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

Structure of Sda1 nuclease apoprotein as an EGFP fixed-arm fusion

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: R.354, R.383, N.390 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.390 Water bridges: A:N.355 Salt bridges: A:R.354, A:R.383 SO4.2: 4 residues within 4Å: Chain A: K.305, W.311, D.360, R.361 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.361 Water bridges: A:D.360, A:D.360 Salt bridges: A:K.305, A:R.361 SO4.3: 6 residues within 4Å: Chain A: S.362, G.363, A.366, D.367, N.386 Ligands: EDO.9 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.363, A:D.367, A:N.386, A:N.386 Water bridges: A:S.368 Salt bridges: A:K.305 SO4.4: 5 residues within 4Å: Chain A: K.44, Y.277, S.426, Q.549 Ligands: EDO.7 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.426, A:S.426, A:Q.549 Water bridges: A:Q.462 Salt bridges: A:K.44 SO4.5: 5 residues within 4Å: Chain A: V.526, H.557, H.558, S.559, T.560 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.560 Salt bridges: A:H.557 SO4.6: 5 residues within 4Å: Chain A: V.58, P.59, W.60, P.61, H.140 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.58, A:W.60 Salt bridges: A:H.140

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

EDO.7: 4 residues within 4Å: Chain A: Y.42, K.44, Y.277 Ligands: SO4.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.44 EDO.8: 2 residues within 4Å: Chain A: Y.247, R.248 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.248 EDO.9: 8 residues within 4Å: Chain A: K.305, D.367, G.371, R.372, P.373, N.377, L.378 Ligands: SO4.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.305, A:K.305, A:D.367, A:D.367 EDO.10: 6 residues within 4Å: Chain A: H.78, N.242, F.243, E.282, Y.284, K.418 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.242

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.11: 3 residues within 4Å: Chain A: H.149, F.166, K.167 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.167, A:K.167 Salt bridges: A:H.149 ACT.12: 3 residues within 4Å: Chain A: A.232, A.233, R.449 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.232 Hydrogen bonds: A:A.233 Salt bridges: A:R.449 ACT.13: 3 residues within 4Å: Chain A: W.311, N.341, R.361 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.341 Water bridges: A:S.339, A:S.339 Salt bridges: A:R.361 ACT.14: 2 residues within 4Å: Chain A: K.343, Y.357 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.357 Salt bridges: A:K.343

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Moon, A.F. et al., Structural characterization of the virulence factor Sda1 nuclease from Streptococcus pyogenes. Nucleic Acids Res. (2016)

Release Date

2016-03-30

Peptides

Green fluorescent protein,Extracellular streptodornase D: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Green fluorescent protein,Extracellular streptodornase D

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