SMTL ID : 7yrk.1

Crystal structure of the hen egg lysozyme-2-oxidobenzylidene-threoninato-copper (II) complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 0.92 Å

Oligo State

monomer

Ligands

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 10 residues within 4Å: Chain A: D.70, L.74, Q.75, I.76, N.77, W.81, I.116, A.125, W.126, V.127 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.75, A:N.77, A:W.81, A:A.125 Water bridges: A:N.77 EDO.7: 3 residues within 4Å: Chain A: A.28, A.29, R.32 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.29

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 2 residues within 4Å: Chain A: Y.41, G.122 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain A: R.23, K.51, F.56, W.141 Ligand excluded by PLIP CL.5: 5 residues within 4Å: Chain A: N.83, G.85, R.86, T.87, S.90 Ligand excluded by PLIP CL.6: 5 residues within 4Å: Chain A: S.42, G.44, V.138, Q.139, I.142 Ligand excluded by PLIP

1 x JI6: (6~{S})-6-[(1~{R})-1-oxidanylethyl]-2,4-dioxa-7$l^{4}-aza-3$l^{3}-cupratricyclo[7.4.0.0^{3,7}]trideca-1(13),7,9,11-tetraen-5-one(Non-covalent)

JI6.3: 4 residues within 4Å: Chain A: R.32, H.33, D.105, T.107 8 PLIP interactions: 8 interactions with chain A, Hydrophobic interactions: A:T.107 Hydrogen bonds: A:R.32, A:R.32 Water bridges: A:I.106 Salt bridges: A:R.32, A:H.33 Metal complexes: A:H.33, A:T.107

3 x NA: SODIUM ION(Non-functional Binders)

NA.8: 2 residues within 4Å: Chain A: T.61, T.69 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.61 NA.9: 2 residues within 4Å: Chain A: E.53, N.62 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.53 NA.10: 2 residues within 4Å: Chain A: N.62, R.63 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.63

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Furuya, T. et al., A novel hybrid protein composed of superoxide-dismutase-active Cu(II) complex and lysozyme. Sci Rep (2023)

Release Date

2023-05-10

Peptides

Lysozyme C: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lysozyme C

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