SMTL ID : 1wmz.3 (2 other biounits)

Crystal Structure of C-type Lectin CEL-I complexed with N-acetyl-D-galactosamine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

3 x NGA: 2-acetamido-2-deoxy-beta-D-galactopyranose(Non-covalent)

NGA.1: 10 residues within 4Å: Chain A: Q.70, Q.101, D.103, W.105, E.109, Q.113, R.115, N.123, D.124 Ligands: CA.3 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Q.70 Hydrogen bonds: A:Q.101, A:R.115, A:N.123, A:N.123 Water bridges: A:N.125 Salt bridges: A:R.115 NGA.9: 10 residues within 4Å: Chain C: Q.70, Q.101, D.103, W.105, E.109, Q.113, R.115, N.123, D.124 Ligands: CA.11 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:Q.70 Hydrogen bonds: C:Q.101, C:R.115, C:N.123, C:N.123 Water bridges: C:N.125 Salt bridges: C:R.115 NGA.13: 10 residues within 4Å: Chain D: Q.70, Q.101, D.103, W.105, E.109, Q.113, R.115, N.123, D.124 Ligands: CA.15 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:Q.70 Hydrogen bonds: D:Q.101, D:R.115, D:N.123, D:N.123 Water bridges: D:N.125 Salt bridges: D:R.115

12 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: D.77, E.81, N.104, E.109, D.110 Ligands: CA.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.77, A:D.77, A:E.81, A:D.110, H2O.2 CA.3: 6 residues within 4Å: Chain A: Q.101, D.103, E.109, N.123, D.124 Ligands: NGA.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.103, A:E.109, A:D.124, A:D.124 CA.4: 3 residues within 4Å: Chain A: E.81, D.110 Ligands: CA.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.81, A:D.110, H2O.1 CA.6: 6 residues within 4Å: Chain B: D.77, E.81, N.104, E.109, D.110 Ligands: CA.8 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.77, B:D.77, B:E.81, B:E.81, H2O.7 CA.7: 6 residues within 4Å: Chain B: Q.101, D.103, E.109, N.123, D.124 Ligands: A2G.5 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.103, B:E.109, B:D.124, B:D.124 CA.8: 3 residues within 4Å: Chain B: E.81, D.110 Ligands: CA.6 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.81, B:D.110, B:D.110, H2O.6, H2O.6 CA.10: 6 residues within 4Å: Chain C: D.77, E.81, N.104, E.109, D.110 Ligands: CA.12 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.77, C:D.77, C:E.81, C:D.110, H2O.11 CA.11: 6 residues within 4Å: Chain C: Q.101, D.103, E.109, N.123, D.124 Ligands: NGA.9 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.103, C:E.109, C:D.124, C:D.124 CA.12: 3 residues within 4Å: Chain C: E.81, D.110 Ligands: CA.10 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.81, C:D.110, C:D.110, H2O.8, H2O.12 CA.14: 6 residues within 4Å: Chain D: D.77, E.81, N.104, E.109, D.110 Ligands: CA.16 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.77, D:E.81, D:E.81, D:D.110, H2O.15 CA.15: 6 residues within 4Å: Chain D: Q.101, D.103, E.109, N.123, D.124 Ligands: NGA.13 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.103, D:E.109, D:D.124, D:D.124 CA.16: 3 residues within 4Å: Chain D: E.81, D.110 Ligands: CA.14 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.81, D:D.110, D:D.110, H2O.13, H2O.16

1 x A2G: 2-acetamido-2-deoxy-alpha-D-galactopyranose(Non-covalent)

A2G.5: 12 residues within 4Å: Chain B: Q.70, Q.101, D.103, W.105, E.109, Q.113, R.115, N.123, D.124 Chain C: N.80, D.83 Ligands: CA.7 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:Q.70 Hydrogen bonds: B:Q.101, B:E.109, B:R.115, B:N.123, C:N.80, C:D.83 Water bridges: B:N.125

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sugawara, H. et al., Characteristic Recognition of N-Acetylgalactosamine by an Invertebrate C-type Lectin, CEL-I, Revealed by X-ray Crystallographic Analysis. J.Biol.Chem. (2004)

Release Date

2004-09-07

Peptides

lectin CEL-I, N-acetyl-D-galactosamine-specific C-type: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

lectin CEL-I, N-acetyl-D-galactosamine-specific C-type

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