SMTL ID : 9g7k.1 (1 other biounit)

Staphylococcus aureus MazF in complex with Nanobody 12

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

hetero-2-2-mer

Ligands

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

CL.1: 3 residues within 4Å: Chain A: R.37, T.60, R.62 Ligand excluded by PLIP CL.3: 3 residues within 4Å: Chain B: E.75, Y.79, S.108 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain D: S.7, G.8 Ligand excluded by PLIP CL.12: 1 residues within 4Å: Chain D: G.26 Ligand excluded by PLIP

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

SO4.2: 5 residues within 4Å: Chain A: S.26, P.27, V.28, G.34, G.35 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.28, A:G.35 Water bridges: A:G.34 SO4.4: 4 residues within 4Å: Chain B: R.37, T.60, G.61, R.62 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.60, B:G.61, B:R.62 Water bridges: B:R.37, B:R.37 Salt bridges: B:R.37 SO4.5: 2 residues within 4Å: Chain B: K.49, Y.50 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.50, B:Y.50 SO4.6: 5 residues within 4Å: Chain B: S.26, P.27, V.28, G.34, G.35 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.28, B:G.35 SO4.7: 1 residues within 4Å: Chain B: Y.50 No protein-ligand interaction detected (PLIP) SO4.8: 4 residues within 4Å: Chain C: R.72, D.73, N.74, A.75 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.74, C:N.74, C:A.75 SO4.9: 1 residues within 4Å: Chain C: S.17 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.17 SO4.10: 3 residues within 4Å: Chain C: T.58, Y.60, K.65 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.60 Water bridges: C:K.65 Salt bridges: C:K.65

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Prolic-Kalinsek, M. et al., Nanobody-mediated activation and inhibition of Staphylococcus aureus MazF. To Be Published

Release Date

2024-07-31

Peptides

Endoribonuclease MazF: AB
Nanobody 12: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Endoribonuclease MazF

Nanobody 12

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