SMTL ID : 7qe3.2 (1 other biounit)

Se-M variant of B-trefoil lectin from Salpingoeca rosetta in complex with GalNAc

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

3 x 1JW: (2S)-hexane-1,2,6-triol(Non-covalent)

1JW.1: 10 residues within 4Å: Chain A: H.53, P.54, H.55, G.56, G.57, V.68, H.70, G.72, R.77, N.161 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.56, A:R.77 1JW.2: 12 residues within 4Å: Chain A: D.64, H.104, P.105, K.106, G.107, G.108, V.117, H.119, S.121, P.122, R.124, T.127 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.105, A:G.107, A:S.121, A:R.124 1JW.3: 9 residues within 4Å: Chain A: E.113, H.150, P.151, H.152, G.153, G.154, V.165, Y.167, R.171 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.167, A:Y.167 Hydrogen bonds: A:E.113, A:H.150, A:G.153, A:R.171, A:R.171

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 3 residues within 4Å: Chain A: K.106, T.115, R.163 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.106, A:T.115, A:T.115 EDO.6: 6 residues within 4Å: Chain A: K.245, V.246, G.247, G.268, S.269, W.270 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.246, A:G.247, A:G.247, A:W.270

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.5: 6 residues within 4Å: Chain A: K.109, V.110, G.111, K.112, E.126, Y.147 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.112 Water bridges: A:V.110

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Notova, S. et al., The choanoflagellate pore-forming lectin SaroL-1 punches holes in cancer cells by targeting the tumor-related glycosphingolipid Gb3. Commun Biol (2022)

Release Date

2022-09-14

Peptides

Sarol-1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
BBB

Sarol-1

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