SMTL ID : 9g7k.2 (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

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

CL.1: 2 residues within 4Å: Chain A: R.37, G.61 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain B: P.27, V.28 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain C: N.52, G.54, G.55, G.56 Ligand excluded by PLIP CL.8: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.9: 1 residues within 4Å: Chain C: R.114 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain C: G.10, L.11 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain C: S.7, G.8 Ligands: SO4.12 Ligand excluded by PLIP

12 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 SO4.3: 6 residues within 4Å: Chain A: V.28, Q.29, G.30 Chain B: K.98 Chain C: D.115, D.118 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: C:D.118, A:G.30 Salt bridges: B:K.98 SO4.4: 3 residues within 4Å: Chain A: Y.79, S.108, K.111 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.79, A:S.108 Salt bridges: A:K.111 SO4.6: 5 residues within 4Å: Chain B: Q.33, R.37, T.60, R.62 Chain D: F.113 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.33, B:T.60 Water bridges: B:G.34, B:G.34, B:R.37 Salt bridges: B:R.37 SO4.12: 3 residues within 4Å: Chain C: T.124, Q.125 Ligands: CL.11 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.125 SO4.13: 5 residues within 4Å: Chain C: F.27, T.28, Y.32, E.100, Y.119 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:T.28, C:T.28, C:Y.32, C:Y.32, C:Y.119 SO4.14: 3 residues within 4Å: Chain C: T.58, Y.60, T.69 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.58, C:Y.60 SO4.15: 2 residues within 4Å: Chain D: T.58, Y.60 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Y.60 Water bridges: D:T.58 SO4.16: 4 residues within 4Å: Chain D: R.72, D.73, N.74, A.75 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.74, D:A.75 Water bridges: D:N.74 SO4.17: 3 residues within 4Å: Chain D: S.7, G.8, G.9 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.8, D:G.9 SO4.18: 2 residues within 4Å: Chain D: R.19, Y.80 2 PLIP interactions: 2 interactions with chain D Water bridges: D:Y.80 Salt bridges: D:R.19 SO4.19: 3 residues within 4Å: Chain D: F.113, R.114, D.115 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.114, D:R.114, D:D.115

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
E

B
F

C
G

D
H

Endoribonuclease MazF

Nanobody 12

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