SMTL ID : 6m5m.1

SPL-1 - GlcNAc complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-1-1-mer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: T.64, E.66, E.70, E.153 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.64, A:E.66, A:E.70, A:E.153, H2O.3 CA.3: 3 residues within 4Å: Chain A: D.119, D.139, Q.141 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.119, A:D.139, A:D.139, H2O.1, H2O.2 CA.4: 4 residues within 4Å: Chain B: T.65, E.67, E.71, E.154 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.65, B:E.67, B:E.71, B:E.154, H2O.5 CA.6: 6 residues within 4Å: Chain B: K.118, D.120, N.122, N.139, D.140 Ligands: NAG.5 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.120, B:D.140, H2O.5

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.2: 9 residues within 4Å: Chain A: R.117, D.126, L.128, Y.130, I.133, N.138, D.139, H.140, T.146 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:T.146 Hydrogen bonds: A:R.117, A:R.117, A:N.138, A:N.138, A:H.140 Water bridges: A:Q.141 NAG.5: 10 residues within 4Å: Chain B: Y.87, K.118, D.127, L.129, Y.131, N.139, D.140, H.141, T.147 Ligands: CA.6 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:Y.87, B:H.141, B:T.147 Hydrogen bonds: B:K.118, B:N.139, B:H.141 Water bridges: B:E.133, B:D.140 Salt bridges: B:H.86

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Unno, H. et al., Novel carbohydrate-recognition mode of the invertebrate C-type lectin SPL-1 from Saxidomus purpuratus revealed by the GlcNAc-complex crystal in the presence of Ca2. Acta Crystallogr.,Sect.F (2020)

Release Date

2020-06-10

Peptides

N-acetylglucosamine-specific lectin: A
N-acetylglucosamine-specific lectin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

N-acetylglucosamine-specific lectin

N-acetylglucosamine-specific lectin

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