SMTL ID : 5v94.1 (1 other biounit)

Pekin duck egg lysozyme isoform III (DEL-III), cubic form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

5 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 2 residues within 4Å: Chain A: Y.34, R.114 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.114 Salt bridges: A:R.114 PO4.2: 3 residues within 4Å: Chain A: S.4, C.6, E.7 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.4, A:S.4, A:C.6, A:E.7 Water bridges: A:S.4, A:R.128, A:R.128 PO4.3: 2 residues within 4Å: Chain A: R.85, S.86 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.86, A:S.86, A:S.86 Water bridges: A:K.1, A:R.85, A:D.87 Salt bridges: A:R.85 PO4.4: 3 residues within 4Å: Chain A: R.97, R.100 Ligands: PO4.5 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.97 Salt bridges: A:R.97, A:R.100 PO4.5: 4 residues within 4Å: Chain A: R.93, R.97, R.100 Ligands: PO4.4 8 PLIP interactions: 8 interactions with chain A Water bridges: A:R.93, A:R.93, A:R.97, A:R.97, A:R.100 Salt bridges: A:R.93, A:R.97, A:R.100

1 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.6: 3 residues within 4Å: Chain A: N.113, R.114, T.118 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.113, A:R.114, A:R.114

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.7: 6 residues within 4Å: Chain A: E.35, D.52, Q.57, A.107, W.108, V.109 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.35, A:Q.57, A:V.109 Water bridges: A:D.52, A:D.52, A:N.59

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Langley, D.B. et al., Structural basis of antigen recognition: crystal structure of duck egg lysozyme. Acta Crystallogr D Struct Biol (2017)

Release Date

2017-11-15

Peptides

lysozyme isoform III: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

lysozyme isoform III

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