SMTL ID : 5yrl.1

PPL3C-trehalose complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x GLC- GLC: alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose(Non-covalent)

GLC-GLC.1: 8 residues within 4Å: Chain A: G.11, G.12, W.62, Y.89, G.130, C.131, R.132, D.134 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Y.89, A:Y.89 GLC-GLC.2: 8 residues within 4Å: Chain B: G.11, G.12, W.62, Y.89, G.130, C.131, R.132, D.134 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.12, B:G.130, B:C.131, B:R.132, B:R.132

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

SO4.3: 4 residues within 4Å: Chain A: I.60, K.64, K.65, G.66 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.65, A:G.66 Water bridges: A:G.66 SO4.4: 2 residues within 4Å: Chain A: R.50, Q.51 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.51 Water bridges: A:Q.51 Salt bridges: A:R.50 SO4.5: 3 residues within 4Å: Chain B: D.13, A.14, R.128 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.14 Water bridges: B:D.13, B:R.128 Salt bridges: B:R.128 SO4.6: 4 residues within 4Å: Chain B: V.70, H.71, E.72, R.100 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.70, B:E.72 Salt bridges: B:H.71, B:R.100 SO4.7: 3 residues within 4Å: Chain B: E.5, Y.6, R.137 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.6 Water bridges: B:R.137, B:R.137, B:R.137 Salt bridges: B:R.137

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Nakae, S. et al., Structures of jacalin-related lectin PPL3 regulating pearl shell biomineralization. Proteins (2018)

Release Date

2018-08-29

Peptides

PPL3-b: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PPL3-b

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