SMTL ID : 2zqo.1 (1 other biounit)

Crystal structure of the earthworm R-type lectin C-half in complex with GalNAc

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

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

NGA.1: 9 residues within 4Å: Chain A: D.16, I.17, E.18, G.19, Q.20, I.29, W.31, K.34, N.41 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Q.20 Hydrogen bonds: A:D.16, A:G.19, A:K.34, A:K.34, A:N.41 Water bridges: A:W.31 NGA.2: 7 residues within 4Å: Chain A: D.100, I.101, I.102, K.103, W.115, H.118, N.122 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.100, A:K.103, A:H.118, A:N.122 Water bridges: A:S.104 Salt bridges: A:K.103

1 x CD: CADMIUM ION(Non-covalent)

CD.3: 2 residues within 4Å: Chain A: H.111 Ligands: IMD.5 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.111, H2O.4, H2O.5

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 2 residues within 4Å: Chain A: N.87, K.124 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.87, A:N.87 Water bridges: A:K.124, A:K.124, A:K.124 Salt bridges: A:K.124

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.5: 3 residues within 4Å: Chain A: G.109, H.111 Ligands: CD.3 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.111

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Suzuki, R. et al., Sugar-complex structures of the C-half domain of the galactose-binding lectin EW29 from the earthworm Lumbricus terrestris. Acta Crystallogr.,Sect.D (2009)

Release Date

2008-09-02

Peptides

29-kDa galactose-binding lectin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

29-kDa galactose-binding lectin

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