SMTL ID : 6a7s.1

Ca2+-independent C-type lectin SPL-2 from Saxidomus purpuratus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

NGA.1: 7 residues within 4Å: Chain A: Y.87, K.118, D.127, L.129, Y.131, N.139, H.141 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.87 Hydrogen bonds: A:K.118, A:N.139, A:N.139, A:H.141 Water bridges: A:N.122 NGA.5: 7 residues within 4Å: Chain B: Y.87, K.118, D.127, L.129, Y.131, N.139, H.141 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Y.87 Hydrogen bonds: B:K.118, B:N.139, B:N.139, B:H.141 Water bridges: B:N.122

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.2: 7 residues within 4Å: Chain A: T.65, E.67, D.105, E.154, I.155, D.156 Ligands: CA.3 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:T.65, A:T.65, A:D.105, A:D.105, A:E.154, A:E.154 Water bridges: A:S.38, A:Y.40, A:D.156 TRS.6: 7 residues within 4Å: Chain B: T.65, E.67, D.105, E.154, I.155, D.156 Ligands: CA.7 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:T.65, B:T.65, B:D.105, B:E.154, B:E.154 Water bridges: B:S.38, B:E.71, B:D.156

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain A: T.65, E.67, E.71, E.154 Ligands: TRS.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.65, A:E.67, A:E.154, A:E.154, H2O.3 CA.7: 5 residues within 4Å: Chain B: T.65, E.67, E.71, E.154 Ligands: TRS.6 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.65, B:E.67, B:E.154, B:E.154, H2O.7

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 2 residues within 4Å: Chain A: P.116, G.117 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.117 Water bridges: A:G.115 SO4.8: 2 residues within 4Å: Chain B: P.116, G.117 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.117 Water bridges: B:G.115

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Unno, H. et al., Novel Ca2+-independent carbohydrate recognition of the C-type lectins, SPL-1 and SPL-2, from the bivalve Saxidomus purpuratus. Protein Sci. (2019)

Release Date

2019-03-20

Peptides

N-acetylglucosamine-specific lectin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

N-acetylglucosamine-specific lectin

Related Entries With Identical Sequence