SMTL ID : 5yrg.1

PPL3A-isomaltose complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 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: 9 residues within 4Å: Chain A: 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 A Hydrogen bonds: A:K.88, A:Y.89, A:G.12, A:C.131, A:R.132, A:R.132 Water bridges: A:Y.89 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 6 PLIP interactions: 6 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:K.88, B:Y.89, B:D.134

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

SO4.3: 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 SO4.4: 1 residues within 4Å: Chain A: R.104 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.104, A:R.104 Salt bridges: A:R.104 SO4.5: 1 residues within 4Å: Chain B: R.128 4 PLIP interactions: 4 interactions with chain B Water bridges: B:A.14, B:R.128, B:R.128 Salt bridges: B:R.128 SO4.6: 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:R.50, 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-A: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PPL3-A

PPL3-A

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