SMTL ID : 7yl5.1 (1 other biounit)

Cell surface protein YwfG protein complexed with mannose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

monomer

Ligands

1 x CA: CALCIUM ION(Non-covalent)

CA.1: 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

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

MAN.2: 9 residues within 4Å: Chain A: A.110, D.111, G.129, Y.148, N.150, G.244, A.245, F.246 Ligands: SO4.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.245, A:F.246, A:F.246

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

SO4.3: 4 residues within 4Å: Chain A: L.46, F.49, Q.50, R.51 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.46, A:R.51 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:A.318, 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: 3 residues within 4Å: Chain A: R.329, G.355, D.358 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.358 Salt bridges: A:R.329 SO4.7: 3 residues within 4Å: Chain A: Q.480, L.481, K.482 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.481, A:K.482 Salt bridges: A:K.482 SO4.8: 4 residues within 4Å: Chain A: Y.148, N.150, V.152 Ligands: MAN.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.148, A:N.150 SO4.9: 1 residues within 4Å: Chain A: G.120 No protein-ligand interaction detected (PLIP) SO4.10: 2 residues within 4Å: Chain A: S.408, S.409 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.409, A:S.409 SO4.11: 3 residues within 4Å: Chain A: K.474, G.475, E.476 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.473, A:G.475, A:E.476 Salt bridges: A:K.474

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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