SMTL ID : 5f8w.1

Crystal structure of a Crenomytilus grayanus lectin in complex with galactose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.56 Å

Oligo State

homo-dimer

Ligands

1 x GAL: beta-D-galactopyranose(Non-covalent)

GAL.1: 10 residues within 4Å: Chain A: E.75, H.108, P.109, K.110, G.111, G.112, V.123, H.125, D.127, H.129 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.109, A:G.111, A:D.127, A:H.129

5 x GLA: alpha-D-galactopyranose(Non-covalent)

GLA.2: 10 residues within 4Å: Chain A: H.16, P.17, Y.18, G.19, G.20, V.31, H.33, D.35, H.37, N.119 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:P.17, A:G.19, A:D.35, A:H.37 Water bridges: A:N.119, A:N.119 Salt bridges: A:H.33 GLA.3: 10 residues within 4Å: Chain A: N.27, H.64, P.65, Y.66, G.67, G.68, V.79, H.81, D.83, H.85 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:H.64, A:P.65, A:G.67, A:D.83, A:H.85 Water bridges: A:G.67 Salt bridges: A:H.81 GLA.4: 11 residues within 4Å: Chain B: N.27, H.64, P.65, Y.66, G.67, G.68, V.79, H.81, D.83, H.85 Ligands: GOL.7 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:P.65, B:G.67, B:H.85 Water bridges: B:N.27, B:G.67, B:R.87, B:R.87, B:R.87 Salt bridges: B:H.81 GLA.5: 10 residues within 4Å: Chain B: E.75, H.108, P.109, K.110, G.111, G.112, V.123, H.125, D.127, H.129 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:H.108, B:P.109, B:G.111, B:D.127, B:H.129 Water bridges: B:H.129 Salt bridges: B:H.125 GLA.6: 11 residues within 4Å: Chain B: H.16, P.17, Y.18, G.19, G.20, V.31, H.33, D.35, H.37, N.119 Ligands: GOL.8 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:H.16, B:P.17, B:G.19, B:H.37 Water bridges: B:G.19, B:H.37, B:R.39, B:R.39, B:N.119 Salt bridges: B:H.33

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 4 residues within 4Å: Chain B: N.27, Y.66, G.67 Ligands: GLA.4 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.27 Water bridges: B:G.67 GOL.8: 4 residues within 4Å: Chain B: Y.18, G.19, N.119 Ligands: GLA.6 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.119, B:N.119

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Liao, J.-H. et al., A Multivalent Marine Lectin from Crenomytilus grayanus Possesses Anti-cancer Activity through Recognizing Globotriose Gb3. J.Am.Chem.Soc. (2016)

Release Date

2016-04-06

Peptides

GalNAc/Gal-specific lectin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

GalNAc/Gal-specific lectin

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