SMTL ID : 5yrf.1

PPL3A-trehalose complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-1-1-mer

Ligands

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

GLC-GLC.1: 9 residues within 4Å: Chain B: G.11, G.12, W.62, Y.89, W.129, G.130, C.131, R.132, D.134 2 PLIP interactions: 2 interactions with chain B Water bridges: B:Y.89, B:Y.89

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

GLC.2: 9 residues within 4Å: Chain A: G.11, G.12, Y.89, W.129, G.130, C.131, R.132, D.134 Ligands: GLC.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.12, A:Y.89, A:C.131, A:R.132, A:R.132 Water bridges: A:G.11, A:D.134 GLC.3: 1 residues within 4Å: Ligands: GLC.2 No protein-ligand interaction detected (PLIP)

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

SO4.4: 3 residues within 4Å: Chain A: D.13, A.14, R.128 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.14 Water bridges: A:R.128, A:R.128, A:R.128 Salt bridges: A:R.128 SO4.5: 1 residues within 4Å: Chain A: R.50 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.50 SO4.6: 2 residues within 4Å: Chain A: R.28, R.43 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.28, A:R.28 Salt bridges: A:R.28, A:R.43 SO4.7: 3 residues within 4Å: Chain B: K.41, R.50, Q.51 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Q.51 Water bridges: B:K.41, B:K.41, B:K.41, B:R.50 Salt bridges: B:K.41, B:R.50

Links

RCSB   PDBe   PDBe-KB   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-A: A
PPL3-A: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PPL3-A

PPL3-A

Related Entries With Identical Sequence