107, H2O.2 CA.13: 6 residues within 4Å: Chain C: E.99, N.101, E.106, N.117, D.118 Ligands: MAN-MAN-NAG-MAN-NAG.2 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.99, C:E.106, C:D.118, C:D.118 CA.14: 3 residues within 4Å: Chain C: E.76, E.105, D.107 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.76, C:E.105, C:D.107, C:D.107, H2O.2 CA.15: 6 residues within 4Å: Chain D: D.72, E.76, N.102, E.106, D.107 Ligands: CA.17 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.72, D:D.72, D:E.106, D:D.107, H2O.4 CA.16: 6 residues within 4Å: Chain D: E.99, N.101, E.106, N.117, D.118 Ligands: MAN-MAN-NAG-MAN-NAG.3 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.99, D:E.106, D:D.118, D:D.118 CA.17: 4 residues within 4Å: Chain D: E.76, E.105, D.107 Ligands: CA.15 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.76, D:E.105, D:D.107, H2O.4, H2O.4 CA.18: 6 residues within 4Å: Chain E: D.72, E.76, N.102, E.106, D.107 Ligands: CA.20 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.72, E:E.76, E:E.106, E:D.107, H2O.5 CA.19: 6 residues within 4Å: Chain E: E.99, N.101, E.106, N.117, D.118 Ligands: MAN-MAN-NAG-MAN-NAG.4 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:E.99, E:E.106, E:D.118, E:D.118 CA.20: 5 residues within 4Å: Chain E: E.76, N.102, E.105, D.107 Ligands: CA.18 5 PLIP interactions: 2 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:E.76, E:E.105, H2O.5, H2O.5, H2O.5 CA.21: 6 residues within 4Å: Chain F: D.72, E.76, N.102, E.106, D.107 Ligands: CA.23 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.72, F:E.76, F:E.106, F:D.107, H2O.6 CA.22: 6 residues within 4Å: Chain F: E.99, N.101, E.106, N.117, D.118 Ligands: MAN-MAN-NAG-MAN-NAG.3 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:E.99, F:E.106, F:D.118, F:D.118 CA.23: 4 residues within 4Å: Chain F: E.76, E.105, D.107 Ligands: CA.21 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.76, F:E.105, F:D.107, H2O.6, H2O.6 CA.24: 7 residues within 4Å: Chain G: D.72, E.76, N.102, E.105, E.106, D.107 Ligands: CA.26 5 PLIP interactions: 4 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:D.72, G:D.72, G:E.106, G:D.107, H2O.7 CA.25: 6 residues within 4Å: Chain G: E.99, N.101, E.106, N.117, D.118 Ligands: MAN-MAN-NAG-MAN-NAG.5 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:E.99, G:E.106, G:D.118, G:D.118 CA.26: 4 residues within 4Å: Chain G: E.76, E.105, D.107 Ligands: CA.24 5 PLIP interactions: 4 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:E.76, G:E.105, G:D.107, G:D.107, H2O.7 CA.27: 5 residues within 4Å: Chain H: D.72, E.76, N.102, E.106, D.107 5 PLIP interactions: 4 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:D.72, H:D.72, H:E.76, H:D.107, H2O.8 CA.28: 6 residues within 4Å: Chain H: E.99, N.101, E.106, N.117, D.118 Ligands: MAN-MAN-NAG-MAN-NAG.5 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:E.99, H:E.106, H:D.118, H:D.118 CA.29: 3 residues within 4Å: Chain H: E.76, E.105, D.107 5 PLIP interactions: 3 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:E.76, H:E.105, H:D.107, H2O.8, H2O.8 CA.30: 7 residues within 4Å: Chain I: D.72, E.76, N.102, E.105, E.106, D.107 Ligands: CA.32 5 PLIP interactions: 4 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:D.72, I:E.76, I:E.106, I:D.107, H2O.9 CA.31: 6 residues within 4Å: Chain I: E.99, N.101, E.106, N.117, D.118 Ligands: MAN-MAN-NAG-MAN-NAG.2 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:E.99, I:E.106, I:D.118, I:D.118 CA.32: 4 residues within 4Å: Chain I: E.76, E.105, D.107 Ligands: CA.30 5 PLIP interactions: 3 interactions with chain I, 2 Ligand-Water interactions Metal complexes: I:E.76, I:E.105, I:D.107, H2O.9, H2O.9 CA.33: 6 residues within 4Å: Chain J: D.72, E.76, N.102, E.105, E.106, D.107 5 PLIP interactions: 4 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:D.72, J:E.76, J:E.106, J:D.107, H2O.10 CA.34: 6 residues within 4Å: Chain J: E.99, N.101, E.106, N.117, D.118 Ligands: MAN-MAN-NAG-MAN-NAG.1 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:E.99, J:E.106, J:D.118, J:D.118 CA.35: 3 residues within 4Å: Chain J: E.76, E.105, D.107 5 PLIP interactions: 4 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:E.76, J:E.105, J:D.107, J:D.107, H2O.10

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Feinberg, H. et al., Structural basis for selective recognition of oligosaccharides by DC-SIGN and DC-SIGNR. Science (2001)

Release Date

2001-12-21

Peptides

mDC-SIGN1B type I isoform: ABCDEFGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

mDC-SIGN1B type I isoform