SMTL ID : 5yrj.1

PPL3B-isomaltose complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-1-mer

Ligands

2 x BGC- GLC: alpha-D-glucopyranose-(1-6)-beta-D-glucopyranose(Non-covalent)

BGC-GLC.1: 10 residues within 4Å: Chain A: G.11, G.12, W.62, K.88, Y.89, W.129, G.130, C.131, R.132, D.134 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.88, A:Y.89, A:G.12, A:C.131, A:R.132, A:R.132 BGC-GLC.2: 9 residues within 4Å: Chain B: G.11, G.12, W.62, K.88, Y.89, G.130, C.131, R.132, D.134 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.88, B:Y.89, B:G.12, B:C.131, B:R.132, B:R.132 Water bridges: B:Y.89

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

SO4.3: 2 residues within 4Å: Chain A: R.28, R.43 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.28, A:R.43 SO4.4: 4 residues within 4Å: Chain A: V.70, H.71, E.72, R.100 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.70, A:E.72 Water bridges: A:H.71 Salt bridges: A:H.71, A:R.100 SO4.5: 1 residues within 4Å: Chain A: R.104 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.104 SO4.6: 1 residues within 4Å: Chain B: R.128 3 PLIP interactions: 3 interactions with chain B Water bridges: B:A.14, B:R.128 Salt bridges: B:R.128 SO4.7: 3 residues within 4Å: Chain B: K.41, R.50, Q.51 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.51 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-b: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PPL3-a

PPL3-b

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