SMTL ID : 9g48.1

Staphylococcus aureus MazF in complex with Nanobody 6

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.14 Å

Oligo State

hetero-2-2-mer

Ligands

5 x CD: CADMIUM ION(Non-covalent)

CD.1: 2 residues within 4Å: Chain A: E.75, D.84 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.75, A:D.84, A:D.84, H2O.1, H2O.1 CD.2: 1 residues within 4Å: Chain A: D.110 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.110, A:D.110, H2O.2, H2O.2 CD.4: 2 residues within 4Å: Chain B: E.75, D.84 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.75, B:D.84, B:D.84, H2O.3, H2O.3 CD.5: 1 residues within 4Å: Chain D: E.45 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.45, H2O.2, H2O.7, H2O.7 CD.6: 1 residues within 4Å: Chain D: E.90 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.90, D:E.90

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.3: 3 residues within 4Å: Chain A: S.26, G.34, G.35 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:S.26

1 x PG0: 2-(2-METHOXYETHOXY)ETHANOL(Non-functional Binders)

PG0.7: 4 residues within 4Å: Chain D: Q.40, R.46, Y.96, W.122 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.40, D:R.46 Water bridges: D:R.46

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

2024-07-24

Peptides

Endoribonuclease MazF: AB
Nanobody 6: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Endoribonuclease MazF

Nanobody 6

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