SMTL ID : 7yl6.1 (1 other biounit)

Cell surface protein YwfG protein complexed with alpha-1,2-mannobiose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.95 Å

Oligo State

monomer

Ligands

1 x MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose(Non-covalent)

MAN-MAN.1: 14 residues within 4Å: Chain A: S.75, Q.76, A.110, D.111, P.128, G.129, G.130, Y.148, N.150, T.243, G.244, A.245, F.246 Ligands: SO4.7 No protein-ligand interaction detected (PLIP)

1 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: D.146, Y.148, N.150, D.160 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.146, A:D.146, A:Y.148, A:D.160

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

SO4.3: 5 residues within 4Å: Chain A: L.46, F.49, Q.50, R.51, K.83 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.51, A:K.83 Salt bridges: A:R.51 SO4.4: 3 residues within 4Å: Chain A: A.317, A.318, N.319 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.319, A:N.319, A:N.319 SO4.5: 3 residues within 4Å: Chain A: A.279, Q.280, K.297 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.280 Salt bridges: A:K.297 SO4.6: 4 residues within 4Å: Chain A: D.479, Q.480, L.481, K.482 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.481, A:K.482, A:K.482 SO4.7: 5 residues within 4Å: Chain A: Y.148, N.150, G.151, V.152 Ligands: MAN-MAN.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.148, A:N.150, A:G.151, A:V.152

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tsuchiya, W. et al., Cell-surface protein YwfG of Lactococcus lactis binds to alpha-1,2-linked mannose. Plos One (2023)

Release Date

2023-06-07

Peptides

GRAM_POS_ANCHORING domain-containing protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GRAM_POS_ANCHORING domain-containing protein

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