SMTL ID : 5h4s.1

Crystal structure of a rhamnose-binding lectin SUL-I from the toxopneustid sea urchin Toxopneustes pileolus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

6 x RAM: alpha-L-rhamnopyranose(Non-covalent)

RAM.1: 8 residues within 4Å: Chain A: E.7, N.71, D.76, R.79, G.80, V.81, Y.82, K.83 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.82 Hydrogen bonds: A:E.7, A:N.71, A:N.71, A:G.80, A:K.83 RAM.2: 10 residues within 4Å: Chain A: E.104, S.140, N.171, D.176, C.178, I.179, G.180, T.181, Y.182, K.183 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.104, A:N.171, A:N.171, A:G.180, A:K.183 Water bridges: A:D.176, A:D.176 RAM.3: 9 residues within 4Å: Chain A: E.199, N.263, D.268, C.270, V.271, G.272, T.273, Y.274, K.275 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.199, A:N.263, A:N.263, A:G.272, A:K.275 Water bridges: A:D.268 RAM.5: 8 residues within 4Å: Chain B: E.7, N.71, D.76, R.79, G.80, V.81, Y.82, K.83 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Y.82 Hydrogen bonds: B:E.7, B:N.71, B:N.71, B:G.80, B:K.83 RAM.6: 10 residues within 4Å: Chain B: E.104, S.140, N.171, D.176, C.178, I.179, G.180, T.181, Y.182, K.183 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.104, B:N.171, B:N.171, B:G.180, B:K.183 Water bridges: B:D.176 RAM.7: 9 residues within 4Å: Chain B: E.199, N.263, D.268, C.270, V.271, G.272, T.273, Y.274, K.275 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:E.199, B:N.263, B:N.263, B:G.272, B:K.275 Water bridges: B:D.268, B:D.268

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

PO4.4: 3 residues within 4Å: Chain A: R.162, S.163, E.164 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.163, A:E.164, A:E.164 Salt bridges: A:R.162 PO4.8: 3 residues within 4Å: Chain B: R.162, S.163, E.164 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.163, B:E.164, B:E.164 Salt bridges: B:R.162

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Hatakeyama, T. et al., Carbohydrate recognition by the rhamnose-binding lectin SUL-I with a novel three-domain structure isolated from the venom of globiferous pedicellariae of the flower sea urchin Toxopneustes pileolus. Protein Sci. (2017)

Release Date

2017-05-17

Peptides

L-rhamnose-binding lectin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

L-rhamnose-binding lectin