SMTL ID : 5f90.1

Crystal structure of a Crenomytilus grayanus lectin in complex with Gb3 allyl

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.64 Å

Oligo State

homo-dimer

Ligands

3 x BGC- GAL- GLA: alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose

BGC-GAL-GLA.1: 11 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 Ligands: 5VQ.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.119, A:N.119, A:H.16, A:P.17, A:G.19, A:H.37 Water bridges: A:H.33 BGC-GAL-GLA.3: 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: 5VQ.8 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.119, B:N.119, B:P.17, B:G.19, B:D.35, B:H.37 Water bridges: B:G.19, B:R.39, B:R.39, B:R.39 BGC-GAL-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: 5VQ.9 7 PLIP interactions: 7 interactions with chain B Water bridges: B:N.27, B:Y.66, B:G.67 Hydrogen bonds: B:N.27, B:N.27, B:H.64, B:P.65, B:G.67, B:D.83, B:H.85, B:R.87

2 x GAL- GLA: alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose(Non-covalent)

GAL-GLA.2: 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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.27, A:N.27, A:G.67, A:H.85 Water bridges: A:G.67 GAL-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 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.111, B:P.109, B:G.111, B:H.129 Water bridges: B:E.75

1 x LMR: (2S)-2-hydroxybutanedioic acid(Non-covalent)

LMR.6: 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 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:H.108, A:G.111, A:D.127, A:H.129 Water bridges: A:E.75, A:H.125 Salt bridges: A:H.108, A:H.125, A:H.125, A:H.129

3 x 5VQ: 2-Propen-1-ol(Non-functional Binders)

5VQ.7: 1 residues within 4Å: Ligands: BGC-GAL-GLA.1 No protein-ligand interaction detected (PLIP) 5VQ.8: 1 residues within 4Å: Ligands: BGC-GAL-GLA.3 No protein-ligand interaction detected (PLIP) 5VQ.9: 1 residues within 4Å: Ligands: BGC-GAL-GLA.4 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   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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